Warning: Permanently added '44.192.98.127' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/7328197-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.72 PID: 6710 Logging PID: 6711 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 7328197, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'd75c9ef765d5cd19839c260849d377c894e7837b', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:9/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.83-6', 'project_dirname': 'openblas-0.3.23:pr:9', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/gui1ty', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'https://src.fedoraproject.org/user/gui1ty', 'tags': [], 'task_id': '7328197-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:9/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:9/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython'... Running: git checkout d75c9ef765d5cd19839c260849d377c894e7837b -- cmd: ['git', 'checkout', 'd75c9ef765d5cd19839c260849d377c894e7837b', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython rc: 0 stdout: stderr: Note: switching to 'd75c9ef765d5cd19839c260849d377c894e7837b'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at d75c9ef automatic import of python-biopython Running: copr-distgit-client sources % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 18.5M 100 18.5M 0 0 398M 0 --:--:-- --:--:-- --:--:-- 402M INFO: Reading stdout from command: md5sum biopython-1.83.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713531086.045918 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.5 starting (python version = 3.12.1, NVR = mock-5.5-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713531086.045918 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython/python-biopython.spec) Config(fedora-39-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.5 INFO: Mock Version: 5.5 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1713531086.045918/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1713531086.045918/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/48993fa572e1a71d7e9478116c0d5525782bf9df68dbf0c4f9c027e079323498/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/48993fa572e1a71d7e9478116c0d5525782bf9df68dbf0c4f9c027e079323498/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 106 MB/s | 17 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 109 MB/s | 75 MB 00:00 fedora 54 MB/s | 89 MB 00:01 updates 28 MB/s | 35 MB 00:01 Last metadata expiration check: 0:00:02 ago on Fri Apr 19 12:52:04 2024. Package python3-dnf-4.19.2-1.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: python3-dnf-plugins-core noarch 4.6.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 491 k dnf-data noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k python3-dnf noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 553 k yum noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs x86_64 1:1.14.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 156 k python3-dateutil noarch 1:2.8.2-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus x86_64 1.3.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 145 k python3-distro noarch 1.9.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd x86_64 235-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 100 k Transaction Summary ========================================================================================================================= Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): dbus-libs-1.14.10-3.fc40.x86_64.rpm 1.7 MB/s | 156 kB 00:00 (2/11): python3-dbus-1.3.2-6.fc40.x86_64.rpm 1.5 MB/s | 145 kB 00:00 (3/11): python3-dateutil-2.8.2-13.fc40.noarch.r 3.3 MB/s | 345 kB 00:00 (4/11): python3-distro-1.9.0-3.fc40.noarch.rpm 1.4 MB/s | 45 kB 00:00 (5/11): python3-six-1.16.0-14.fc40.noarch.rpm 1.8 MB/s | 41 kB 00:00 (6/11): python3-dnf-plugins-core-4.6.0-1.fc41.n 7.8 MB/s | 302 kB 00:00 (7/11): dnf-data-4.19.2-1.fc41.noarch.rpm 2.0 MB/s | 40 kB 00:00 (8/11): python3-systemd-235-9.fc40.x86_64.rpm 3.0 MB/s | 100 kB 00:00 (9/11): dnf-4.19.2-1.fc41.noarch.rpm 15 MB/s | 491 kB 00:00 (10/11): yum-4.19.2-1.fc41.noarch.rpm 1.7 MB/s | 37 kB 00:00 (11/11): python3-dnf-4.19.2-1.fc41.noarch.rpm 8.7 MB/s | 553 kB 00:00 -------------------------------------------------------------------------------- Total 10 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.19.2-1.fc41.noarch 1/15 Upgrading : python3-dnf-4.19.2-1.fc41.noarch 2/15 Upgrading : dnf-4.19.2-1.fc41.noarch 3/15 Running scriptlet: dnf-4.19.2-1.fc41.noarch 3/15 Installing : python3-systemd-235-9.fc40.x86_64 4/15 Installing : python3-six-1.16.0-14.fc40.noarch 5/15 Installing : python3-dateutil-1:2.8.2-13.fc40.noarch 6/15 Installing : python3-distro-1.9.0-3.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-3.fc40.x86_64 8/15 Installing : python3-dbus-1.3.2-6.fc40.x86_64 9/15 Installing : python3-dnf-plugins-core-4.6.0-1.fc41.noarch 10/15 Upgrading : yum-4.19.2-1.fc41.noarch 11/15 Cleanup : yum-4.19.2-1.fc39.noarch 12/15 Running scriptlet: dnf-4.19.2-1.fc39.noarch 13/15 Cleanup : dnf-4.19.2-1.fc39.noarch 13/15 Running scriptlet: dnf-4.19.2-1.fc39.noarch 13/15 Cleanup : python3-dnf-4.19.2-1.fc39.noarch 14/15 Cleanup : dnf-data-4.19.2-1.fc39.noarch 15/15 Running scriptlet: dnf-data-4.19.2-1.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-3.fc40.x86_64 1/15 Verifying : python3-dateutil-1:2.8.2-13.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-6.fc40.x86_64 3/15 Verifying : python3-distro-1.9.0-3.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.6.0-1.fc41.noarch 5/15 Verifying : python3-six-1.16.0-14.fc40.noarch 6/15 Verifying : python3-systemd-235-9.fc40.x86_64 7/15 Verifying : dnf-4.19.2-1.fc41.noarch 8/15 Verifying : dnf-4.19.2-1.fc39.noarch 9/15 Verifying : dnf-data-4.19.2-1.fc41.noarch 10/15 Verifying : dnf-data-4.19.2-1.fc39.noarch 11/15 Verifying : python3-dnf-4.19.2-1.fc41.noarch 12/15 Verifying : python3-dnf-4.19.2-1.fc39.noarch 13/15 Verifying : yum-4.19.2-1.fc41.noarch 14/15 Verifying : yum-4.19.2-1.fc39.noarch 15/15 Upgraded: dnf-4.19.2-1.fc41.noarch dnf-data-4.19.2-1.fc41.noarch python3-dnf-4.19.2-1.fc41.noarch yum-4.19.2-1.fc41.noarch Installed: dbus-libs-1:1.14.10-3.fc40.x86_64 python3-dateutil-1:2.8.2-13.fc40.noarch python3-dbus-1.3.2-6.fc40.x86_64 python3-distro-1.9.0-3.fc40.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch python3-six-1.16.0-14.fc40.noarch python3-systemd-235-9.fc40.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1713531086.045918/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc41.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch yum-4.19.2-1.fc41.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 224 MB/s | 17 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 94 MB/s | 75 MB 00:00 fedora 57 MB/s | 89 MB 00:01 updates 46 MB/s | 35 MB 00:00 Last metadata expiration check: 0:00:02 ago on Fri Apr 19 12:52:51 2024. Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash x86_64 5.2.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 x86_64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k coreutils x86_64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M cpio x86_64 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 285 k diffutils x86_64 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 397 k fedora-release-common noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k findutils x86_64 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482 k gawk x86_64 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M glibc-minimal-langpack x86_64 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 109 k grep x86_64 3.11-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 290 k gzip x86_64 1.13-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 164 k info x86_64 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 182 k patch x86_64 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 131 k redhat-rpm-config noarch 288-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build x86_64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 70 k sed x86_64 4.9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309 k shadow-utils x86_64 2:4.15.1-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 M tar x86_64 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 847 k unzip x86_64 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 185 k util-linux x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M which x86_64 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k xz x86_64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 532 k Installing dependencies: alternatives x86_64 1.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k ansible-srpm-macros noarch 1-15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs x86_64 4.0.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 126 k authselect x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 141 k authselect-libs x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 205 k basesystem noarch 11-20.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils x86_64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.3 M binutils-gold x86_64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 783 k bzip2-libs x86_64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 862 k coreutils-common x86_64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib x86_64 2.9.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82 k crypto-policies noarch 20240320-1.git58e3d95.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 65 k curl x86_64 8.7.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 306 k cyrus-sasl-lib x86_64 2.1.28-19.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 789 k debugedit x86_64 5.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 79 k dwz x86_64 0.15-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 138 k ed x86_64 1.20.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82 k efi-srpm-macros noarch 5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils x86_64 0.191-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 525 k elfutils-debuginfod-client x86_64 0.191-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k elfutils-default-yama-scope noarch 0.191-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf x86_64 0.191-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 209 k elfutils-libs x86_64 0.191-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 258 k fedora-gpg-keys noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k fedora-release noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k fedora-release-identity-basic noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k fedora-repos noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.3 k fedora-repos-rawhide noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.9 k file x86_64 5.45-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 49 k file-libs x86_64 5.45-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 763 k filesystem x86_64 3.18-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M fonts-srpm-macros noarch 1:2.0.5-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k forge-srpm-macros noarch 0.3.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 19 k fpc-srpm-macros noarch 1.3-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.8 k gdb-minimal x86_64 14.2-4.fc41 copr_base 4.3 M gdbm x86_64 1:1.23-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 147 k gdbm-libs x86_64 1:1.23-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 56 k ghc-srpm-macros noarch 1.9.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.0 k glibc x86_64 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.2 M glibc-common x86_64 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 391 k glibc-gconv-extra x86_64 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 M gmp x86_64 1:6.3.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 317 k gnat-srpm-macros noarch 6-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.8 k go-srpm-macros noarch 3.6.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k jansson x86_64 2.13.1-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 44 k kernel-srpm-macros noarch 1.0-23.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.8 k keyutils-libs x86_64 1.6.3-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k krb5-libs x86_64 1.21.2-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 751 k libacl x86_64 2.3.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 24 k libarchive x86_64 3.7.2-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 407 k libattr x86_64 2.5.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k libblkid x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 124 k libbrotli x86_64 1.1.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 338 k libcap x86_64 2.69-8.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 85 k libcap-ng x86_64 0.8.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libcom_err x86_64 1.47.0-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k libcurl x86_64 8.7.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 352 k libeconf x86_64 0.6.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libevent x86_64 2.1.12-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 257 k libfdisk x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 159 k libffi x86_64 3.4.6-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k libgcc x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 126 k libgomp x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 346 k libidn2 x86_64 2.3.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112 k libmount x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 155 k libnghttp2 x86_64 1.61.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 76 k libnsl2 x86_64 2.0.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 30 k libpkgconf x86_64 2.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k libpsl x86_64 0.21.5-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 64 k libpwquality x86_64 1.4.5-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 108 k libselinux x86_64 3.6-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 88 k libsemanage x86_64 3.6-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 116 k libsepol x86_64 3.6-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 340 k libsmartcols x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83 k libssh x86_64 0.10.6-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 212 k libssh-config noarch 0.10.6-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.1 k libstdc++ x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 881 k libtasn1 x86_64 4.19.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 74 k libtirpc x86_64 1.3.4-1.rc3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 92 k libtool-ltdl x86_64 2.4.7-10.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 36 k libunistring x86_64 1.1-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 545 k libutempter x86_64 1.2.1-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 k libuuid x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 28 k libverto x86_64 0.3.2-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k libxcrypt x86_64 4.4.36-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 118 k libxml2 x86_64 2.12.6-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 686 k libzstd x86_64 1.5.6-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309 k lua-libs x86_64 5.4.6-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 132 k lua-srpm-macros noarch 1-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.7 k lz4-libs x86_64 1.9.4-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 67 k mpfr x86_64 4.2.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 349 k ncurses-base noarch 6.4-12.20240127.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 64 k ncurses-libs x86_64 6.4-12.20240127.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 332 k ocaml-srpm-macros noarch 9-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.1 k openblas-srpm-macros noarch 2-17.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.7 k openldap x86_64 2.6.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 254 k openssl-libs x86_64 1:3.2.1-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.3 M p11-kit x86_64 0.25.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 476 k p11-kit-trust x86_64 0.25.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 132 k package-notes-srpm-macros noarch 0.5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.9 k pam x86_64 1.6.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 517 k pam-libs x86_64 1.6.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 57 k pcre2 x86_64 10.43-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 242 k pcre2-syntax noarch 10.43-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 149 k perl-srpm-macros noarch 1-53.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.4 k pkgconf x86_64 2.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k pkgconf-m4 noarch 2.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k pkgconf-pkg-config x86_64 2.1.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.7 k popt x86_64 1.19-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 60 k publicsuffix-list-dafsa noarch 20240107-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 58 k pyproject-srpm-macros noarch 1.12.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k python-srpm-macros noarch 3.12-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 24 k qt5-srpm-macros noarch 5.15.13-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.5 k qt6-srpm-macros noarch 6.7.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.0 k readline x86_64 8.2-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 213 k rpm x86_64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 512 k rpm-build-libs x86_64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 95 k rpm-libs x86_64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309 k rpm-sequoia x86_64 1.6.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 847 k rust-srpm-macros noarch 26.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k setup noarch 2.14.5-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 148 k sqlite-libs x86_64 3.45.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 706 k systemd-libs x86_64 255.4-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 708 k util-linux-core x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 520 k xxhash-libs x86_64 0.8.2-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k xz-libs x86_64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 110 k zig-srpm-macros noarch 1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 k zip x86_64 3.0-40.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 265 k zlib-ng-compat x86_64 2.1.6-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 77 k zstd x86_64 1.5.6-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 479 k Installing Groups: Buildsystem building group Transaction Summary ======================================================================================================================================== Install 153 Packages Total download size: 52 M Installed size: 179 M Downloading Packages: (1/153): alternatives-1.26-3.fc40.x86_64.rpm 538 kB/s | 40 kB 00:00 (2/153): ansible-srpm-macros-1-15.fc41.noarch.r 236 kB/s | 21 kB 00:00 (3/153): gdb-minimal-14.2-4.fc41.x86_64.rpm 40 MB/s | 4.3 MB 00:00 (4/153): audit-libs-4.0.1-1.fc41.x86_64.rpm 3.6 MB/s | 126 kB 00:00 (5/153): authselect-libs-1.5.0-5.fc41.x86_64.rp 5.5 MB/s | 205 kB 00:00 (6/153): authselect-1.5.0-5.fc41.x86_64.rpm 2.2 MB/s | 141 kB 00:00 (7/153): basesystem-11-20.fc40.noarch.rpm 169 kB/s | 7.2 kB 00:00 (8/153): bash-5.2.26-3.fc40.x86_64.rpm 41 MB/s | 1.8 MB 00:00 (9/153): bzip2-1.0.8-18.fc40.x86_64.rpm 2.4 MB/s | 52 kB 00:00 (10/153): binutils-gold-2.42.50-6.fc41.x86_64.r 9.9 MB/s | 783 kB 00:00 (11/153): bzip2-libs-1.0.8-18.fc40.x86_64.rpm 2.0 MB/s | 41 kB 00:00 (12/153): ca-certificates-2023.2.62_v7.0.401-6. 32 MB/s | 862 kB 00:00 (13/153): coreutils-9.5-1.fc41.x86_64.rpm 37 MB/s | 1.1 MB 00:00 (14/153): cpio-2.15-1.fc40.x86_64.rpm 13 MB/s | 285 kB 00:00 (15/153): coreutils-common-9.5-1.fc41.x86_64.rp 68 MB/s | 2.1 MB 00:00 (16/153): binutils-2.42.50-6.fc41.x86_64.rpm 43 MB/s | 6.3 MB 00:00 (17/153): cracklib-2.9.11-5.fc40.x86_64.rpm 3.3 MB/s | 82 kB 00:00 (18/153): crypto-policies-20240320-1.git58e3d95 2.5 MB/s | 65 kB 00:00 (19/153): curl-8.7.1-1.fc41.x86_64.rpm 12 MB/s | 306 kB 00:00 (20/153): debugedit-5.0-14.fc40.x86_64.rpm 3.7 MB/s | 79 kB 00:00 (21/153): cyrus-sasl-lib-2.1.28-19.fc40.x86_64. 27 MB/s | 789 kB 00:00 (22/153): diffutils-3.10-5.fc40.x86_64.rpm 17 MB/s | 397 kB 00:00 (23/153): dwz-0.15-6.fc40.x86_64.rpm 6.2 MB/s | 138 kB 00:00 (24/153): ed-1.20.1-1.fc41.x86_64.rpm 3.8 MB/s | 82 kB 00:00 (25/153): efi-srpm-macros-5-11.fc40.noarch.rpm 1.1 MB/s | 22 kB 00:00 (26/153): elfutils-debuginfod-client-0.191-5.fc 1.9 MB/s | 38 kB 00:00 (27/153): elfutils-0.191-5.fc41.x86_64.rpm 23 MB/s | 525 kB 00:00 (28/153): elfutils-default-yama-scope-0.191-5.f 657 kB/s | 13 kB 00:00 (29/153): elfutils-libelf-0.191-5.fc41.x86_64.r 9.5 MB/s | 209 kB 00:00 (30/153): elfutils-libs-0.191-5.fc41.x86_64.rpm 11 MB/s | 258 kB 00:00 (31/153): fedora-gpg-keys-41-0.1.noarch.rpm 5.5 MB/s | 121 kB 00:00 (32/153): fedora-release-41-0.9.noarch.rpm 534 kB/s | 11 kB 00:00 (33/153): fedora-release-identity-basic-41-0.9. 744 kB/s | 12 kB 00:00 (34/153): fedora-release-common-41-0.9.noarch.r 849 kB/s | 22 kB 00:00 (35/153): fedora-repos-41-0.1.noarch.rpm 431 kB/s | 9.3 kB 00:00 (36/153): fedora-repos-rawhide-41-0.1.noarch.rp 443 kB/s | 8.9 kB 00:00 (37/153): file-5.45-5.fc41.x86_64.rpm 2.4 MB/s | 49 kB 00:00 (38/153): file-libs-5.45-5.fc41.x86_64.rpm 29 MB/s | 763 kB 00:00 (39/153): findutils-4.9.0-8.fc40.x86_64.rpm 21 MB/s | 482 kB 00:00 (40/153): filesystem-3.18-9.fc41.x86_64.rpm 40 MB/s | 1.1 MB 00:00 (41/153): fpc-srpm-macros-1.3-12.fc40.noarch.rp 541 kB/s | 7.8 kB 00:00 (42/153): forge-srpm-macros-0.3.1-1.fc41.noarch 952 kB/s | 19 kB 00:00 (43/153): fonts-srpm-macros-2.0.5-14.fc40.noarc 1.0 MB/s | 27 kB 00:00 (44/153): gawk-5.3.0-3.fc40.x86_64.rpm 43 MB/s | 1.1 MB 00:00 (45/153): gdbm-1.23-6.fc40.x86_64.rpm 6.9 MB/s | 147 kB 00:00 (46/153): gdbm-libs-1.23-6.fc40.x86_64.rpm 2.6 MB/s | 56 kB 00:00 (47/153): glibc-common-2.39.9000-12.fc41.x86_64 22 MB/s | 391 kB 00:00 (48/153): ghc-srpm-macros-1.9.1-1.fc41.noarch.r 328 kB/s | 9.0 kB 00:00 (49/153): glibc-2.39.9000-12.fc41.x86_64.rpm 74 MB/s | 2.2 MB 00:00 (50/153): glibc-gconv-extra-2.39.9000-12.fc41.x 55 MB/s | 1.6 MB 00:00 (51/153): glibc-minimal-langpack-2.39.9000-12.f 4.8 MB/s | 109 kB 00:00 (52/153): gmp-6.3.0-1.fc41.x86_64.rpm 14 MB/s | 317 kB 00:00 (53/153): gnat-srpm-macros-6-5.fc40.noarch.rpm 421 kB/s | 8.8 kB 00:00 (54/153): go-srpm-macros-3.6.0-1.fc41.noarch.rp 1.3 MB/s | 28 kB 00:00 (55/153): grep-3.11-7.fc40.x86_64.rpm 12 MB/s | 290 kB 00:00 (56/153): gzip-1.13-1.fc40.x86_64.rpm 7.8 MB/s | 164 kB 00:00 (57/153): jansson-2.13.1-9.fc40.x86_64.rpm 2.5 MB/s | 44 kB 00:00 (58/153): info-7.1-2.fc40.x86_64.rpm 6.7 MB/s | 182 kB 00:00 (59/153): kernel-srpm-macros-1.0-23.fc41.noarch 474 kB/s | 9.8 kB 00:00 (60/153): krb5-libs-1.21.2-5.fc40.x86_64.rpm 34 MB/s | 751 kB 00:00 (61/153): keyutils-libs-1.6.3-3.fc40.x86_64.rpm 1.2 MB/s | 31 kB 00:00 (62/153): libacl-2.3.2-1.fc40.x86_64.rpm 1.2 MB/s | 24 kB 00:00 (63/153): libarchive-3.7.2-3.fc41.x86_64.rpm 17 MB/s | 407 kB 00:00 (64/153): libattr-2.5.2-3.fc40.x86_64.rpm 583 kB/s | 18 kB 00:00 (65/153): libblkid-2.40-13.fc41.x86_64.rpm 5.8 MB/s | 124 kB 00:00 (66/153): libbrotli-1.1.0-3.fc40.x86_64.rpm 15 MB/s | 338 kB 00:00 (67/153): libcap-ng-0.8.5-1.fc41.x86_64.rpm 1.6 MB/s | 32 kB 00:00 (68/153): libcap-2.69-8.fc41.x86_64.rpm 3.6 MB/s | 85 kB 00:00 (69/153): libcom_err-1.47.0-5.fc40.x86_64.rpm 1.2 MB/s | 25 kB 00:00 (70/153): libeconf-0.6.2-1.fc41.x86_64.rpm 1.6 MB/s | 32 kB 00:00 (71/153): libcurl-8.7.1-1.fc41.x86_64.rpm 11 MB/s | 352 kB 00:00 (72/153): libfdisk-2.40-13.fc41.x86_64.rpm 6.7 MB/s | 159 kB 00:00 (73/153): libevent-2.1.12-12.fc40.x86_64.rpm 7.5 MB/s | 257 kB 00:00 (74/153): libffi-3.4.6-1.fc41.x86_64.rpm 1.7 MB/s | 40 kB 00:00 (75/153): libgcc-14.0.1-0.15.fc41.x86_64.rpm 5.2 MB/s | 126 kB 00:00 (76/153): libgomp-14.0.1-0.15.fc41.x86_64.rpm 10 MB/s | 346 kB 00:00 (77/153): libidn2-2.3.7-1.fc40.x86_64.rpm 4.2 MB/s | 112 kB 00:00 (78/153): libmount-2.40-13.fc41.x86_64.rpm 5.2 MB/s | 155 kB 00:00 (79/153): libnghttp2-1.61.0-1.fc41.x86_64.rpm 3.7 MB/s | 76 kB 00:00 (80/153): libnsl2-2.0.1-1.fc40.x86_64.rpm 1.4 MB/s | 30 kB 00:00 (81/153): libpwquality-1.4.5-9.fc40.x86_64.rpm 6.9 MB/s | 108 kB 00:00 (82/153): libpsl-0.21.5-3.fc40.x86_64.rpm 2.9 MB/s | 64 kB 00:00 (83/153): libpkgconf-2.1.0-1.fc40.x86_64.rpm 1.4 MB/s | 38 kB 00:00 (84/153): libselinux-3.6-4.fc40.x86_64.rpm 3.9 MB/s | 88 kB 00:00 (85/153): libsemanage-3.6-3.fc40.x86_64.rpm 5.4 MB/s | 116 kB 00:00 (86/153): libsepol-3.6-3.fc40.x86_64.rpm 15 MB/s | 340 kB 00:00 (87/153): libsmartcols-2.40-13.fc41.x86_64.rpm 4.0 MB/s | 83 kB 00:00 (88/153): libssh-0.10.6-6.fc41.x86_64.rpm 9.4 MB/s | 212 kB 00:00 (89/153): libssh-config-0.10.6-6.fc41.noarch.rp 466 kB/s | 9.1 kB 00:00 (90/153): libtirpc-1.3.4-1.rc3.fc41.x86_64.rpm 5.9 MB/s | 92 kB 00:00 (91/153): libtasn1-4.19.0-6.fc40.x86_64.rpm 3.5 MB/s | 74 kB 00:00 (92/153): libstdc++-14.0.1-0.15.fc41.x86_64.rpm 26 MB/s | 881 kB 00:00 (93/153): libtool-ltdl-2.4.7-10.fc40.x86_64.rpm 1.5 MB/s | 36 kB 00:00 (94/153): libutempter-1.2.1-13.fc40.x86_64.rpm 1.6 MB/s | 26 kB 00:00 (95/153): libunistring-1.1-7.fc41.x86_64.rpm 19 MB/s | 545 kB 00:00 (96/153): libuuid-2.40-13.fc41.x86_64.rpm 1.3 MB/s | 28 kB 00:00 (97/153): libverto-0.3.2-8.fc40.x86_64.rpm 955 kB/s | 21 kB 00:00 (98/153): libxcrypt-4.4.36-5.fc40.x86_64.rpm 5.4 MB/s | 118 kB 00:00 (99/153): libxml2-2.12.6-1.fc41.x86_64.rpm 28 MB/s | 686 kB 00:00 (100/153): libzstd-1.5.6-1.fc41.x86_64.rpm 14 MB/s | 309 kB 00:00 (101/153): lua-libs-5.4.6-5.fc40.x86_64.rpm 5.7 MB/s | 132 kB 00:00 (102/153): lua-srpm-macros-1-13.fc40.noarch.rpm 432 kB/s | 8.7 kB 00:00 (103/153): lz4-libs-1.9.4-6.fc40.x86_64.rpm 3.2 MB/s | 67 kB 00:00 (104/153): mpfr-4.2.1-3.fc40.x86_64.rpm 15 MB/s | 349 kB 00:00 (105/153): ncurses-base-6.4-12.20240127.fc40.no 3.0 MB/s | 64 kB 00:00 (106/153): ocaml-srpm-macros-9-3.fc40.noarch.rp 558 kB/s | 9.1 kB 00:00 (107/153): ncurses-libs-6.4-12.20240127.fc40.x8 12 MB/s | 332 kB 00:00 (108/153): openblas-srpm-macros-2-17.fc41.noarc 365 kB/s | 7.7 kB 00:00 (109/153): openldap-2.6.7-1.fc40.x86_64.rpm 9.1 MB/s | 254 kB 00:00 (110/153): p11-kit-0.25.3-4.fc40.x86_64.rpm 19 MB/s | 476 kB 00:00 (111/153): openssl-libs-3.2.1-6.fc41.x86_64.rpm 60 MB/s | 2.3 MB 00:00 (112/153): p11-kit-trust-0.25.3-4.fc40.x86_64.r 5.5 MB/s | 132 kB 00:00 (113/153): package-notes-srpm-macros-0.5-11.fc4 488 kB/s | 9.9 kB 00:00 (114/153): pam-libs-1.6.1-1.fc41.x86_64.rpm 3.7 MB/s | 57 kB 00:00 (115/153): pam-1.6.1-1.fc41.x86_64.rpm 18 MB/s | 517 kB 00:00 (116/153): patch-2.7.6-24.fc40.x86_64.rpm 6.1 MB/s | 131 kB 00:00 (117/153): pcre2-syntax-10.43-1.fc41.noarch.rpm 9.6 MB/s | 149 kB 00:00 (118/153): pcre2-10.43-1.fc41.x86_64.rpm 9.0 MB/s | 242 kB 00:00 (119/153): perl-srpm-macros-1-53.fc40.noarch.rp 401 kB/s | 8.4 kB 00:00 (120/153): pkgconf-m4-2.1.0-1.fc40.noarch.rpm 937 kB/s | 14 kB 00:00 (121/153): pkgconf-2.1.0-1.fc40.x86_64.rpm 1.6 MB/s | 43 kB 00:00 (122/153): pkgconf-pkg-config-2.1.0-1.fc40.x86_ 488 kB/s | 9.7 kB 00:00 (123/153): popt-1.19-6.fc40.x86_64.rpm 2.8 MB/s | 60 kB 00:00 (124/153): publicsuffix-list-dafsa-20240107-3.f 2.8 MB/s | 58 kB 00:00 (125/153): pyproject-srpm-macros-1.12.0-1.fc40. 670 kB/s | 14 kB 00:00 (126/153): python-srpm-macros-3.12-9.fc41.noarc 1.2 MB/s | 24 kB 00:00 (127/153): qt5-srpm-macros-5.15.13-1.fc41.noarc 427 kB/s | 8.5 kB 00:00 (128/153): qt6-srpm-macros-6.7.0-1.fc41.noarch. 460 kB/s | 9.0 kB 00:00 (129/153): readline-8.2-8.fc40.x86_64.rpm 9.3 MB/s | 213 kB 00:00 (130/153): redhat-rpm-config-288-1.fc41.noarch. 3.3 MB/s | 75 kB 00:00 (131/153): rpm-4.19.1.1-1.fc40.x86_64.rpm 22 MB/s | 512 kB 00:00 (132/153): rpm-build-libs-4.19.1.1-1.fc40.x86_6 4.6 MB/s | 95 kB 00:00 (133/153): rpm-build-4.19.1.1-1.fc40.x86_64.rpm 2.6 MB/s | 70 kB 00:00 (134/153): rpm-libs-4.19.1.1-1.fc40.x86_64.rpm 13 MB/s | 309 kB 00:00 (135/153): rust-srpm-macros-26.2-1.fc41.noarch. 608 kB/s | 13 kB 00:00 (136/153): rpm-sequoia-1.6.0-2.fc40.x86_64.rpm 29 MB/s | 847 kB 00:00 (137/153): sed-4.9-1.fc40.x86_64.rpm 10 MB/s | 309 kB 00:00 (138/153): setup-2.14.5-2.fc40.noarch.rpm 6.7 MB/s | 148 kB 00:00 (139/153): shadow-utils-4.15.1-2.fc41.x86_64.rp 49 MB/s | 1.3 MB 00:00 (140/153): tar-1.35-3.fc40.x86_64.rpm 41 MB/s | 847 kB 00:00 (141/153): sqlite-libs-3.45.2-1.fc41.x86_64.rpm 21 MB/s | 706 kB 00:00 (142/153): systemd-libs-255.4-1.fc41.x86_64.rpm 21 MB/s | 708 kB 00:00 (143/153): util-linux-core-2.40-13.fc41.x86_64. 29 MB/s | 520 kB 00:00 (144/153): unzip-6.0-63.fc40.x86_64.rpm 6.8 MB/s | 185 kB 00:00 (145/153): util-linux-2.40-13.fc41.x86_64.rpm 43 MB/s | 1.2 MB 00:00 (146/153): which-2.21-41.fc40.x86_64.rpm 2.0 MB/s | 41 kB 00:00 (147/153): xxhash-libs-0.8.2-2.fc40.x86_64.rpm 1.6 MB/s | 37 kB 00:00 (148/153): xz-5.4.6-3.fc41.x86_64.rpm 22 MB/s | 532 kB 00:00 (149/153): xz-libs-5.4.6-3.fc41.x86_64.rpm 5.3 MB/s | 110 kB 00:00 (150/153): zip-3.0-40.fc40.x86_64.rpm 12 MB/s | 265 kB 00:00 (151/153): zlib-ng-compat-2.1.6-2.fc40.x86_64.r 4.8 MB/s | 77 kB 00:00 (152/153): zig-srpm-macros-1-2.fc40.noarch.rpm 288 kB/s | 8.0 kB 00:00 (153/153): zstd-1.5.6-1.fc41.x86_64.rpm 17 MB/s | 479 kB 00:00 -------------------------------------------------------------------------------- Total 38 MB/s | 52 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-9.fc41.x86_64 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.15.fc41.x86_64 1/153 Running scriptlet: libgcc-14.0.1-0.15.fc41.x86_64 1/153 Installing : crypto-policies-20240320-1.git58e3d95.fc41.noarc 2/153 Running scriptlet: crypto-policies-20240320-1.git58e3d95.fc41.noarc 2/153 Installing : fedora-release-identity-basic-41-0.9.noarch 3/153 Installing : fedora-repos-rawhide-41-0.1.noarch 4/153 Installing : fedora-gpg-keys-41-0.1.noarch 5/153 Installing : fedora-repos-41-0.1.noarch 6/153 Installing : fedora-release-common-41-0.9.noarch 7/153 Installing : fedora-release-41-0.9.noarch 8/153 Installing : setup-2.14.5-2.fc40.noarch 9/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-2.fc40.noarch 9/153 Installing : filesystem-3.18-9.fc41.x86_64 10/153 Installing : basesystem-11-20.fc40.noarch 11/153 Installing : rust-srpm-macros-26.2-1.fc41.noarch 12/153 Installing : qt6-srpm-macros-6.7.0-1.fc41.noarch 13/153 Installing : qt5-srpm-macros-5.15.13-1.fc41.noarch 14/153 Installing : publicsuffix-list-dafsa-20240107-3.fc40.noarch 15/153 Installing : pkgconf-m4-2.1.0-1.fc40.noarch 16/153 Installing : perl-srpm-macros-1-53.fc40.noarch 17/153 Installing : pcre2-syntax-10.43-1.fc41.noarch 18/153 Installing : package-notes-srpm-macros-0.5-11.fc40.noarch 19/153 Installing : openblas-srpm-macros-2-17.fc41.noarch 20/153 Installing : ocaml-srpm-macros-9-3.fc40.noarch 21/153 Installing : ncurses-base-6.4-12.20240127.fc40.noarch 22/153 Installing : glibc-gconv-extra-2.39.9000-12.fc41.x86_64 23/153 Running scriptlet: glibc-gconv-extra-2.39.9000-12.fc41.x86_64 23/153 Installing : glibc-minimal-langpack-2.39.9000-12.fc41.x86_64 24/153 Installing : glibc-common-2.39.9000-12.fc41.x86_64 25/153 Running scriptlet: glibc-2.39.9000-12.fc41.x86_64 26/153 Installing : glibc-2.39.9000-12.fc41.x86_64 26/153 Running scriptlet: glibc-2.39.9000-12.fc41.x86_64 26/153 Installing : ncurses-libs-6.4-12.20240127.fc40.x86_64 27/153 Installing : bash-5.2.26-3.fc40.x86_64 28/153 Running scriptlet: bash-5.2.26-3.fc40.x86_64 28/153 Installing : zlib-ng-compat-2.1.6-2.fc40.x86_64 29/153 Installing : xz-libs-1:5.4.6-3.fc41.x86_64 30/153 Installing : bzip2-libs-1.0.8-18.fc40.x86_64 31/153 Installing : readline-8.2-8.fc40.x86_64 32/153 Installing : libstdc++-14.0.1-0.15.fc41.x86_64 33/153 Installing : libuuid-2.40-13.fc41.x86_64 34/153 Installing : libzstd-1.5.6-1.fc41.x86_64 35/153 Installing : elfutils-libelf-0.191-5.fc41.x86_64 36/153 Installing : popt-1.19-6.fc40.x86_64 37/153 Installing : libblkid-2.40-13.fc41.x86_64 38/153 Installing : gmp-1:6.3.0-1.fc41.x86_64 39/153 Installing : libattr-2.5.2-3.fc40.x86_64 40/153 Installing : libacl-2.3.2-1.fc40.x86_64 41/153 Installing : libxcrypt-4.4.36-5.fc40.x86_64 42/153 Installing : gdbm-libs-1:1.23-6.fc40.x86_64 43/153 Installing : libeconf-0.6.2-1.fc41.x86_64 44/153 Installing : lz4-libs-1.9.4-6.fc40.x86_64 45/153 Installing : mpfr-4.2.1-3.fc40.x86_64 46/153 Installing : gawk-5.3.0-3.fc40.x86_64 47/153 Installing : dwz-0.15-6.fc40.x86_64 48/153 Installing : unzip-6.0-63.fc40.x86_64 49/153 Installing : file-libs-5.45-5.fc41.x86_64 50/153 Installing : file-5.45-5.fc41.x86_64 51/153 Installing : alternatives-1.26-3.fc40.x86_64 52/153 Installing : jansson-2.13.1-9.fc40.x86_64 53/153 Installing : libcap-ng-0.8.5-1.fc41.x86_64 54/153 Installing : audit-libs-4.0.1-1.fc41.x86_64 55/153 Installing : pam-libs-1.6.1-1.fc41.x86_64 56/153 Installing : libcap-2.69-8.fc41.x86_64 57/153 Installing : systemd-libs-255.4-1.fc41.x86_64 58/153 Installing : libcom_err-1.47.0-5.fc40.x86_64 59/153 Installing : libsepol-3.6-3.fc40.x86_64 60/153 Installing : libsmartcols-2.40-13.fc41.x86_64 61/153 Installing : libtasn1-4.19.0-6.fc40.x86_64 62/153 Installing : libunistring-1.1-7.fc41.x86_64 63/153 Installing : libidn2-2.3.7-1.fc40.x86_64 64/153 Installing : lua-libs-5.4.6-5.fc40.x86_64 65/153 Installing : pcre2-10.43-1.fc41.x86_64 66/153 Installing : libselinux-3.6-4.fc40.x86_64 67/153 Installing : sed-4.9-1.fc40.x86_64 68/153 Installing : grep-3.11-7.fc40.x86_64 69/153 Installing : findutils-1:4.9.0-8.fc40.x86_64 70/153 Installing : xz-1:5.4.6-3.fc41.x86_64 71/153 Installing : libmount-2.40-13.fc41.x86_64 72/153 Installing : util-linux-core-2.40-13.fc41.x86_64 73/153 Installing : libsemanage-3.6-3.fc40.x86_64 74/153 Installing : shadow-utils-2:4.15.1-2.fc41.x86_64 75/153 Running scriptlet: libutempter-1.2.1-13.fc40.x86_64 76/153 Installing : libutempter-1.2.1-13.fc40.x86_64 76/153 Installing : tar-2:1.35-3.fc40.x86_64 77/153 Installing : libpsl-0.21.5-3.fc40.x86_64 78/153 Installing : zip-3.0-40.fc40.x86_64 79/153 Installing : zstd-1.5.6-1.fc41.x86_64 80/153 Installing : cyrus-sasl-lib-2.1.28-19.fc40.x86_64 81/153 Installing : gdbm-1:1.23-6.fc40.x86_64 82/153 Installing : libfdisk-2.40-13.fc41.x86_64 83/153 Installing : bzip2-1.0.8-18.fc40.x86_64 84/153 Installing : libxml2-2.12.6-1.fc41.x86_64 85/153 Installing : sqlite-libs-3.45.2-1.fc41.x86_64 86/153 Installing : ed-1.20.1-1.fc41.x86_64 87/153 Installing : patch-2.7.6-24.fc40.x86_64 88/153 Installing : elfutils-default-yama-scope-0.191-5.fc41.noarch 89/153 Running scriptlet: elfutils-default-yama-scope-0.191-5.fc41.noarch 89/153 Installing : cpio-2.15-1.fc40.x86_64 90/153 Installing : diffutils-3.10-5.fc40.x86_64 91/153 Installing : keyutils-libs-1.6.3-3.fc40.x86_64 92/153 Installing : libbrotli-1.1.0-3.fc40.x86_64 93/153 Installing : libffi-3.4.6-1.fc41.x86_64 94/153 Installing : p11-kit-0.25.3-4.fc40.x86_64 95/153 Installing : p11-kit-trust-0.25.3-4.fc40.x86_64 96/153 Running scriptlet: p11-kit-trust-0.25.3-4.fc40.x86_64 96/153 Installing : libgomp-14.0.1-0.15.fc41.x86_64 97/153 Installing : libnghttp2-1.61.0-1.fc41.x86_64 98/153 Installing : libpkgconf-2.1.0-1.fc40.x86_64 99/153 Installing : pkgconf-2.1.0-1.fc40.x86_64 100/153 Installing : pkgconf-pkg-config-2.1.0-1.fc40.x86_64 101/153 Installing : libtool-ltdl-2.4.7-10.fc40.x86_64 102/153 Installing : libverto-0.3.2-8.fc40.x86_64 103/153 Installing : xxhash-libs-0.8.2-2.fc40.x86_64 104/153 Installing : libssh-config-0.10.6-6.fc41.noarch 105/153 Installing : kernel-srpm-macros-1.0-23.fc41.noarch 106/153 Installing : gnat-srpm-macros-6-5.fc40.noarch 107/153 Installing : ghc-srpm-macros-1.9.1-1.fc41.noarch 108/153 Installing : fpc-srpm-macros-1.3-12.fc40.noarch 109/153 Installing : coreutils-common-9.5-1.fc41.x86_64 110/153 Installing : openssl-libs-1:3.2.1-6.fc41.x86_64 111/153 Installing : coreutils-9.5-1.fc41.x86_64 112/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 113/153 Installing : ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 113/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 113/153 Installing : krb5-libs-1.21.2-5.fc40.x86_64 114/153 Installing : libtirpc-1.3.4-1.rc3.fc41.x86_64 115/153 Installing : authselect-libs-1.5.0-5.fc41.x86_64 116/153 Installing : gzip-1.13-1.fc40.x86_64 117/153 Installing : libarchive-3.7.2-3.fc41.x86_64 118/153 Installing : cracklib-2.9.11-5.fc40.x86_64 119/153 Installing : libpwquality-1.4.5-9.fc40.x86_64 120/153 Installing : authselect-1.5.0-5.fc41.x86_64 121/153 Installing : libnsl2-2.0.1-1.fc40.x86_64 122/153 Installing : pam-1.6.1-1.fc41.x86_64 123/153 Installing : libssh-0.10.6-6.fc41.x86_64 124/153 Installing : libevent-2.1.12-12.fc40.x86_64 125/153 Installing : openldap-2.6.7-1.fc40.x86_64 126/153 Installing : libcurl-8.7.1-1.fc41.x86_64 127/153 Installing : elfutils-libs-0.191-5.fc41.x86_64 128/153 Installing : elfutils-debuginfod-client-0.191-5.fc41.x86_64 129/153 Installing : binutils-gold-2.42.50-6.fc41.x86_64 130/153 Running scriptlet: binutils-gold-2.42.50-6.fc41.x86_64 130/153 Installing : binutils-2.42.50-6.fc41.x86_64 131/153 Running scriptlet: binutils-2.42.50-6.fc41.x86_64 131/153 Installing : gdb-minimal-14.2-4.fc41.x86_64 132/153 Installing : elfutils-0.191-5.fc41.x86_64 133/153 Installing : debugedit-5.0-14.fc40.x86_64 134/153 Installing : curl-8.7.1-1.fc41.x86_64 135/153 Installing : rpm-sequoia-1.6.0-2.fc40.x86_64 136/153 Installing : rpm-libs-4.19.1.1-1.fc40.x86_64 137/153 Running scriptlet: rpm-4.19.1.1-1.fc40.x86_64 138/153 Installing : rpm-4.19.1.1-1.fc40.x86_64 138/153 Installing : efi-srpm-macros-5-11.fc40.noarch 139/153 Installing : lua-srpm-macros-1-13.fc40.noarch 140/153 Installing : zig-srpm-macros-1-2.fc40.noarch 141/153 Installing : rpm-build-libs-4.19.1.1-1.fc40.x86_64 142/153 Installing : ansible-srpm-macros-1-15.fc41.noarch 143/153 Installing : fonts-srpm-macros-1:2.0.5-14.fc40.noarch 144/153 Installing : forge-srpm-macros-0.3.1-1.fc41.noarch 145/153 Installing : go-srpm-macros-3.6.0-1.fc41.noarch 146/153 Installing : python-srpm-macros-3.12-9.fc41.noarch 147/153 Installing : redhat-rpm-config-288-1.fc41.noarch 148/153 Installing : rpm-build-4.19.1.1-1.fc40.x86_64 149/153 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 150/153 Installing : util-linux-2.40-13.fc41.x86_64 151/153 Running scriptlet: util-linux-2.40-13.fc41.x86_64 151/153 Installing : which-2.21-41.fc40.x86_64 152/153 Installing : info-7.1-2.fc40.x86_64 153/153 Running scriptlet: filesystem-3.18-9.fc41.x86_64 153/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.5.0-5.fc41.x86_64 153/153 Running scriptlet: rpm-4.19.1.1-1.fc40.x86_64 153/153 Running scriptlet: info-7.1-2.fc40.x86_64 153/153 Installed: alternatives-1.26-3.fc40.x86_64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.x86_64 authselect-1.5.0-5.fc41.x86_64 authselect-libs-1.5.0-5.fc41.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.42.50-6.fc41.x86_64 binutils-gold-2.42.50-6.fc41.x86_64 bzip2-1.0.8-18.fc40.x86_64 bzip2-libs-1.0.8-18.fc40.x86_64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.x86_64 coreutils-common-9.5-1.fc41.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.x86_64 cyrus-sasl-lib-2.1.28-19.fc40.x86_64 debugedit-5.0-14.fc40.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.1-1.fc41.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-5.fc41.x86_64 elfutils-debuginfod-client-0.191-5.fc41.x86_64 elfutils-default-yama-scope-0.191-5.fc41.noarch elfutils-libelf-0.191-5.fc41.x86_64 elfutils-libs-0.191-5.fc41.x86_64 fedora-gpg-keys-41-0.1.noarch fedora-release-41-0.9.noarch fedora-release-common-41-0.9.noarch fedora-release-identity-basic-41-0.9.noarch fedora-repos-41-0.1.noarch fedora-repos-rawhide-41-0.1.noarch file-5.45-5.fc41.x86_64 file-libs-5.45-5.fc41.x86_64 filesystem-3.18-9.fc41.x86_64 findutils-1:4.9.0-8.fc40.x86_64 fonts-srpm-macros-1:2.0.5-14.fc40.noarch forge-srpm-macros-0.3.1-1.fc41.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-14.2-4.fc41.x86_64 gdbm-1:1.23-6.fc40.x86_64 gdbm-libs-1:1.23-6.fc40.x86_64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-12.fc41.x86_64 glibc-common-2.39.9000-12.fc41.x86_64 glibc-gconv-extra-2.39.9000-12.fc41.x86_64 glibc-minimal-langpack-2.39.9000-12.fc41.x86_64 gmp-1:6.3.0-1.fc41.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.x86_64 gzip-1.13-1.fc40.x86_64 info-7.1-2.fc40.x86_64 jansson-2.13.1-9.fc40.x86_64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.2-5.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.2-3.fc41.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40-13.fc41.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.69-8.fc41.x86_64 libcap-ng-0.8.5-1.fc41.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.7.1-1.fc41.x86_64 libeconf-0.6.2-1.fc41.x86_64 libevent-2.1.12-12.fc40.x86_64 libfdisk-2.40-13.fc41.x86_64 libffi-3.4.6-1.fc41.x86_64 libgcc-14.0.1-0.15.fc41.x86_64 libgomp-14.0.1-0.15.fc41.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40-13.fc41.x86_64 libnghttp2-1.61.0-1.fc41.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.0-1.fc40.x86_64 libpsl-0.21.5-3.fc40.x86_64 libpwquality-1.4.5-9.fc40.x86_64 libselinux-3.6-4.fc40.x86_64 libsemanage-3.6-3.fc40.x86_64 libsepol-3.6-3.fc40.x86_64 libsmartcols-2.40-13.fc41.x86_64 libssh-0.10.6-6.fc41.x86_64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.4-1.rc3.fc41.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc41.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40-13.fc41.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.6-1.fc41.x86_64 libzstd-1.5.6-1.fc41.x86_64 lua-libs-5.4.6-5.fc40.x86_64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.x86_64 mpfr-4.2.1-3.fc40.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.x86_64 openssl-libs-1:3.2.1-6.fc41.x86_64 p11-kit-0.25.3-4.fc40.x86_64 p11-kit-trust-0.25.3-4.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.x86_64 pam-libs-1.6.1-1.fc41.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.43-1.fc41.x86_64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.x86_64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-9.fc41.noarch qt5-srpm-macros-5.15.13-1.fc41.noarch qt6-srpm-macros-6.7.0-1.fc41.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.x86_64 rpm-build-4.19.1.1-1.fc40.x86_64 rpm-build-libs-4.19.1.1-1.fc40.x86_64 rpm-libs-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.6.0-2.fc40.x86_64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.x86_64 setup-2.14.5-2.fc40.noarch shadow-utils-2:4.15.1-2.fc41.x86_64 sqlite-libs-3.45.2-1.fc41.x86_64 systemd-libs-255.4-1.fc41.x86_64 tar-2:1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40-13.fc41.x86_64 util-linux-core-2.40-13.fc41.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-1:5.4.6-3.fc41.x86_64 xz-libs-1:5.4.6-3.fc41.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.6-2.fc40.x86_64 zstd-1.5.6-1.fc41.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-3.fc40.x86_64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.x86_64 authselect-1.5.0-5.fc41.x86_64 authselect-libs-1.5.0-5.fc41.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.42.50-6.fc41.x86_64 binutils-gold-2.42.50-6.fc41.x86_64 bzip2-1.0.8-18.fc40.x86_64 bzip2-libs-1.0.8-18.fc40.x86_64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.x86_64 coreutils-common-9.5-1.fc41.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.x86_64 cyrus-sasl-lib-2.1.28-19.fc40.x86_64 debugedit-5.0-14.fc40.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.1-1.fc41.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-5.fc41.x86_64 elfutils-debuginfod-client-0.191-5.fc41.x86_64 elfutils-default-yama-scope-0.191-5.fc41.noarch elfutils-libelf-0.191-5.fc41.x86_64 elfutils-libs-0.191-5.fc41.x86_64 fedora-gpg-keys-41-0.1.noarch fedora-release-41-0.9.noarch fedora-release-common-41-0.9.noarch fedora-release-identity-basic-41-0.9.noarch fedora-repos-41-0.1.noarch fedora-repos-rawhide-41-0.1.noarch file-5.45-5.fc41.x86_64 file-libs-5.45-5.fc41.x86_64 filesystem-3.18-9.fc41.x86_64 findutils-4.9.0-8.fc40.x86_64 fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.3.1-1.fc41.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-14.2-4.fc41.x86_64 gdbm-1.23-6.fc40.x86_64 gdbm-libs-1.23-6.fc40.x86_64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-12.fc41.x86_64 glibc-common-2.39.9000-12.fc41.x86_64 glibc-gconv-extra-2.39.9000-12.fc41.x86_64 glibc-minimal-langpack-2.39.9000-12.fc41.x86_64 gmp-6.3.0-1.fc41.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.x86_64 gzip-1.13-1.fc40.x86_64 info-7.1-2.fc40.x86_64 jansson-2.13.1-9.fc40.x86_64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.2-5.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.2-3.fc41.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40-13.fc41.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.69-8.fc41.x86_64 libcap-ng-0.8.5-1.fc41.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.7.1-1.fc41.x86_64 libeconf-0.6.2-1.fc41.x86_64 libevent-2.1.12-12.fc40.x86_64 libfdisk-2.40-13.fc41.x86_64 libffi-3.4.6-1.fc41.x86_64 libgcc-14.0.1-0.15.fc41.x86_64 libgomp-14.0.1-0.15.fc41.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40-13.fc41.x86_64 libnghttp2-1.61.0-1.fc41.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.0-1.fc40.x86_64 libpsl-0.21.5-3.fc40.x86_64 libpwquality-1.4.5-9.fc40.x86_64 libselinux-3.6-4.fc40.x86_64 libsemanage-3.6-3.fc40.x86_64 libsepol-3.6-3.fc40.x86_64 libsmartcols-2.40-13.fc41.x86_64 libssh-0.10.6-6.fc41.x86_64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.4-1.rc3.fc41.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc41.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40-13.fc41.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.6-1.fc41.x86_64 libzstd-1.5.6-1.fc41.x86_64 lua-libs-5.4.6-5.fc40.x86_64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.x86_64 mpfr-4.2.1-3.fc40.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.x86_64 openssl-libs-3.2.1-6.fc41.x86_64 p11-kit-0.25.3-4.fc40.x86_64 p11-kit-trust-0.25.3-4.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.x86_64 pam-libs-1.6.1-1.fc41.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.43-1.fc41.x86_64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.x86_64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-9.fc41.noarch qt5-srpm-macros-5.15.13-1.fc41.noarch qt6-srpm-macros-6.7.0-1.fc41.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.x86_64 rpm-build-4.19.1.1-1.fc40.x86_64 rpm-build-libs-4.19.1.1-1.fc40.x86_64 rpm-libs-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.6.0-2.fc40.x86_64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.x86_64 setup-2.14.5-2.fc40.noarch shadow-utils-4.15.1-2.fc41.x86_64 sqlite-libs-3.45.2-1.fc41.x86_64 systemd-libs-255.4-1.fc41.x86_64 tar-1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40-13.fc41.x86_64 util-linux-core-2.40-13.fc41.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-5.4.6-3.fc41.x86_64 xz-libs-5.4.6-3.fc41.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.6-2.fc40.x86_64 zstd-1.5.6-1.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-qh5thz05/python-biopython/python-biopython.spec) Config(child) 1 minutes 43 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.83-6.fc41.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1713531086.045918/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1713531086.045918/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1713531086.045918/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc41.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch yum-4.19.2-1.fc41.noarch Finish: chroot init Start: build phase for python-biopython-1.83-6.fc41.src.rpm Start: build setup for python-biopython-1.83-6.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 87 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 86 kB/s | 3.8 kB 00:00 fedora 87 kB/s | 24 kB 00:00 updates 81 kB/s | 22 kB 00:00 Dependencies resolved. ============================================================================================================================== Package Arch Version Repository Size ============================================================================================================================== Installing: gcc x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 M pyproject-rpm-macros noarch 1.12.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-devel x86_64 3.12.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 275 k python3-reportlab noarch 4.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.2 M Installing dependencies: abattis-cantarell-vf-fonts noarch 0.301-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 120 k annobin-docs noarch 12.49-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 89 k annobin-plugin-gcc x86_64 12.49-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 961 k cairo x86_64 1.18.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 709 k cpp x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 M default-fonts-core-sans noarch 4.0-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k dejavu-sans-fonts noarch 2.37-23.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 M expat x86_64 2.6.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 113 k fontconfig x86_64 2.15.0-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 256 k fonts-filesystem noarch 1:2.0.5-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.2 k freetype x86_64 2.13.2-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 410 k fribidi x86_64 1.0.13-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 91 k gc x86_64 8.2.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 110 k gcc-plugin-annobin x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 48 k glib2 x86_64 2.80.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.0 M glibc-devel x86_64 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 119 k glibc-headers-x86 noarch 2.39.9000-12.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 539 k gnutls x86_64 3.8.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M google-noto-fonts-common noarch 20240401-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k google-noto-sans-vf-fonts noarch 20240401-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 594 k graphite2 x86_64 1.3.14-15.fc40 copr_base 95 k guile30 x86_64 3.0.7-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 M harfbuzz x86_64 8.4.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M jbigkit-libs x86_64 2.1-29.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 53 k kernel-headers x86_64 6.9.0-0.rc4.37.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M lcms2 x86_64 2.16-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 180 k libX11 x86_64 1.8.9-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 648 k libX11-common noarch 1.8.9-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 145 k libXau x86_64 1.0.11-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 32 k libXext x86_64 1.3.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k libXrender x86_64 0.9.11-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k libb2 x86_64 0.98.1-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k libimagequant x86_64 4.0.3-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 306 k libjpeg-turbo x86_64 3.0.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 227 k liblerc x86_64 4.0.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 210 k libmpc x86_64 1.3.1-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 71 k libpng x86_64 2:1.6.40-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 120 k libraqm x86_64 0.8.0-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 20 k libtiff x86_64 4.6.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 332 k libwebp x86_64 1.4.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 291 k libxcb x86_64 1.17.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 234 k libxcrypt-devel x86_64 4.4.36-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 k make x86_64 1:4.4.1-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 580 k mpdecimal x86_64 2.5.1-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 89 k nettle x86_64 3.9.1-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 425 k openjpeg2 x86_64 2.5.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 186 k pixman x86_64 0.43.4-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 293 k python-pip-wheel noarch 24.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.5 M python-rpm-macros noarch 3.12-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k python3 x86_64 3.12.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k python3-chardet noarch 5.2.0-8.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 273 k python3-libs x86_64 3.12.3-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.8 M python3-olefile noarch 0.47-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 73 k python3-packaging noarch 24.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 116 k python3-pillow x86_64 10.3.0-1.fc41 copr_base 907 k python3-rpm-generators noarch 14-10.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 30 k python3-rpm-macros noarch 3.12-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k tzdata noarch 2024a-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 431 k xml-common noarch 0.6.3-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k Transaction Summary ============================================================================================================================== Install 63 Packages Total download size: 89 M Installed size: 307 M Downloading Packages: (1/63): python3-pillow-10.3.0-1.fc41.x86_64.rpm 12 MB/s | 907 kB 00:00 (2/63): abattis-cantarell-vf-fonts-0.301-12.fc4 1.5 MB/s | 120 kB 00:00 (3/63): annobin-docs-12.49-1.fc41.noarch.rpm 2.7 MB/s | 89 kB 00:00 (4/63): cairo-1.18.0-3.fc40.x86_64.rpm 17 MB/s | 709 kB 00:00 (5/63): annobin-plugin-gcc-12.49-1.fc41.x86_64. 9.1 MB/s | 961 kB 00:00 (6/63): cpp-14.0.1-0.15.fc41.x86_64.rpm 170 MB/s | 12 MB 00:00 (7/63): default-fonts-core-sans-4.0-12.fc40.noa 723 kB/s | 25 kB 00:00 (8/63): expat-2.6.2-1.fc41.x86_64.rpm 5.4 MB/s | 113 kB 00:00 (9/63): dejavu-sans-fonts-2.37-23.fc40.noarch.r 50 MB/s | 1.3 MB 00:00 (10/63): fontconfig-2.15.0-4.fc40.x86_64.rpm 12 MB/s | 256 kB 00:00 (11/63): fonts-filesystem-2.0.5-14.fc40.noarch. 409 kB/s | 8.2 kB 00:00 (12/63): fribidi-1.0.13-4.fc40.x86_64.rpm 3.6 MB/s | 91 kB 00:00 (13/63): freetype-2.13.2-5.fc40.x86_64.rpm 12 MB/s | 410 kB 00:00 (14/63): graphite2-1.3.14-15.fc40.x86_64.rpm 314 kB/s | 95 kB 00:00 (15/63): gc-8.2.2-6.fc40.x86_64.rpm 5.3 MB/s | 110 kB 00:00 (16/63): glib2-2.80.0-1.fc41.x86_64.rpm 66 MB/s | 3.0 MB 00:00 (17/63): gcc-plugin-annobin-14.0.1-0.15.fc41.x8 663 kB/s | 48 kB 00:00 (18/63): glibc-devel-2.39.9000-12.fc41.x86_64.r 4.8 MB/s | 119 kB 00:00 (19/63): glibc-headers-x86-2.39.9000-12.fc41.no 23 MB/s | 539 kB 00:00 (20/63): google-noto-fonts-common-20240401-1.fc 812 kB/s | 17 kB 00:00 (21/63): gnutls-3.8.5-1.fc41.x86_64.rpm 19 MB/s | 1.1 MB 00:00 (22/63): google-noto-sans-vf-fonts-20240401-1.f 24 MB/s | 594 kB 00:00 (23/63): harfbuzz-8.4.0-1.fc41.x86_64.rpm 28 MB/s | 1.0 MB 00:00 (24/63): guile30-3.0.7-12.fc40.x86_64.rpm 121 MB/s | 8.0 MB 00:00 (25/63): jbigkit-libs-2.1-29.fc40.x86_64.rpm 1.9 MB/s | 53 kB 00:00 (26/63): lcms2-2.16-3.fc40.x86_64.rpm 7.6 MB/s | 180 kB 00:00 (27/63): kernel-headers-6.9.0-0.rc4.37.fc41.x86 48 MB/s | 1.4 MB 00:00 (28/63): libX11-1.8.9-1.fc41.x86_64.rpm 26 MB/s | 648 kB 00:00 (29/63): libX11-common-1.8.9-1.fc41.noarch.rpm 6.9 MB/s | 145 kB 00:00 (30/63): libXext-1.3.6-1.fc40.x86_64.rpm 1.9 MB/s | 39 kB 00:00 (31/63): libXau-1.0.11-6.fc40.x86_64.rpm 1.4 MB/s | 32 kB 00:00 (32/63): libXrender-0.9.11-6.fc40.x86_64.rpm 1.3 MB/s | 27 kB 00:00 (33/63): libb2-0.98.1-11.fc40.x86_64.rpm 1.1 MB/s | 25 kB 00:00 (34/63): gcc-14.0.1-0.15.fc41.x86_64.rpm 107 MB/s | 37 MB 00:00 (35/63): libjpeg-turbo-3.0.2-1.fc40.x86_64.rpm 5.0 MB/s | 227 kB 00:00 (36/63): libimagequant-4.0.3-3.fc40.x86_64.rpm 5.7 MB/s | 306 kB 00:00 (37/63): liblerc-4.0.0-6.fc40.x86_64.rpm 9.3 MB/s | 210 kB 00:00 (38/63): libmpc-1.3.1-5.fc40.x86_64.rpm 3.4 MB/s | 71 kB 00:00 (39/63): libpng-1.6.40-3.fc40.x86_64.rpm 5.3 MB/s | 120 kB 00:00 (40/63): libraqm-0.8.0-7.fc40.x86_64.rpm 900 kB/s | 20 kB 00:00 (41/63): libtiff-4.6.0-2.fc40.x86_64.rpm 13 MB/s | 332 kB 00:00 (42/63): libwebp-1.4.0-1.fc41.x86_64.rpm 13 MB/s | 291 kB 00:00 (43/63): libxcb-1.17.0-1.fc41.x86_64.rpm 11 MB/s | 234 kB 00:00 (44/63): libxcrypt-devel-4.4.36-5.fc40.x86_64.r 1.3 MB/s | 29 kB 00:00 (45/63): make-4.4.1-6.fc40.x86_64.rpm 22 MB/s | 580 kB 00:00 (46/63): mpdecimal-2.5.1-9.fc40.x86_64.rpm 3.7 MB/s | 89 kB 00:00 (47/63): nettle-3.9.1-6.fc40.x86_64.rpm 19 MB/s | 425 kB 00:00 (48/63): openjpeg2-2.5.2-1.fc41.x86_64.rpm 7.7 MB/s | 186 kB 00:00 (49/63): pixman-0.43.4-1.fc41.x86_64.rpm 13 MB/s | 293 kB 00:00 (50/63): pyproject-rpm-macros-1.12.0-1.fc40.noa 1.7 MB/s | 41 kB 00:00 (51/63): python-rpm-macros-3.12-9.fc41.noarch.r 833 kB/s | 18 kB 00:00 (52/63): python3-3.12.3-2.fc41.x86_64.rpm 1.3 MB/s | 27 kB 00:00 (53/63): python-pip-wheel-24.0-2.fc41.noarch.rp 40 MB/s | 1.5 MB 00:00 (54/63): python3-chardet-5.2.0-8.fc41.noarch.rp 11 MB/s | 273 kB 00:00 (55/63): python3-devel-3.12.3-2.fc41.x86_64.rpm 12 MB/s | 275 kB 00:00 (56/63): python3-olefile-0.47-3.fc40.noarch.rpm 3.0 MB/s | 73 kB 00:00 (57/63): python3-packaging-24.0-1.fc41.noarch.r 5.5 MB/s | 116 kB 00:00 (58/63): python3-rpm-generators-14-10.fc40.noar 1.1 MB/s | 30 kB 00:00 (59/63): python3-reportlab-4.2.0-1.fc41.noarch. 62 MB/s | 3.2 MB 00:00 (60/63): python3-rpm-macros-3.12-9.fc41.noarch. 413 kB/s | 13 kB 00:00 (61/63): tzdata-2024a-5.fc41.noarch.rpm 17 MB/s | 431 kB 00:00 (62/63): python3-libs-3.12.3-2.fc41.x86_64.rpm 72 MB/s | 8.8 MB 00:00 (63/63): xml-common-0.6.3-63.fc40.noarch.rpm 1.3 MB/s | 31 kB 00:00 -------------------------------------------------------------------------------- Total 98 MB/s | 89 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : fonts-filesystem-1:2.0.5-14.fc40.noarch 1/63 Installing : python-rpm-macros-3.12-9.fc41.noarch 2/63 Installing : python3-rpm-macros-3.12-9.fc41.noarch 3/63 Installing : libwebp-1.4.0-1.fc41.x86_64 4/63 Installing : libpng-2:1.6.40-3.fc40.x86_64 5/63 Installing : libmpc-1.3.1-5.fc40.x86_64 6/63 Installing : libjpeg-turbo-3.0.2-1.fc40.x86_64 7/63 Installing : cpp-14.0.1-0.15.fc41.x86_64 8/63 Installing : pyproject-rpm-macros-1.12.0-1.fc40.noarch 9/63 Installing : abattis-cantarell-vf-fonts-0.301-12.fc40.noarch 10/63 Installing : dejavu-sans-fonts-2.37-23.fc40.noarch 11/63 Running scriptlet: xml-common-0.6.3-63.fc40.noarch 12/63 Installing : xml-common-0.6.3-63.fc40.noarch 12/63 Installing : tzdata-2024a-5.fc41.noarch 13/63 Installing : python-pip-wheel-24.0-2.fc41.noarch 14/63 Installing : pixman-0.43.4-1.fc41.x86_64 15/63 Installing : openjpeg2-2.5.2-1.fc41.x86_64 16/63 Installing : nettle-3.9.1-6.fc40.x86_64 17/63 Installing : gnutls-3.8.5-1.fc41.x86_64 18/63 Installing : glib2-2.80.0-1.fc41.x86_64 19/63 Installing : mpdecimal-2.5.1-9.fc40.x86_64 20/63 Installing : liblerc-4.0.0-6.fc40.x86_64 21/63 Installing : libimagequant-4.0.3-3.fc40.x86_64 22/63 Installing : libb2-0.98.1-11.fc40.x86_64 23/63 Installing : libXau-1.0.11-6.fc40.x86_64 24/63 Installing : libxcb-1.17.0-1.fc41.x86_64 25/63 Installing : libX11-common-1.8.9-1.fc41.noarch 26/63 Installing : libX11-1.8.9-1.fc41.x86_64 27/63 Installing : libXext-1.3.6-1.fc40.x86_64 28/63 Installing : libXrender-0.9.11-6.fc40.x86_64 29/63 Installing : lcms2-2.16-3.fc40.x86_64 30/63 Installing : kernel-headers-6.9.0-0.rc4.37.fc41.x86_64 31/63 Installing : jbigkit-libs-2.1-29.fc40.x86_64 32/63 Installing : libtiff-4.6.0-2.fc40.x86_64 33/63 Installing : google-noto-fonts-common-20240401-1.fc41.noarch 34/63 Installing : google-noto-sans-vf-fonts-20240401-1.fc41.noarch 35/63 Installing : default-fonts-core-sans-4.0-12.fc40.noarch 36/63 Installing : glibc-headers-x86-2.39.9000-12.fc41.noarch 37/63 Installing : libxcrypt-devel-4.4.36-5.fc40.x86_64 38/63 Installing : glibc-devel-2.39.9000-12.fc41.x86_64 39/63 Installing : gc-8.2.2-6.fc40.x86_64 40/63 Installing : guile30-3.0.7-12.fc40.x86_64 41/63 Installing : make-1:4.4.1-6.fc40.x86_64 42/63 Installing : gcc-14.0.1-0.15.fc41.x86_64 43/63 Running scriptlet: gcc-14.0.1-0.15.fc41.x86_64 43/63 Installing : fribidi-1.0.13-4.fc40.x86_64 44/63 Installing : expat-2.6.2-1.fc41.x86_64 45/63 Installing : python3-3.12.3-2.fc41.x86_64 46/63 Installing : python3-libs-3.12.3-2.fc41.x86_64 47/63 Installing : python3-chardet-5.2.0-8.fc41.noarch 48/63 Installing : python3-olefile-0.47-3.fc40.noarch 49/63 Installing : python3-packaging-24.0-1.fc41.noarch 50/63 Installing : python3-rpm-generators-14-10.fc40.noarch 51/63 Installing : annobin-docs-12.49-1.fc41.noarch 52/63 Installing : graphite2-1.3.14-15.fc40.x86_64 53/63 Installing : cairo-1.18.0-3.fc40.x86_64 54/63 Installing : harfbuzz-8.4.0-1.fc41.x86_64 55/63 Installing : freetype-2.13.2-5.fc40.x86_64 56/63 Installing : fontconfig-2.15.0-4.fc40.x86_64 57/63 Running scriptlet: fontconfig-2.15.0-4.fc40.x86_64 57/63 Installing : libraqm-0.8.0-7.fc40.x86_64 58/63 Installing : python3-pillow-10.3.0-1.fc41.x86_64 59/63 Installing : python3-reportlab-4.2.0-1.fc41.noarch 60/63 Installing : annobin-plugin-gcc-12.49-1.fc41.x86_64 61/63 Running scriptlet: annobin-plugin-gcc-12.49-1.fc41.x86_64 61/63 Installing : python3-devel-3.12.3-2.fc41.x86_64 62/63 Installing : gcc-plugin-annobin-14.0.1-0.15.fc41.x86_64 63/63 Running scriptlet: gcc-plugin-annobin-14.0.1-0.15.fc41.x86_64 63/63 Running scriptlet: fontconfig-2.15.0-4.fc40.x86_64 63/63 Running scriptlet: gcc-plugin-annobin-14.0.1-0.15.fc41.x86_64 63/63 Installed: abattis-cantarell-vf-fonts-0.301-12.fc40.noarch annobin-docs-12.49-1.fc41.noarch annobin-plugin-gcc-12.49-1.fc41.x86_64 cairo-1.18.0-3.fc40.x86_64 cpp-14.0.1-0.15.fc41.x86_64 default-fonts-core-sans-4.0-12.fc40.noarch dejavu-sans-fonts-2.37-23.fc40.noarch expat-2.6.2-1.fc41.x86_64 fontconfig-2.15.0-4.fc40.x86_64 fonts-filesystem-1:2.0.5-14.fc40.noarch freetype-2.13.2-5.fc40.x86_64 fribidi-1.0.13-4.fc40.x86_64 gc-8.2.2-6.fc40.x86_64 gcc-14.0.1-0.15.fc41.x86_64 gcc-plugin-annobin-14.0.1-0.15.fc41.x86_64 glib2-2.80.0-1.fc41.x86_64 glibc-devel-2.39.9000-12.fc41.x86_64 glibc-headers-x86-2.39.9000-12.fc41.noarch gnutls-3.8.5-1.fc41.x86_64 google-noto-fonts-common-20240401-1.fc41.noarch google-noto-sans-vf-fonts-20240401-1.fc41.noarch graphite2-1.3.14-15.fc40.x86_64 guile30-3.0.7-12.fc40.x86_64 harfbuzz-8.4.0-1.fc41.x86_64 jbigkit-libs-2.1-29.fc40.x86_64 kernel-headers-6.9.0-0.rc4.37.fc41.x86_64 lcms2-2.16-3.fc40.x86_64 libX11-1.8.9-1.fc41.x86_64 libX11-common-1.8.9-1.fc41.noarch libXau-1.0.11-6.fc40.x86_64 libXext-1.3.6-1.fc40.x86_64 libXrender-0.9.11-6.fc40.x86_64 libb2-0.98.1-11.fc40.x86_64 libimagequant-4.0.3-3.fc40.x86_64 libjpeg-turbo-3.0.2-1.fc40.x86_64 liblerc-4.0.0-6.fc40.x86_64 libmpc-1.3.1-5.fc40.x86_64 libpng-2:1.6.40-3.fc40.x86_64 libraqm-0.8.0-7.fc40.x86_64 libtiff-4.6.0-2.fc40.x86_64 libwebp-1.4.0-1.fc41.x86_64 libxcb-1.17.0-1.fc41.x86_64 libxcrypt-devel-4.4.36-5.fc40.x86_64 make-1:4.4.1-6.fc40.x86_64 mpdecimal-2.5.1-9.fc40.x86_64 nettle-3.9.1-6.fc40.x86_64 openjpeg2-2.5.2-1.fc41.x86_64 pixman-0.43.4-1.fc41.x86_64 pyproject-rpm-macros-1.12.0-1.fc40.noarch python-pip-wheel-24.0-2.fc41.noarch python-rpm-macros-3.12-9.fc41.noarch python3-3.12.3-2.fc41.x86_64 python3-chardet-5.2.0-8.fc41.noarch python3-devel-3.12.3-2.fc41.x86_64 python3-libs-3.12.3-2.fc41.x86_64 python3-olefile-0.47-3.fc40.noarch python3-packaging-24.0-1.fc41.noarch python3-pillow-10.3.0-1.fc41.x86_64 python3-reportlab-4.2.0-1.fc41.noarch python3-rpm-generators-14-10.fc40.noarch python3-rpm-macros-3.12-9.fc41.noarch tzdata-2024a-5.fc41.noarch xml-common-0.6.3-63.fc40.noarch Complete! Finish: build setup for python-biopython-1.83-6.fc41.src.rpm Start: rpmbuild python-biopython-1.83-6.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.YVKh3U + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf biopython-1.83 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.83.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd biopython-1.83 + rm -rf /builddir/build/BUILD/biopython-1.83-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/biopython-1.83-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/4683.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/4696.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/4706.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.vWO8Mm + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + echo 'python3dist(wheel)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement not satisfied: setuptools >= 40.8 Handling wheel from default build backend Requirement not satisfied: wheel Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 70 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 61 kB/s | 3.8 kB 00:00 fedora 90 kB/s | 24 kB 00:00 updates 81 kB/s | 22 kB 00:00 Package gcc-14.0.1-0.15.fc41.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-packaging-24.0-1.fc41.noarch is already installed. Package python3-reportlab-4.2.0-1.fc41.noarch is already installed. Dependencies resolved. ================================================================================================================== Package Arch Version Repository Size ================================================================================================================== Installing: python3-pip noarch 24.0-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 M python3-setuptools noarch 69.2.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M python3-wheel noarch 1:0.43.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 149 k Transaction Summary ================================================================================================================== Install 3 Packages Total download size: 4.5 M Installed size: 22 M Downloading Packages: (1/3): python3-wheel-0.43.0-1.fc41.noarch.rpm 1.6 MB/s | 149 kB 00:00 (2/3): python3-setuptools-69.2.0-1.fc41.noarch. 14 MB/s | 1.4 MB 00:00 (3/3): python3-pip-24.0-2.fc41.noarch.rpm 16 MB/s | 2.9 MB 00:00 -------------------------------------------------------------------------------- Total 24 MB/s | 4.5 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-wheel-1:0.43.0-1.fc41.noarch 1/3 Installing : python3-setuptools-69.2.0-1.fc41.noarch 2/3 Installing : python3-pip-24.0-2.fc41.noarch 3/3 Running scriptlet: python3-pip-24.0-2.fc41.noarch 3/3 Installed: python3-pip-24.0-2.fc41.noarch python3-setuptools-69.2.0-1.fc41.noarch python3-wheel-1:0.43.0-1.fc41.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.LQPIf4 + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + echo 'python3dist(wheel)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.2.0) Handling wheel from default build backend Requirement satisfied: wheel (installed: wheel 0.43.0) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement not satisfied: numpy + cat /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/LICENSE.rst' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/top_level.txt' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 90 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 52 kB/s | 3.8 kB 00:00 fedora 87 kB/s | 24 kB 00:00 updates 84 kB/s | 22 kB 00:00 Package gcc-14.0.1-0.15.fc41.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-packaging-24.0-1.fc41.noarch is already installed. Package python3-pip-24.0-2.fc41.noarch is already installed. Package python3-reportlab-4.2.0-1.fc41.noarch is already installed. Package python3-setuptools-69.2.0-1.fc41.noarch is already installed. Package python3-wheel-1:0.43.0-1.fc41.noarch is already installed. Dependencies resolved. ========================================================================================================================== Package Arch Version Repository Size ========================================================================================================================== Installing: python3-numpy x86_64 1:1.26.4-3.fc41 copr_base 7.2 M Installing dependencies: flexiblas x86_64 3.4.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k flexiblas-netlib x86_64 3.4.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.2 M flexiblas-openblas-openmp x86_64 3.4.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k libgfortran x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 932 k libquadmath x86_64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 195 k openblas x86_64 0.3.26-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k openblas-openmp x86_64 0.3.26-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 5.1 M Transaction Summary ========================================================================================================================== Install 8 Packages Total download size: 17 M Installed size: 97 M Downloading Packages: (1/8): python3-numpy-1.26.4-3.fc41.x86_64.rpm 162 MB/s | 7.2 MB 00:00 (2/8): flexiblas-3.4.2-1.fc41.x86_64.rpm 493 kB/s | 25 kB 00:00 (3/8): flexiblas-openblas-openmp-3.4.2-1.fc41.x 1.0 MB/s | 18 kB 00:00 (4/8): libgfortran-14.0.1-0.15.fc41.x86_64.rpm 17 MB/s | 932 kB 00:00 (5/8): openblas-0.3.26-4.fc40.x86_64.rpm 2.6 MB/s | 39 kB 00:00 (6/8): openblas-openmp-0.3.26-4.fc40.x86_64.rpm 115 MB/s | 5.1 MB 00:00 (7/8): libquadmath-14.0.1-0.15.fc41.x86_64.rpm 1.6 MB/s | 195 kB 00:00 (8/8): flexiblas-netlib-3.4.2-1.fc41.x86_64.rpm 13 MB/s | 3.2 MB 00:00 -------------------------------------------------------------------------------- Total 65 MB/s | 17 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libgfortran-14.0.1-0.15.fc41.x86_64 1/8 Installing : openblas-0.3.26-4.fc40.x86_64 2/8 Installing : openblas-openmp-0.3.26-4.fc40.x86_64 3/8 Installing : libquadmath-14.0.1-0.15.fc41.x86_64 4/8 Installing : flexiblas-netlib-3.4.2-1.fc41.x86_64 5/8 Installing : flexiblas-openblas-openmp-3.4.2-1.fc41.x86_64 6/8 Installing : flexiblas-3.4.2-1.fc41.x86_64 7/8 Installing : python3-numpy-1:1.26.4-3.fc41.x86_64 8/8 Running scriptlet: python3-numpy-1:1.26.4-3.fc41.x86_64 8/8 Installed: flexiblas-3.4.2-1.fc41.x86_64 flexiblas-netlib-3.4.2-1.fc41.x86_64 flexiblas-openblas-openmp-3.4.2-1.fc41.x86_64 libgfortran-14.0.1-0.15.fc41.x86_64 libquadmath-14.0.1-0.15.fc41.x86_64 openblas-0.3.26-4.fc40.x86_64 openblas-openmp-0.3.26-4.fc40.x86_64 python3-numpy-1:1.26.4-3.fc41.x86_64 Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.1jcxpQ + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + echo 'python3dist(wheel)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.2.0) Handling wheel from default build backend Requirement satisfied: wheel (installed: wheel 0.43.0) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 1.26.4) + cat /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/LICENSE.rst' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/top_level.txt' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 90 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 61 kB/s | 3.8 kB 00:00 fedora 88 kB/s | 24 kB 00:00 updates 83 kB/s | 22 kB 00:00 Package gcc-14.0.1-0.15.fc41.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc40.noarch is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-devel-3.12.3-2.fc41.x86_64 is already installed. Package python3-numpy-1:1.26.4-3.fc41.x86_64 is already installed. Package python3-packaging-24.0-1.fc41.noarch is already installed. Package python3-pip-24.0-2.fc41.noarch is already installed. Package python3-reportlab-4.2.0-1.fc41.noarch is already installed. Package python3-setuptools-69.2.0-1.fc41.noarch is already installed. Package python3-wheel-1:0.43.0-1.fc41.noarch is already installed. Dependencies resolved. Nothing to do. Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1713484800 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.8KGeFw + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + echo 'python3dist(wheel)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.2.0) Handling wheel from default build backend Requirement satisfied: wheel (installed: wheel 0.43.0) running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.43.0) running dist_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 1.26.4) + cat /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/LICENSE.rst' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/top_level.txt' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0WARYT + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.83 + mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir Processing /builddir/build/BUILD/biopython-1.83 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info writing /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/dependency_links.txt writing requirements to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-5q3jp3q4/biopython-1.83.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: biopython Building wheel for biopython (pyproject.toml): started Running command Building wheel for biopython (pyproject.toml) running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/Bio copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/File.py -> build/lib.linux-x86_64-cpython-312/Bio creating build/lib.linux-x86_64-cpython-312/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-312/Bio/Affy creating build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-312/Bio/Align creating build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/Applications creating build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices creating build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-312/Bio/AlignIO creating build/lib.linux-x86_64-cpython-312/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Alphabet creating build/lib.linux-x86_64-cpython-312/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Application creating build/lib.linux-x86_64-cpython-312/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-312/Bio/Blast creating build/lib.linux-x86_64-cpython-312/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/CAPS creating build/lib.linux-x86_64-cpython-312/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Cluster creating build/lib.linux-x86_64-cpython-312/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/codonalign creating build/lib.linux-x86_64-cpython-312/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Compass creating build/lib.linux-x86_64-cpython-312/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-312/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-312/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-312/Bio/Data creating build/lib.linux-x86_64-cpython-312/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-312/Bio/Emboss creating build/lib.linux-x86_64-cpython-312/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-312/Bio/Entrez creating build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-312/Bio/ExPASy creating build/lib.linux-x86_64-cpython-312/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/GenBank creating build/lib.linux-x86_64-cpython-312/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-312/Bio/Geo creating build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics creating build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram creating build/lib.linux-x86_64-cpython-312/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-312/Bio/HMM creating build/lib.linux-x86_64-cpython-312/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Gene creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map creating build/lib.linux-x86_64-cpython-312/Bio/PDB creating build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf creating build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML creating build/lib.linux-x86_64-cpython-312/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Medline creating build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs creating build/lib.linux-x86_64-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/applications creating build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar creating build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-312/Bio/Nexus creating build/lib.linux-x86_64-cpython-312/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-312/Bio/NMR creating build/lib.linux-x86_64-cpython-312/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway creating build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-312/Bio/PDB creating build/lib.linux-x86_64-cpython-312/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-312/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-312/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/phenotype creating build/lib.linux-x86_64-cpython-312/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen creating build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop creating build/lib.linux-x86_64-cpython-312/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-312/Bio/Restriction creating build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-312/Bio/SCOP creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO creating build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO creating build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO creating build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-312/Bio/SeqUtils creating build/lib.linux-x86_64-cpython-312/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing creating build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications creating build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer creating build/lib.linux-x86_64-cpython-312/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-312/Bio/SwissProt creating build/lib.linux-x86_64-cpython-312/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/TogoWS creating build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo creating build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications creating build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML creating build/lib.linux-x86_64-cpython-312/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/UniGene creating build/lib.linux-x86_64-cpython-312/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-312/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-312/Bio/UniProt creating build/lib.linux-x86_64-cpython-312/BioSQL copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-312/BioSQL copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-312/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-312/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-312/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-312/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/py.typed -> build/lib.linux-x86_64-cpython-312/Bio copying Bio/Align/_codonaligner.c -> build/lib.linux-x86_64-cpython-312/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-x86_64-cpython-312/Bio/Align creating build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-312/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-312/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-312/Bio/Cluster creating build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs creating build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-312/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-312/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-312/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-312/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-x86_64-cpython-312/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/Bio creating build/temp.linux-x86_64-cpython-312/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Align/_codonaligner.c -o build/temp.linux-x86_64-cpython-312/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Align/_codonaligner.cpython-312-x86_64-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-x86_64-cpython-312/Bio/Align/_pairwisealigner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Align/_pairwisealigner.cpython-312-x86_64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-312/Bio/cpairwise2module.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/cpairwise2.cpython-312-x86_64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-x86_64-cpython-312/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-312/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.cpython-312-x86_64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-x86_64-cpython-312/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-312/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.cpython-312-x86_64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-x86_64-cpython-312/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-312/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/Cluster/_cluster.cpython-312-x86_64-linux-gnu.so building 'Bio.PDB.kdtrees' extension creating build/temp.linux-x86_64-cpython-312/Bio/PDB gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-312/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.cpython-312-x86_64-linux-gnu.so building 'Bio.PDB.ccealign' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-312/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealign.cpython-312-x86_64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-x86_64-cpython-312/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/py.typed -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/BioSeq.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/BioSeqDatabase.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/DBUtils.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/Loader.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-312/BioSQL/__init__.py -> build/bdist.linux-x86_64/wheel/BioSQL creating build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/cpairwise2.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/py.typed -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/cpairwise2module.c -> build/bdist.linux-x86_64/wheel/Bio creating build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-312/Bio/UniProt/GOA.py -> build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-312/Bio/UniProt/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/UniProt creating build/bdist.linux-x86_64/wheel/Bio/UniGene copying build/lib.linux-x86_64-cpython-312/Bio/UniGene/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/UniGene creating build/bdist.linux-x86_64/wheel/Bio/Phylo creating build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML creating build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/BaseTree.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/CDAO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/CDAOIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Consensus.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NeXML.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/Newick.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NewickIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/NexusIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PhyloXML.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_io.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-312/Bio/Phylo/_utils.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo creating build/bdist.linux-x86_64/wheel/Bio/TogoWS copying build/lib.linux-x86_64-cpython-312/Bio/TogoWS/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/TogoWS creating build/bdist.linux-x86_64/wheel/Bio/SwissProt copying build/lib.linux-x86_64-cpython-312/Bio/SwissProt/KeyWList.py -> build/bdist.linux-x86_64/wheel/Bio/SwissProt copying build/lib.linux-x86_64-cpython-312/Bio/SwissProt/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SwissProt creating build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer copying build/lib.linux-x86_64-cpython-312/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer creating build/bdist.linux-x86_64/wheel/Bio/Sequencing creating build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Ace.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/Phd.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-312/Bio/Sequencing/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing creating build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-312/Bio/SeqUtils/lcc.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils creating build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/AbiIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/AceIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/GckIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/IgIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/NibIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PdbIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PhdIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/PirIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/QualityIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SffIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SwissIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/TabIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/_index.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-312/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/hit.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_model/query.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/BlatIO.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_index.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-312/Bio/SearchIO/_utils.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO creating build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Cla.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Des.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Dom.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Hie.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Raf.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/Residues.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-312/Bio/SCOP/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP creating build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/PrintFormat.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/Restriction.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-312/Bio/Restriction/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction creating build/bdist.linux-x86_64/wheel/Bio/PopGen creating build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-312/Bio/PopGen/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen creating build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/phen_micro.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-312/Bio/phenotype/pm_fitting.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype creating build/bdist.linux-x86_64/wheel/Bio/Pathway creating build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-312/Bio/Pathway/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway creating build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-312/Bio/NMR/NOEtools.py -> build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-312/Bio/NMR/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-312/Bio/NMR/xpktools.py -> build/bdist.linux-x86_64/wheel/Bio/NMR creating build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/cnexus.c -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Nexus.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Nodes.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/StandardData.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/Trees.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-312/Bio/Nexus/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus creating build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/_pwm.c -> build/bdist.linux-x86_64/wheel/Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-312/Bio/motifs/jaspar/db.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar creating build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-312/Bio/motifs/applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-312/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-312/Bio/motifs/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/alignace.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/clusterbuster.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/mast.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/matrix.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/meme.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/minimal.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/pfm.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/thresholds.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/transfac.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-312/Bio/motifs/xms.py -> build/bdist.linux-x86_64/wheel/Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/Medline copying build/lib.linux-x86_64-cpython-312/Bio/Medline/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Medline creating build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealign.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/kdtrees.c -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ccealignmodule.c -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Atom.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Chain.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/DSSP.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Dice.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Entity.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/FragmentMapper.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/HSExposure.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/MMCIFParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Model.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/NACCESS.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBExceptions.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBList.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PDBParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PICIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/PSEA.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Polypeptide.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Residue.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ResidueDepth.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/SASA.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/SCADIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Selection.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Structure.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/StructureAlignment.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/StructureBuilder.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/Superimposer.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/cealign.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ic_data.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/ic_rebuild.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/internal_coords.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmcifio.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/qcprot.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-312/Bio/PDB/vectors.py -> build/bdist.linux-x86_64/wheel/Bio/PDB creating build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-312/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf creating build/bdist.linux-x86_64/wheel/Bio/KEGG creating build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Map copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Map/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Map creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/REST.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG copying build/lib.linux-x86_64-cpython-312/Bio/KEGG/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG creating build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-312/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-312/Bio/HMM/MarkovModel.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-312/Bio/HMM/Trainer.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-312/Bio/HMM/Utilities.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-312/Bio/HMM/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/HMM creating build/bdist.linux-x86_64/wheel/Bio/Graphics creating build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/Comparative.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/Distribution.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/KGML_vis.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-312/Bio/Graphics/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics creating build/bdist.linux-x86_64/wheel/Bio/Geo copying build/lib.linux-x86_64-cpython-312/Bio/Geo/Record.py -> build/bdist.linux-x86_64/wheel/Bio/Geo copying build/lib.linux-x86_64-cpython-312/Bio/Geo/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Geo creating build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/Record.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/Scanner.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-312/Bio/GenBank/utils.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank creating build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Enzyme.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Prodoc.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/Prosite.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-312/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy creating build/bdist.linux-x86_64/wheel/Bio/Entrez creating build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs creating build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isolat1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isogrk1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isocyr2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isocyr1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isobox.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsr.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamso.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsn.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsc.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsb.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/isoamsa.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/htmltable.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/format.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esummary_gene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esummary-v1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/esearch.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/epost.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/elink.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/einfo.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/egquery.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSummary_041029.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSpell.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eSearch_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eLink_101123.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eLink_090910.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/eInfo_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/display.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/default-mixes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/default-classes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/common.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/chars.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/backmatter.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/articlemeta.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-modules.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-models.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivecustom-classes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/archivearticle.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/SP_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/SP_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PRF_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PIR_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/PDB_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/OMSSA.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NSE.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NSE.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Project.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-link1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-format1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-display1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-common1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/HomoloGene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/GenBank_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/EMBL_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/Parser.py -> build/bdist.linux-x86_64/wheel/Bio/Entrez copying build/lib.linux-x86_64-cpython-312/Bio/Entrez/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Entrez creating build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/Applications.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/Primer3.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-312/Bio/Emboss/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss creating build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-312/Bio/Data/CodonTable.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-312/Bio/Data/IUPACData.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-312/Bio/Data/PDBData.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-312/Bio/Data/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Data creating build/bdist.linux-x86_64/wheel/Bio/Compass copying build/lib.linux-x86_64-cpython-312/Bio/Compass/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Compass creating build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/codonalignment.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-312/Bio/codonalign/codonseq.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign creating build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/_cluster.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/clustermodule.c -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/cluster.h -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/cluster.c -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-312/Bio/Cluster/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Cluster creating build/bdist.linux-x86_64/wheel/Bio/CAPS copying build/lib.linux-x86_64-cpython-312/Bio/CAPS/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/CAPS creating build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-312/Bio/Blast/Applications.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-312/Bio/Blast/NCBIWWW.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-312/Bio/Blast/NCBIXML.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-312/Bio/Blast/Record.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-312/Bio/Blast/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Blast creating build/bdist.linux-x86_64/wheel/Bio/Application copying build/lib.linux-x86_64-cpython-312/Bio/Application/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Application creating build/bdist.linux-x86_64/wheel/Bio/Alphabet copying build/lib.linux-x86_64-cpython-312/Bio/Alphabet/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Alphabet creating build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MafIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MauveIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/MsfIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/NexusIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-312/Bio/AlignIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO creating build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/_pairwisealigner.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/_codonaligner.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/_pairwisealigner.c -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/_codonaligner.c -> build/bdist.linux-x86_64/wheel/Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/NUC.4.4 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-312/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices creating build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Prank.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-312/Bio/Align/AlignInfo.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/a2m.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/analysis.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/bed.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigbed.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigmaf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/bigpsl.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/chain.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/clustal.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/emboss.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/exonerate.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/fasta.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/hhr.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/maf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/mauve.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/msf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/nexus.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/phylip.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/psl.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/sam.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/stockholm.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-312/Bio/Align/tabular.py -> build/bdist.linux-x86_64/wheel/Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-312/Bio/Affy/CelFile.py -> build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-312/Bio/Affy/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-312/Bio/File.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/LogisticRegression.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/MarkovModel.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/MaxEntropy.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/NaiveBayes.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/Seq.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/SeqFeature.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/SeqRecord.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/__init__.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/_utils.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/bgzf.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/kNN.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-312/Bio/pairwise2.py -> build/bdist.linux-x86_64/wheel/Bio running install_egg_info Copying biopython.egg-info to build/bdist.linux-x86_64/wheel/biopython-1.83-py3.12.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/biopython-1.83.dist-info/WHEEL creating '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-wheel-e6lpfvif/.tmp-ngkg0qsq/biopython-1.83-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'Bio/File.py' adding 'Bio/LogisticRegression.py' adding 'Bio/MarkovModel.py' adding 'Bio/MaxEntropy.py' adding 'Bio/NaiveBayes.py' adding 'Bio/Seq.py' adding 'Bio/SeqFeature.py' adding 'Bio/SeqRecord.py' adding 'Bio/__init__.py' adding 'Bio/_utils.py' adding 'Bio/bgzf.py' adding 'Bio/cpairwise2.cpython-312-x86_64-linux-gnu.so' adding 'Bio/cpairwise2module.c' adding 'Bio/kNN.py' adding 'Bio/pairwise2.py' adding 'Bio/py.typed' adding 'Bio/Affy/CelFile.py' adding 'Bio/Affy/__init__.py' adding 'Bio/Align/AlignInfo.py' adding 'Bio/Align/__init__.py' adding 'Bio/Align/_codonaligner.c' adding 'Bio/Align/_codonaligner.cpython-312-x86_64-linux-gnu.so' adding 'Bio/Align/_pairwisealigner.c' adding 'Bio/Align/_pairwisealigner.cpython-312-x86_64-linux-gnu.so' adding 'Bio/Align/a2m.py' adding 'Bio/Align/analysis.py' adding 'Bio/Align/bed.py' adding 'Bio/Align/bigbed.py' adding 'Bio/Align/bigmaf.py' adding 'Bio/Align/bigpsl.py' adding 'Bio/Align/chain.py' adding 'Bio/Align/clustal.py' adding 'Bio/Align/emboss.py' adding 'Bio/Align/exonerate.py' adding 'Bio/Align/fasta.py' adding 'Bio/Align/hhr.py' adding 'Bio/Align/interfaces.py' adding 'Bio/Align/maf.py' adding 'Bio/Align/mauve.py' adding 'Bio/Align/msf.py' adding 'Bio/Align/nexus.py' adding 'Bio/Align/phylip.py' adding 'Bio/Align/psl.py' adding 'Bio/Align/sam.py' adding 'Bio/Align/stockholm.py' adding 'Bio/Align/tabular.py' adding 'Bio/Align/Applications/_ClustalOmega.py' adding 'Bio/Align/Applications/_Clustalw.py' adding 'Bio/Align/Applications/_Dialign.py' adding 'Bio/Align/Applications/_MSAProbs.py' adding 'Bio/Align/Applications/_Mafft.py' adding 'Bio/Align/Applications/_Muscle.py' adding 'Bio/Align/Applications/_Prank.py' adding 'Bio/Align/Applications/_Probcons.py' adding 'Bio/Align/Applications/_TCoffee.py' adding 'Bio/Align/Applications/__init__.py' adding 'Bio/Align/substitution_matrices/__init__.py' adding 'Bio/Align/substitution_matrices/data/BENNER22' adding 'Bio/Align/substitution_matrices/data/BENNER6' adding 'Bio/Align/substitution_matrices/data/BENNER74' adding 'Bio/Align/substitution_matrices/data/BLASTN' adding 'Bio/Align/substitution_matrices/data/BLASTP' adding 'Bio/Align/substitution_matrices/data/BLOSUM45' adding 'Bio/Align/substitution_matrices/data/BLOSUM50' adding 'Bio/Align/substitution_matrices/data/BLOSUM62' adding 'Bio/Align/substitution_matrices/data/BLOSUM80' adding 'Bio/Align/substitution_matrices/data/BLOSUM90' adding 'Bio/Align/substitution_matrices/data/DAYHOFF' adding 'Bio/Align/substitution_matrices/data/FENG' adding 'Bio/Align/substitution_matrices/data/GENETIC' adding 'Bio/Align/substitution_matrices/data/GONNET1992' adding 'Bio/Align/substitution_matrices/data/HOXD70' adding 'Bio/Align/substitution_matrices/data/JOHNSON' adding 'Bio/Align/substitution_matrices/data/JONES' adding 'Bio/Align/substitution_matrices/data/LEVIN' adding 'Bio/Align/substitution_matrices/data/MCLACHLAN' adding 'Bio/Align/substitution_matrices/data/MDM78' adding 'Bio/Align/substitution_matrices/data/MEGABLAST' adding 'Bio/Align/substitution_matrices/data/NUC.4.4' adding 'Bio/Align/substitution_matrices/data/PAM250' adding 'Bio/Align/substitution_matrices/data/PAM30' adding 'Bio/Align/substitution_matrices/data/PAM70' adding 'Bio/Align/substitution_matrices/data/RAO' adding 'Bio/Align/substitution_matrices/data/RISLER' adding 'Bio/Align/substitution_matrices/data/SCHNEIDER' adding 'Bio/Align/substitution_matrices/data/STR' adding 'Bio/Align/substitution_matrices/data/TRANS' adding 'Bio/AlignIO/ClustalIO.py' adding 'Bio/AlignIO/EmbossIO.py' adding 'Bio/AlignIO/FastaIO.py' adding 'Bio/AlignIO/Interfaces.py' adding 'Bio/AlignIO/MafIO.py' adding 'Bio/AlignIO/MauveIO.py' adding 'Bio/AlignIO/MsfIO.py' adding 'Bio/AlignIO/NexusIO.py' adding 'Bio/AlignIO/PhylipIO.py' adding 'Bio/AlignIO/StockholmIO.py' adding 'Bio/AlignIO/__init__.py' adding 'Bio/Alphabet/__init__.py' adding 'Bio/Application/__init__.py' adding 'Bio/Blast/Applications.py' adding 'Bio/Blast/NCBIWWW.py' adding 'Bio/Blast/NCBIXML.py' adding 'Bio/Blast/Record.py' adding 'Bio/Blast/__init__.py' adding 'Bio/CAPS/__init__.py' adding 'Bio/Cluster/__init__.py' adding 'Bio/Cluster/_cluster.cpython-312-x86_64-linux-gnu.so' adding 'Bio/Cluster/cluster.c' adding 'Bio/Cluster/cluster.h' adding 'Bio/Cluster/clustermodule.c' adding 'Bio/Compass/__init__.py' adding 'Bio/Data/CodonTable.py' adding 'Bio/Data/IUPACData.py' adding 'Bio/Data/PDBData.py' adding 'Bio/Data/__init__.py' adding 'Bio/Emboss/Applications.py' adding 'Bio/Emboss/Primer3.py' adding 'Bio/Emboss/PrimerSearch.py' adding 'Bio/Emboss/__init__.py' adding 'Bio/Entrez/Parser.py' adding 'Bio/Entrez/__init__.py' adding 'Bio/Entrez/DTDs/BITS-embedded-index2.ent' adding 'Bio/Entrez/DTDs/BITS-question-answer2.ent' adding 'Bio/Entrez/DTDs/Docsum_3_0.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_0.mod.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_1.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_1.mod.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_2.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_2.mod.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_3.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_3.mod.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_4.dtd' adding 'Bio/Entrez/DTDs/Docsum_3_4.mod.dtd' adding 'Bio/Entrez/DTDs/EMBL_General.dtd' adding 'Bio/Entrez/DTDs/EMBL_General.mod.dtd' adding 'Bio/Entrez/DTDs/GenBank_General.dtd' adding 'Bio/Entrez/DTDs/GenBank_General.mod.dtd' adding 'Bio/Entrez/DTDs/HomoloGene.dtd' adding 'Bio/Entrez/DTDs/HomoloGene.mod.dtd' adding 'Bio/Entrez/DTDs/INSD_INSDSeq.dtd' adding 'Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd' adding 'Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent' adding 'Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent' adding 'Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd' adding 'Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent' adding 'Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent' adding 'Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent' adding 'Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent' adding 'Bio/Entrez/DTDs/JATS-articlemeta1-3.ent' adding 'Bio/Entrez/DTDs/JATS-backmatter1-3.ent' adding 'Bio/Entrez/DTDs/JATS-chars1-3.ent' adding 'Bio/Entrez/DTDs/JATS-common-atts1-3.ent' adding 'Bio/Entrez/DTDs/JATS-common1-3.ent' adding 'Bio/Entrez/DTDs/JATS-default-classes1-3.ent' adding 'Bio/Entrez/DTDs/JATS-default-mixes1-3.ent' adding 'Bio/Entrez/DTDs/JATS-display1-3.ent' adding 'Bio/Entrez/DTDs/JATS-format1-3.ent' adding 'Bio/Entrez/DTDs/JATS-funding1-3.ent' adding 'Bio/Entrez/DTDs/JATS-journalmeta1-3.ent' adding 'Bio/Entrez/DTDs/JATS-link1-3.ent' adding 'Bio/Entrez/DTDs/JATS-list1-3.ent' adding 'Bio/Entrez/DTDs/JATS-math1-3.ent' adding 'Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent' adding 'Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent' adding 'Bio/Entrez/DTDs/JATS-modules1-3.ent' adding 'Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent' adding 'Bio/Entrez/DTDs/JATS-notat1-3.ent' adding 'Bio/Entrez/DTDs/JATS-para1-3.ent' adding 'Bio/Entrez/DTDs/JATS-phrase1-3.ent' adding 'Bio/Entrez/DTDs/JATS-references1-3.ent' adding 'Bio/Entrez/DTDs/JATS-related-object1-3.ent' adding 'Bio/Entrez/DTDs/JATS-section1-3.ent' adding 'Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent' adding 'Bio/Entrez/DTDs/MMDB.dtd' adding 'Bio/Entrez/DTDs/MMDB.mod.dtd' adding 'Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd' adding 'Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd' adding 'Bio/Entrez/DTDs/MMDB_Features.dtd' adding 'Bio/Entrez/DTDs/MMDB_Features.mod.dtd' adding 'Bio/Entrez/DTDs/MMDB_Structural_model.dtd' adding 'Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Access.dtd' adding 'Bio/Entrez/DTDs/NCBI_Access.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Biblio.dtd' adding 'Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_BioSource.dtd' adding 'Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_BioTree.dtd' adding 'Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Blast4.dtd' adding 'Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_BlastDL.dtd' adding 'Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.dtd' adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Cdd.dtd' adding 'Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Cn3d.dtd' adding 'Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Entity.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Entrez2.dtd' adding 'Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Entrezgene.dtd' adding 'Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_FeatDef.dtd' adding 'Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_GBSeq.dtd' adding 'Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Gene.dtd' adding 'Bio/Entrez/DTDs/NCBI_Gene.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_General.dtd' adding 'Bio/Entrez/DTDs/NCBI_General.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_ID1Access.dtd' adding 'Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_ID2Access.dtd' adding 'Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_MedArchive.dtd' adding 'Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Medlars.dtd' adding 'Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Medline.dtd' adding 'Bio/Entrez/DTDs/NCBI_Medline.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Mim.dtd' adding 'Bio/Entrez/DTDs/NCBI_Mim.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Mime.dtd' adding 'Bio/Entrez/DTDs/NCBI_Mime.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_ObjPrt.dtd' adding 'Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Organism.dtd' adding 'Bio/Entrez/DTDs/NCBI_Organism.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_PCAssay.dtd' adding 'Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_PCSubstance.dtd' adding 'Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Project.dtd' adding 'Bio/Entrez/DTDs/NCBI_Project.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Protein.dtd' adding 'Bio/Entrez/DTDs/NCBI_Protein.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Pub.dtd' adding 'Bio/Entrez/DTDs/NCBI_Pub.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_PubMed.dtd' adding 'Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_RNA.dtd' adding 'Bio/Entrez/DTDs/NCBI_RNA.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Remap.dtd' adding 'Bio/Entrez/DTDs/NCBI_Remap.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Rsite.dtd' adding 'Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_ScoreMat.dtd' adding 'Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_SeqCode.dtd' adding 'Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_SeqTable.dtd' adding 'Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seq_split.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqalign.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqfeat.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqloc.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqres.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqset.dtd' adding 'Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Sequence.dtd' adding 'Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Submit.dtd' adding 'Bio/Entrez/DTDs/NCBI_Submit.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Systems.dtd' adding 'Bio/Entrez/DTDs/NCBI_TSeq.dtd' adding 'Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_TxInit.dtd' adding 'Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_Variation.dtd' adding 'Bio/Entrez/DTDs/NCBI_Variation.mod.dtd' adding 'Bio/Entrez/DTDs/NCBI_all.dtd' adding 'Bio/Entrez/DTDs/NSE.dtd' adding 'Bio/Entrez/DTDs/NSE.mod.dtd' adding 'Bio/Entrez/DTDs/OMSSA.dtd' adding 'Bio/Entrez/DTDs/OMSSA.mod.dtd' adding 'Bio/Entrez/DTDs/PDB_General.dtd' adding 'Bio/Entrez/DTDs/PDB_General.mod.dtd' adding 'Bio/Entrez/DTDs/PIR_General.dtd' adding 'Bio/Entrez/DTDs/PIR_General.mod.dtd' adding 'Bio/Entrez/DTDs/PRF_General.dtd' adding 'Bio/Entrez/DTDs/PRF_General.mod.dtd' adding 'Bio/Entrez/DTDs/SP_General.dtd' adding 'Bio/Entrez/DTDs/SP_General.mod.dtd' adding 'Bio/Entrez/DTDs/XHTMLtablesetup.ent' adding 'Bio/Entrez/DTDs/archivearticle.dtd' adding 'Bio/Entrez/DTDs/archivecustom-classes.ent' adding 'Bio/Entrez/DTDs/archivecustom-mixes.ent' adding 'Bio/Entrez/DTDs/archivecustom-models.ent' adding 'Bio/Entrez/DTDs/archivecustom-modules.ent' adding 'Bio/Entrez/DTDs/articlemeta.ent' adding 'Bio/Entrez/DTDs/backmatter.ent' adding 'Bio/Entrez/DTDs/bookdoc_100301.dtd' adding 'Bio/Entrez/DTDs/bookdoc_110101.dtd' adding 'Bio/Entrez/DTDs/bookdoc_120101.dtd' adding 'Bio/Entrez/DTDs/bookdoc_130101.dtd' adding 'Bio/Entrez/DTDs/bookdoc_140101.dtd' adding 'Bio/Entrez/DTDs/bookdoc_150101.dtd' adding 'Bio/Entrez/DTDs/chars.ent' adding 'Bio/Entrez/DTDs/common.ent' adding 'Bio/Entrez/DTDs/default-classes.ent' adding 'Bio/Entrez/DTDs/default-mixes.ent' adding 'Bio/Entrez/DTDs/display.ent' adding 'Bio/Entrez/DTDs/eInfo_020511.dtd' adding 'Bio/Entrez/DTDs/eLink_090910.dtd' adding 'Bio/Entrez/DTDs/eLink_101123.dtd' adding 'Bio/Entrez/DTDs/ePost_020511.dtd' adding 'Bio/Entrez/DTDs/eSearch_020511.dtd' adding 'Bio/Entrez/DTDs/eSpell.dtd' adding 'Bio/Entrez/DTDs/eSummary_041029.dtd' adding 'Bio/Entrez/DTDs/egquery.dtd' adding 'Bio/Entrez/DTDs/einfo.dtd' adding 'Bio/Entrez/DTDs/elink.dtd' adding 'Bio/Entrez/DTDs/elink_020122.dtd' adding 'Bio/Entrez/DTDs/epost.dtd' adding 'Bio/Entrez/DTDs/esearch.dtd' adding 'Bio/Entrez/DTDs/esummary-v1.dtd' adding 'Bio/Entrez/DTDs/esummary_gene.dtd' adding 'Bio/Entrez/DTDs/format.ent' adding 'Bio/Entrez/DTDs/htmltable.dtd' adding 'Bio/Entrez/DTDs/isoamsa.ent' adding 'Bio/Entrez/DTDs/isoamsb.ent' adding 'Bio/Entrez/DTDs/isoamsc.ent' adding 'Bio/Entrez/DTDs/isoamsn.ent' adding 'Bio/Entrez/DTDs/isoamso.ent' adding 'Bio/Entrez/DTDs/isoamsr.ent' adding 'Bio/Entrez/DTDs/isobox.ent' adding 'Bio/Entrez/DTDs/isocyr1.ent' adding 'Bio/Entrez/DTDs/isocyr2.ent' adding 'Bio/Entrez/DTDs/isodia.ent' adding 'Bio/Entrez/DTDs/isogrk1.ent' adding 'Bio/Entrez/DTDs/isogrk2.ent' adding 'Bio/Entrez/DTDs/isogrk3.ent' adding 'Bio/Entrez/DTDs/isogrk4.ent' adding 'Bio/Entrez/DTDs/isolat1.ent' adding 'Bio/Entrez/DTDs/isolat2.ent' adding 'Bio/Entrez/DTDs/isomfrk.ent' adding 'Bio/Entrez/DTDs/isomopf.ent' adding 'Bio/Entrez/DTDs/isomscr.ent' adding 'Bio/Entrez/DTDs/isonum.ent' adding 'Bio/Entrez/DTDs/isopub.ent' adding 'Bio/Entrez/DTDs/isotech.ent' adding 'Bio/Entrez/DTDs/journalmeta.ent' adding 'Bio/Entrez/DTDs/link.ent' adding 'Bio/Entrez/DTDs/list.ent' adding 'Bio/Entrez/DTDs/math.ent' adding 'Bio/Entrez/DTDs/mathml-in-pubmed.mod' adding 'Bio/Entrez/DTDs/mathml2-qname-1.mod' adding 'Bio/Entrez/DTDs/mathml2.dtd' adding 'Bio/Entrez/DTDs/mathml3-qname1.mod' adding 'Bio/Entrez/DTDs/mathml3.dtd' adding 'Bio/Entrez/DTDs/mathmlsetup.ent' adding 'Bio/Entrez/DTDs/mmlalias.ent' adding 'Bio/Entrez/DTDs/mmlextra.ent' adding 'Bio/Entrez/DTDs/modules.ent' adding 'Bio/Entrez/DTDs/nlm-articleset-2.0.dtd' adding 'Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd' adding 'Bio/Entrez/DTDs/nlmcommon_011101.dtd' adding 'Bio/Entrez/DTDs/nlmcommon_080101.dtd' adding 'Bio/Entrez/DTDs/nlmcommon_090101.dtd' adding 'Bio/Entrez/DTDs/nlmmedline_011101.dtd' adding 'Bio/Entrez/DTDs/nlmmedline_080101.dtd' adding 'Bio/Entrez/DTDs/nlmmedline_090101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd' adding 'Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd' adding 'Bio/Entrez/DTDs/nlmserials_080101.dtd' adding 'Bio/Entrez/DTDs/nlmserials_100101.dtd' adding 'Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd' adding 'Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd' adding 'Bio/Entrez/DTDs/notat.ent' adding 'Bio/Entrez/DTDs/para.ent' adding 'Bio/Entrez/DTDs/phrase.ent' adding 'Bio/Entrez/DTDs/pmc-1.dtd' adding 'Bio/Entrez/DTDs/pubmed_020114.dtd' adding 'Bio/Entrez/DTDs/pubmed_080101.dtd' adding 'Bio/Entrez/DTDs/pubmed_090101.dtd' adding 'Bio/Entrez/DTDs/pubmed_100101.dtd' adding 'Bio/Entrez/DTDs/pubmed_100301.dtd' adding 'Bio/Entrez/DTDs/pubmed_110101.dtd' adding 'Bio/Entrez/DTDs/pubmed_120101.dtd' adding 'Bio/Entrez/DTDs/pubmed_130101.dtd' adding 'Bio/Entrez/DTDs/pubmed_130501.dtd' adding 'Bio/Entrez/DTDs/pubmed_140101.dtd' adding 'Bio/Entrez/DTDs/pubmed_150101.dtd' adding 'Bio/Entrez/DTDs/pubmed_180101.dtd' adding 'Bio/Entrez/DTDs/pubmed_180601.dtd' adding 'Bio/Entrez/DTDs/pubmed_190101.dtd' adding 'Bio/Entrez/DTDs/references.ent' adding 'Bio/Entrez/DTDs/section.ent' adding 'Bio/Entrez/DTDs/taxon.dtd' adding 'Bio/Entrez/DTDs/xhtml-inlstyle-1.mod' adding 'Bio/Entrez/DTDs/xhtml-table-1.mod' adding 'Bio/Entrez/DTDs/xmlspecchars.ent' adding 'Bio/Entrez/XSDs/IPGReportSet.xsd' adding 'Bio/ExPASy/Enzyme.py' adding 'Bio/ExPASy/Prodoc.py' adding 'Bio/ExPASy/Prosite.py' adding 'Bio/ExPASy/ScanProsite.py' adding 'Bio/ExPASy/__init__.py' adding 'Bio/ExPASy/cellosaurus.py' adding 'Bio/GenBank/Record.py' adding 'Bio/GenBank/Scanner.py' adding 'Bio/GenBank/__init__.py' adding 'Bio/GenBank/utils.py' adding 'Bio/Geo/Record.py' adding 'Bio/Geo/__init__.py' adding 'Bio/Graphics/BasicChromosome.py' adding 'Bio/Graphics/ColorSpiral.py' adding 'Bio/Graphics/Comparative.py' adding 'Bio/Graphics/DisplayRepresentation.py' adding 'Bio/Graphics/Distribution.py' adding 'Bio/Graphics/KGML_vis.py' adding 'Bio/Graphics/__init__.py' adding 'Bio/Graphics/GenomeDiagram/_AbstractDrawer.py' adding 'Bio/Graphics/GenomeDiagram/_CircularDrawer.py' adding 'Bio/Graphics/GenomeDiagram/_Colors.py' adding 'Bio/Graphics/GenomeDiagram/_CrossLink.py' adding 'Bio/Graphics/GenomeDiagram/_Diagram.py' adding 'Bio/Graphics/GenomeDiagram/_Feature.py' adding 'Bio/Graphics/GenomeDiagram/_FeatureSet.py' adding 'Bio/Graphics/GenomeDiagram/_Graph.py' adding 'Bio/Graphics/GenomeDiagram/_GraphSet.py' adding 'Bio/Graphics/GenomeDiagram/_LinearDrawer.py' adding 'Bio/Graphics/GenomeDiagram/_Track.py' adding 'Bio/Graphics/GenomeDiagram/__init__.py' adding 'Bio/HMM/DynamicProgramming.py' adding 'Bio/HMM/MarkovModel.py' adding 'Bio/HMM/Trainer.py' adding 'Bio/HMM/Utilities.py' adding 'Bio/HMM/__init__.py' adding 'Bio/KEGG/REST.py' adding 'Bio/KEGG/__init__.py' adding 'Bio/KEGG/Compound/__init__.py' adding 'Bio/KEGG/Enzyme/__init__.py' adding 'Bio/KEGG/Gene/__init__.py' adding 'Bio/KEGG/KGML/KGML_parser.py' adding 'Bio/KEGG/KGML/KGML_pathway.py' adding 'Bio/KEGG/KGML/__init__.py' adding 'Bio/KEGG/Map/__init__.py' adding 'Bio/Medline/__init__.py' adding 'Bio/NMR/NOEtools.py' adding 'Bio/NMR/__init__.py' adding 'Bio/NMR/xpktools.py' adding 'Bio/Nexus/Nexus.py' adding 'Bio/Nexus/Nodes.py' adding 'Bio/Nexus/StandardData.py' adding 'Bio/Nexus/Trees.py' adding 'Bio/Nexus/__init__.py' adding 'Bio/Nexus/cnexus.c' adding 'Bio/Nexus/cnexus.cpython-312-x86_64-linux-gnu.so' adding 'Bio/PDB/AbstractPropertyMap.py' adding 'Bio/PDB/Atom.py' adding 'Bio/PDB/Chain.py' adding 'Bio/PDB/DSSP.py' adding 'Bio/PDB/Dice.py' adding 'Bio/PDB/Entity.py' adding 'Bio/PDB/FragmentMapper.py' adding 'Bio/PDB/HSExposure.py' adding 'Bio/PDB/MMCIF2Dict.py' adding 'Bio/PDB/MMCIFParser.py' adding 'Bio/PDB/Model.py' adding 'Bio/PDB/NACCESS.py' adding 'Bio/PDB/NeighborSearch.py' adding 'Bio/PDB/PDBExceptions.py' adding 'Bio/PDB/PDBIO.py' adding 'Bio/PDB/PDBList.py' adding 'Bio/PDB/PDBParser.py' adding 'Bio/PDB/PICIO.py' adding 'Bio/PDB/PSEA.py' adding 'Bio/PDB/Polypeptide.py' adding 'Bio/PDB/Residue.py' adding 'Bio/PDB/ResidueDepth.py' adding 'Bio/PDB/SASA.py' adding 'Bio/PDB/SCADIO.py' adding 'Bio/PDB/Selection.py' adding 'Bio/PDB/Structure.py' adding 'Bio/PDB/StructureAlignment.py' adding 'Bio/PDB/StructureBuilder.py' adding 'Bio/PDB/Superimposer.py' adding 'Bio/PDB/__init__.py' adding 'Bio/PDB/ccealign.cpython-312-x86_64-linux-gnu.so' adding 'Bio/PDB/ccealignmodule.c' adding 'Bio/PDB/cealign.py' adding 'Bio/PDB/ic_data.py' adding 'Bio/PDB/ic_rebuild.py' adding 'Bio/PDB/internal_coords.py' adding 'Bio/PDB/kdtrees.c' adding 'Bio/PDB/kdtrees.cpython-312-x86_64-linux-gnu.so' adding 'Bio/PDB/mmcifio.py' adding 'Bio/PDB/parse_pdb_header.py' adding 'Bio/PDB/qcprot.py' adding 'Bio/PDB/vectors.py' adding 'Bio/PDB/mmtf/DefaultParser.py' adding 'Bio/PDB/mmtf/__init__.py' adding 'Bio/PDB/mmtf/mmtfio.py' adding 'Bio/Pathway/__init__.py' adding 'Bio/Pathway/Rep/Graph.py' adding 'Bio/Pathway/Rep/MultiGraph.py' adding 'Bio/Pathway/Rep/__init__.py' adding 'Bio/Phylo/BaseTree.py' adding 'Bio/Phylo/CDAO.py' adding 'Bio/Phylo/CDAOIO.py' adding 'Bio/Phylo/Consensus.py' adding 'Bio/Phylo/NeXML.py' adding 'Bio/Phylo/NeXMLIO.py' adding 'Bio/Phylo/Newick.py' adding 'Bio/Phylo/NewickIO.py' adding 'Bio/Phylo/NexusIO.py' adding 'Bio/Phylo/PhyloXML.py' adding 'Bio/Phylo/PhyloXMLIO.py' adding 'Bio/Phylo/TreeConstruction.py' adding 'Bio/Phylo/__init__.py' adding 'Bio/Phylo/_cdao_owl.py' adding 'Bio/Phylo/_io.py' adding 'Bio/Phylo/_utils.py' adding 'Bio/Phylo/Applications/_Fasttree.py' adding 'Bio/Phylo/Applications/_Phyml.py' adding 'Bio/Phylo/Applications/_Raxml.py' adding 'Bio/Phylo/Applications/__init__.py' adding 'Bio/Phylo/PAML/__init__.py' adding 'Bio/Phylo/PAML/_paml.py' adding 'Bio/Phylo/PAML/_parse_baseml.py' adding 'Bio/Phylo/PAML/_parse_codeml.py' adding 'Bio/Phylo/PAML/_parse_yn00.py' adding 'Bio/Phylo/PAML/baseml.py' adding 'Bio/Phylo/PAML/chi2.py' adding 'Bio/Phylo/PAML/codeml.py' adding 'Bio/Phylo/PAML/yn00.py' adding 'Bio/PopGen/__init__.py' adding 'Bio/PopGen/GenePop/Controller.py' adding 'Bio/PopGen/GenePop/EasyController.py' adding 'Bio/PopGen/GenePop/FileParser.py' adding 'Bio/PopGen/GenePop/LargeFileParser.py' adding 'Bio/PopGen/GenePop/__init__.py' adding 'Bio/Restriction/PrintFormat.py' adding 'Bio/Restriction/Restriction.py' adding 'Bio/Restriction/Restriction_Dictionary.py' adding 'Bio/Restriction/__init__.py' adding 'Bio/SCOP/Cla.py' adding 'Bio/SCOP/Des.py' adding 'Bio/SCOP/Dom.py' adding 'Bio/SCOP/Hie.py' adding 'Bio/SCOP/Raf.py' adding 'Bio/SCOP/Residues.py' adding 'Bio/SCOP/__init__.py' adding 'Bio/SVDSuperimposer/__init__.py' adding 'Bio/SearchIO/BlatIO.py' adding 'Bio/SearchIO/FastaIO.py' adding 'Bio/SearchIO/__init__.py' adding 'Bio/SearchIO/_index.py' adding 'Bio/SearchIO/_utils.py' adding 'Bio/SearchIO/BlastIO/__init__.py' adding 'Bio/SearchIO/BlastIO/blast_tab.py' adding 'Bio/SearchIO/BlastIO/blast_xml.py' adding 'Bio/SearchIO/ExonerateIO/__init__.py' adding 'Bio/SearchIO/ExonerateIO/_base.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_cigar.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_text.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_vulgar.py' adding 'Bio/SearchIO/HHsuiteIO/__init__.py' adding 'Bio/SearchIO/HHsuiteIO/hhsuite2_text.py' adding 'Bio/SearchIO/HmmerIO/__init__.py' adding 'Bio/SearchIO/HmmerIO/_base.py' adding 'Bio/SearchIO/HmmerIO/hmmer2_text.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_domtab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_tab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_text.py' adding 'Bio/SearchIO/InterproscanIO/__init__.py' adding 'Bio/SearchIO/InterproscanIO/interproscan_xml.py' adding 'Bio/SearchIO/_model/__init__.py' adding 'Bio/SearchIO/_model/_base.py' adding 'Bio/SearchIO/_model/hit.py' adding 'Bio/SearchIO/_model/hsp.py' adding 'Bio/SearchIO/_model/query.py' adding 'Bio/SeqIO/AbiIO.py' adding 'Bio/SeqIO/AceIO.py' adding 'Bio/SeqIO/FastaIO.py' adding 'Bio/SeqIO/GckIO.py' adding 'Bio/SeqIO/IgIO.py' adding 'Bio/SeqIO/InsdcIO.py' adding 'Bio/SeqIO/Interfaces.py' adding 'Bio/SeqIO/NibIO.py' adding 'Bio/SeqIO/PdbIO.py' adding 'Bio/SeqIO/PhdIO.py' adding 'Bio/SeqIO/PirIO.py' adding 'Bio/SeqIO/QualityIO.py' adding 'Bio/SeqIO/SeqXmlIO.py' adding 'Bio/SeqIO/SffIO.py' adding 'Bio/SeqIO/SnapGeneIO.py' adding 'Bio/SeqIO/SwissIO.py' adding 'Bio/SeqIO/TabIO.py' adding 'Bio/SeqIO/TwoBitIO.py' adding 'Bio/SeqIO/UniprotIO.py' adding 'Bio/SeqIO/XdnaIO.py' adding 'Bio/SeqIO/__init__.py' adding 'Bio/SeqIO/_index.py' adding 'Bio/SeqIO/_twoBitIO.c' adding 'Bio/SeqIO/_twoBitIO.cpython-312-x86_64-linux-gnu.so' adding 'Bio/SeqUtils/CheckSum.py' adding 'Bio/SeqUtils/IsoelectricPoint.py' adding 'Bio/SeqUtils/MeltingTemp.py' adding 'Bio/SeqUtils/ProtParam.py' adding 'Bio/SeqUtils/ProtParamData.py' adding 'Bio/SeqUtils/__init__.py' adding 'Bio/SeqUtils/lcc.py' adding 'Bio/Sequencing/Ace.py' adding 'Bio/Sequencing/Phd.py' adding 'Bio/Sequencing/__init__.py' adding 'Bio/Sequencing/Applications/_Novoalign.py' adding 'Bio/Sequencing/Applications/__init__.py' adding 'Bio/Sequencing/Applications/_bwa.py' adding 'Bio/Sequencing/Applications/_samtools.py' adding 'Bio/SwissProt/KeyWList.py' adding 'Bio/SwissProt/__init__.py' adding 'Bio/TogoWS/__init__.py' adding 'Bio/UniGene/__init__.py' adding 'Bio/UniProt/GOA.py' adding 'Bio/UniProt/__init__.py' adding 'Bio/codonalign/__init__.py' adding 'Bio/codonalign/codonalignment.py' adding 'Bio/codonalign/codonseq.py' adding 'Bio/motifs/__init__.py' adding 'Bio/motifs/_pwm.c' adding 'Bio/motifs/_pwm.cpython-312-x86_64-linux-gnu.so' adding 'Bio/motifs/alignace.py' adding 'Bio/motifs/clusterbuster.py' adding 'Bio/motifs/mast.py' adding 'Bio/motifs/matrix.py' adding 'Bio/motifs/meme.py' adding 'Bio/motifs/minimal.py' adding 'Bio/motifs/pfm.py' adding 'Bio/motifs/thresholds.py' adding 'Bio/motifs/transfac.py' adding 'Bio/motifs/xms.py' adding 'Bio/motifs/applications/__init__.py' adding 'Bio/motifs/applications/_xxmotif.py' adding 'Bio/motifs/jaspar/__init__.py' adding 'Bio/motifs/jaspar/db.py' adding 'Bio/phenotype/__init__.py' adding 'Bio/phenotype/phen_micro.py' adding 'Bio/phenotype/pm_fitting.py' adding 'BioSQL/BioSeq.py' adding 'BioSQL/BioSeqDatabase.py' adding 'BioSQL/DBUtils.py' adding 'BioSQL/Loader.py' adding 'BioSQL/__init__.py' adding 'BioSQL/py.typed' adding 'biopython-1.83.dist-info/LICENSE' adding 'biopython-1.83.dist-info/LICENSE.rst' adding 'biopython-1.83.dist-info/METADATA' adding 'biopython-1.83.dist-info/WHEEL' adding 'biopython-1.83.dist-info/top_level.txt' adding 'biopython-1.83.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Building wheel for biopython (pyproject.toml): finished with status 'done' Created wheel for biopython: filename=biopython-1.83-cp312-cp312-linux_x86_64.whl size=3074019 sha256=5a74a236e1905cabcb2cbdb49958c0eaf5921a14b27cae223f747e1e83c1bd71 Stored in directory: /builddir/.cache/pip/wheels/8f/13/4d/5683b29d5ae933c1f9b0d0a504ae17c8e39ba4601c20249b2d Successfully built biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.cBT6fu + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.83 ++ ls /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir/biopython-1.83-cp312-cp312-linux_x86_64.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=biopython==1.83 + '[' -z biopython==1.83 ']' + TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir biopython==1.83 Using pip 24.0 from /usr/lib/python3.12/site-packages/pip (python 3.12) Looking in links: /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir Processing ./pyproject-wheeldir/biopython-1.83-cp312-cp312-linux_x86_64.whl Installing collected packages: biopython Successfully installed biopython-1.83 + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin ']' + rm -f /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages ']' + '[' /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages '!=' /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages ']' + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages ']' + site_dirs+=("/usr/lib64/python3.12/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.12/site-packages/biopython-1.83.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 --record /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD --output /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-record + rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD removed '/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD' + rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/REQUESTED removed '/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_PERCENTAGES_COUNT=2 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-modules --buildroot /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 --sitelib /usr/lib/python3.12/site-packages --sitearch /usr/lib64/python3.12/site-packages --python-version 3.12 --pyproject-record /builddir/build/BUILD/python-biopython-1.83-6.fc41.x86_64-pyproject-record --prefix /usr Bio BioSQL + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.83-6.fc41 --unique-debug-suffix -1.83-6.fc41.x86_64 --unique-debug-src-base python-biopython-1.83-6.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/biopython-1.83 find-debuginfo: starting Extracting debug info from 9 files DWARF-compressing 9 files sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-biopython-1.83-6.fc41.x86_64 1246 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ofQ0ek + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd biopython-1.83 ~/build/BUILD/biopython-1.83/Tests ~/build/BUILD/biopython-1.83 + pushd Tests ++ grep -v test_Align_bigbed.py ++ grep -v test_Tutorial.py ++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_chain.py test_Align_clustal.py test_Align_codonalign.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCPSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Ace.py test_Ace ... ok test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser) Test to check that contig parser parses each contig into a contig. ... ok test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Affy.py test_Affy ... ok testAffy3 (test_Affy.AffyTest.testAffy3) ... ok testAffy4 (test_Affy.AffyTest.testAffy4) ... ok testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO.py test_AlignIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files) Check that parsing an empty file returns an empty list. ... ok test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate) Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files) Check that writers can cope with no alignments. ... ok test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments) Check that writers reject records that are not alignments. ... ok test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.647 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_ClustalIO.py test_AlignIO_ClustalIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header) Make sure we can parse the Biopython header. ... ok test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok test_empty (test_AlignIO_ClustalIO.TestClustalIO.test_empty) Checking empty file. ... ok test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header) Make sure we can parse the Kalign header. ... ok test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read) Checking write/read. ... ok test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single) Testing write/read when there is only one sequence. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.033 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.039 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_PhylipIO.py test_AlignIO_PhylipIO ... ok test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.033 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_convert.py test_AlignIO_convert ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type) Converting Clustal to NEXUS with a molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type) Converting Clustal to NEXUS without a molecule type. ... ok test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.106 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignInfo.py test_AlignInfo ... ok test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_Alignment.py test_Align_Alignment ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_mapall (test_Align_Alignment.TestAlign_mapall.test_mapall) ... ok test_nucleotide_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_nucleotide_nucleotide_str) ... ok test_protein_nucleotide_many_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_many_str) ... ok test_protein_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_str) ... ok test_aligned (test_Align_Alignment.TestAlign_out_of_order.test_aligned) ... ok test_array (test_Align_Alignment.TestAlign_out_of_order.test_array) ... ok test_indices (test_Align_Alignment.TestAlign_out_of_order.test_indices) ... ok test_row (test_Align_Alignment.TestAlign_out_of_order.test_row) ... ok test_row_col (test_Align_Alignment.TestAlign_out_of_order.test_row_col) ... ok test_row_iterable (test_Align_Alignment.TestAlign_out_of_order.test_row_iterable) ... ok test_row_slice (test_Align_Alignment.TestAlign_out_of_order.test_row_slice) ... ok test_rows_col (test_Align_Alignment.TestAlign_out_of_order.test_rows_col) ... ok test_rows_cols (test_Align_Alignment.TestAlign_out_of_order.test_rows_cols) ... ok test_str (test_Align_Alignment.TestAlign_out_of_order.test_str) ... ok test_substitutions (test_Align_Alignment.TestAlign_out_of_order.test_substitutions) ... ok test_empty_alignment (test_Align_Alignment.TestAlignment.test_empty_alignment) ... ok test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok test_a2m (test_Align_Alignment.TestAlignment_pairwise_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_pairwise_format.test_bed) ... ok test_clustal (test_Align_Alignment.TestAlignment_pairwise_format.test_clustal) ... ok test_exonerate (test_Align_Alignment.TestAlignment_pairwise_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_pairwise_format.test_fasta) ... ok test_maf (test_Align_Alignment.TestAlignment_pairwise_format.test_maf) ... ok test_phylip (test_Align_Alignment.TestAlignment_pairwise_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_pairwise_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_pairwise_format.test_sam) ... ok test_add (test_Align_Alignment.TestMultipleAlignment.test_add) ... ok test_comparison (test_Align_Alignment.TestMultipleAlignment.test_comparison) ... ok test_indexing_slicing (test_Align_Alignment.TestMultipleAlignment.test_indexing_slicing) ... ok test_sort (test_Align_Alignment.TestMultipleAlignment.test_sort) ... ok test_substitutions (test_Align_Alignment.TestMultipleAlignment.test_substitutions) ... ok test_target_query_properties (test_Align_Alignment.TestMultipleAlignment.test_target_query_properties) ... ok test_add (test_Align_Alignment.TestPairwiseAlignment.test_add) ... ok test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok test_reverse_complement (test_Align_Alignment.TestPairwiseAlignment.test_reverse_complement) ... ok test_sort (test_Align_Alignment.TestPairwiseAlignment.test_sort) ... ok test_substitutions (test_Align_Alignment.TestPairwiseAlignment.test_substitutions) ... ok test_target_query_properties (test_Align_Alignment.TestPairwiseAlignment.test_target_query_properties) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.188 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_a2m.py test_Align_a2m ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bed.py test_Align_bed ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_reading (test_Align_bed.TestAlign_bed12.test_reading) Test parsing alignments in file formats BED3 through BED12. ... ok test_writing (test_Align_bed.TestAlign_bed12.test_writing) Test writing the alignments in bed12.bed as BED3 through BED12. ... ok test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.bed. ... ok test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.bed. ... ok test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.bed. ... ok test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.bed. ... ok test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.bed. ... ok test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.bed. ... ok test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.bed. ... ok test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.bed. ... ok test_reading (test_Align_bed.TestAlign_dna_rna.test_reading) Test parsing dna_rna.bed. ... ok test_writing (test_Align_bed.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.bed. ... ok test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.bed. ... ok test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.bed. ... ok test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.bed. ... ok test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.bed. ... ok test_reading (test_Align_bed.TestAlign_searching.test_reading) Test reading bigbedtest.bed. ... ok test_writing (test_Align_bed.TestAlign_searching.test_writing) Test writing bigbedtest.bed. ... ok test_format (test_Align_bed.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.100 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigmaf.py test_Align_bigmaf ... ok test_reading (test_Align_bigmaf.TestAlign_bundle_without_target.test_reading) Test parsing bundle_without_target.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_bundle_without_target.test_writing) Test writing bundle_without_target.bb. ... ok test_declaration (test_Align_bigmaf.TestAlign_declaration.test_declaration) ... ok test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok test_reading (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_reading) Test parsing file ucsc_mm9_chr10.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_writing) Test writing file ucsc_mm9_chr10.bb. ... ok test_reading (test_Align_bigmaf.TestAlign_ucsc_test.test_reading) Test reading ucsc_test.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_test.test_writing) Test writing ucsc_test.bb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.310 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigpsl.py test_Align_bigpsl ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_reading (test_Align_bigpsl.TestAlign_bigpsl.test_reading) Test parsing bigPsl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_bigpsl.test_writing) Test writing bigPsl.bb. ... ok test_declaration (test_Align_bigpsl.TestAlign_declaration.test_declaration) ... ok test_reading_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl.bb. ... ok test_reading_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl.bb. ... ok test_reading_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl.bb. ... ok test_reading_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl.bb. ... ok test_writing_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_001) Test writing psl_34_001.psl.bb. ... ok test_writing_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_003) Test writing psl_34_003.psl.bb. ... ok test_writing_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_004) Test writing psl_34_004.psl.bb. ... ok test_writing_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_005) Test writing psl_34_005.psl.bb. ... ok test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_dna_rna.test_writing) Test writing dna_rna.psl.bb. ... ok test_reading_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl.bb. ... ok test_reading_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl.bb. ... ok test_writing_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing psl_35_001.psl.bb. ... ok test_writing_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing psl_35_002.psl.bb. ... ok test_search_chromosome (test_Align_bigpsl.TestAlign_searching.test_search_chromosome) ... ok test_search_position (test_Align_bigpsl.TestAlign_searching.test_search_position) ... ok test_search_region (test_Align_bigpsl.TestAlign_searching.test_search_region) ... ok test_three_iterators (test_Align_bigpsl.TestAlign_searching.test_three_iterators) Create three iterators and use them concurrently. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.291 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_chain.py test_Align_chain ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_reading_chain_34_002 (test_Align_chain.TestAlign_dna.test_reading_chain_34_002) Test parsing psl_34_002.chain. ... ok test_reading_psl_34_001 (test_Align_chain.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.chain. ... ok test_reading_psl_34_003 (test_Align_chain.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.chain. ... ok test_reading_psl_34_004 (test_Align_chain.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.chain. ... ok test_reading_psl_34_005 (test_Align_chain.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.chain. ... ok test_writing_chain_34_001 (test_Align_chain.TestAlign_dna.test_writing_chain_34_001) Test writing the alignments in psl_34_001.chain. ... ok test_writing_psl_34_002 (test_Align_chain.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.chain. ... ok test_writing_psl_34_003 (test_Align_chain.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.chain. ... ok test_writing_psl_34_004 (test_Align_chain.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.chain. ... ok test_writing_psl_34_005 (test_Align_chain.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.chain. ... ok test_reading (test_Align_chain.TestAlign_dna_rna.test_reading) Test parsing dna_rna.chain. ... ok test_writing (test_Align_chain.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.chain. ... ok test_format (test_Align_chain.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.108 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_clustal.py test_Align_clustal ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign) Make sure we can parse the Kalign header. ... ok test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_codonalign.py test_Align_codonalign ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_aligner (test_Align_codonalign.TestBasic.test_aligner) ... ok test_alignments (test_Align_codonalign.TestBasic.test_alignments) ... ok test1 (test_Align_codonalign.TestBuildAndIO.test1) ... ok test2 (test_Align_codonalign.TestBuildAndIO.test2) ... ok test3 (test_Align_codonalign.TestBuildAndIO.test3) ... ok test4 (test_Align_codonalign.TestBuildAndIO.test4) ... ok test5 (test_Align_codonalign.TestBuildAndIO.test5) ... ok test_mk (test_Align_codonalign.Test_MK.test_mk) ... ok test_build1 (test_Align_codonalign.Test_build.test_build1) ... ok test_build2 (test_Align_codonalign.Test_build.test_build2) ... ok test_build3 (test_Align_codonalign.Test_build.test_build3) ... ok test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) ... ok ---------------------------------------------------------------------- Ran 1 test in 2.176 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_emboss.py test_Align_emboss ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2) Test parsing a local alignment. ... ok test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_exonerate.py test_Align_exonerate ... ok test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar) Test parsing exn_22_m_affine_local_cigar.exn. ... ok test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar) Test parsing exn_22_m_affine_local_vulgar.exn. ... ok test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar) Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar) Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar) Test parsing exn_22_m_coding2coding_cigar.exn. ... ok test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar) Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar) Test parsing exn_22_m_cigar_fshifts.exn). ... ok test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar) Test parsing exn_22_o_vulgar_fshifts.exn. ... ok test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar) Test parsing exn_22_m_coding2genome_cigar.exn. ... ok test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar) Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar) Test parsing exn_22_m_dna2protein_cigar.exn. ... ok test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar) Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar) Test parsing exn_22_m_est2genome_cigar.exn. ... ok test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar) Test parsing exn_22_m_est2genome_vulgar.exn. ... ok test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar) Test parsing exn_22_o_vulgar_cigar.exn. ... ok test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar) Test parsing exn_22_o_vulgar.exn. ... ok test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar) Test parsing exn_22_q_multiple_cigar.exn. ... ok test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar) Test parsing exn_22_q_multiple_vulgar.exn. ... ok test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar) Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar) Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar) Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar) Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar) Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar) Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar) Test parsing exn_22_m_protein2genome_cigar.exn. ... ok test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar) Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar) Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar) Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar) Test parsing exn_22_m_ungapped_cigar.exn. ... ok test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar) Test parsing exn_22_m_ungapped_vulgar.exn. ... ok test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar) Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar) Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_fasta.py test_Align_fasta ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_clustalw (test_Align_fasta.TestFASTAReadingWriting.test_clustalw) ... ok test_empty (test_Align_fasta.TestFASTAReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_fasta.TestFASTAReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_fasta.TestFASTAReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_fasta.TestFASTAReadingWriting.test_muscle) ... ok test_probcons (test_Align_fasta.TestFASTAReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_hhr.py test_Align_hhr ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_7rbx_A_hhsearch_trunc.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_allx.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.204 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_maf.py test_Align_maf ... ok test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453) Test parsing bug2453.maf. ... ok test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target) Test parsing bundle_without_target.maf. ... ok test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch) Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature) Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10) Test parsing MAF file ucsc_mm9_chr10.maf. ... ok test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad) Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test) Test parsing ucsc_test.maf. ... ok test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453) Test reading and writing bug2453.maf. ... ok test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target) Test reading and writing bundle_without_target.maf. ... ok test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10) Test reading and writing ucsc_mm9_chr10.maf. ... ok test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test) Test reading and writing ucsc_test.maf. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.262 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_mauve.py test_Align_mauve ... ok test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok test_parse (test_Align_mauve.TestSeparateFiles.test_parse) ... ok test_write_read (test_Align_mauve.TestSeparateFiles.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_msf.py test_Align_msf ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_empty (test_Align_msf.TestMSF.test_empty) Checking empty file. ... ok test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.036 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_nexus.py test_Align_nexus ... ok test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_phylip.py test_Align_phylip ... ok test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok test_interlaced (test_Align_phylip.TestPhylipReading.test_interlaced) ... ok test_interlaced2 (test_Align_phylip.TestPhylipReading.test_interlaced2) ... ok test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok test_sequential (test_Align_phylip.TestPhylipReading.test_sequential) ... ok test_sequential2 (test_Align_phylip.TestPhylipReading.test_sequential2) ... ok test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_psl.py test_Align_psl ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002) Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.psl. ... ok test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.psl. ... ok test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.psl. ... ok test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.psl. ... ok test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.psl. ... ok test_reading (test_Align_psl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl. ... ok test_writing (test_Align_psl.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.psl. ... ok test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl. ... ok test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.psl. ... ok test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.psl. ... ok test_format (test_Align_psl.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.261 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_sam.py test_Align_sam ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_4D8I6M (test_Align_sam.TestAlign_clipping.test_4D8I6M) Test alignment starting with deletion followed by insertion. ... ok test_4I8D6M (test_Align_sam.TestAlign_clipping.test_4I8D6M) Test alignment starting with insertion followed by deletion. ... ok test_4S6M (test_Align_sam.TestAlign_clipping.test_4S6M) Test alignment starting with soft clip at non-zero position. ... ok test_4S8D6M (test_Align_sam.TestAlign_clipping.test_4S8D6M) Test alignment starting with soft clip followed by deletion. ... ok test_4S8I6M (test_Align_sam.TestAlign_clipping.test_4S8I6M) Test alignment starting with soft clip followed by insertion. ... ok test_6M (test_Align_sam.TestAlign_clipping.test_6M) Test alignment starting at non-zero position. ... ok test_8D6M_ex1 (test_Align_sam.TestAlign_clipping.test_8D6M_ex1) Test alignment starting with deletion. ... ok test_8D6M_ex2 (test_Align_sam.TestAlign_clipping.test_8D6M_ex2) Test alignment starting with deletion at non-zero position. ... ok test_8I6M_ex1 (test_Align_sam.TestAlign_clipping.test_8I6M_ex1) Test alignment starting with insertion. ... ok test_8I6M_ex2 (test_Align_sam.TestAlign_clipping.test_8I6M_ex2) Test alignment starting with insertion at non-zero position. ... ok test_8S6M (test_Align_sam.TestAlign_clipping.test_8S6M) Test alignment starting with soft clip. ... ok test_reading_psl_34_001 (test_Align_sam.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.sam. ... ok test_reading_psl_34_003 (test_Align_sam.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.sam. ... ok test_reading_psl_34_004 (test_Align_sam.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.sam. ... ok test_reading_psl_34_005 (test_Align_sam.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.sam. ... ok test_writing_psl_34_001 (test_Align_sam.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.sam. ... ok test_writing_psl_34_003 (test_Align_sam.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.sam. ... ok test_writing_psl_34_004 (test_Align_sam.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.sam. ... ok test_writing_psl_34_005 (test_Align_sam.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.sam. ... ok test_reading (test_Align_sam.TestAlign_dna_rna.test_reading) Test parsing dna_rna.sam. ... ok test_reading_psl_comparison (test_Align_sam.TestAlign_dna_rna.test_reading_psl_comparison) Test parsing dna_rna.sam and comparing to dna_rna.psl. ... ok test_writing (test_Align_sam.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.sam. ... ok test_ex1 (test_Align_sam.TestAlign_sambam.test_ex1) ... ok test_ex1_header (test_Align_sam.TestAlign_sambam.test_ex1_header) ... ok test_sam1 (test_Align_sam.TestAlign_sambam.test_sam1) ... ok test_sam2 (test_Align_sam.TestAlign_sambam.test_sam2) ... ok test_format (test_Align_sam.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.207 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_stockholm.py test_Align_stockholm ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_io_nonstandard_annotations (test_Align_stockholm.TestStockholm_reading.test_io_nonstandard_annotations) Test input and output of nonstandard GC, GS and GR annotation lines. ... ok test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ... ok test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ... ok test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ... ok test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ... ok test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ... ok test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ... ok test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ... ok test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ... ok test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ... ok test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ... ok test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ... ok test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ... ok test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ... ok test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ... ok test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ... ok test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ... ok test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ... ok test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ... ok test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.933 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_tabular.py test_Align_tabular ... ok test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.288 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Application.py test_Application ... ok test_echo (test_Application.TestApp.test_echo) ... ok test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.018 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BWA_tool.py test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.087 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_psycopg2.py test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_psycopg2_online.py test_BioSQL_psycopg2_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.087 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_sqlite3.py test_BioSQL_sqlite3 ... ok test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility) Check can re-use an old BioSQL SQLite3 database. ... ok test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932) From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816) From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265) From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1) From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6) From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref) From GenBank file to BioSQL and back to a GenBank file, noref. ... ok test_one_of (common_BioSQL.ClosedLoopTest.test_one_of) From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2) From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items) Check all associated data is deleted from an item. ... ok test_server (common_BioSQL.DeleteTest.test_server) Check BioSeqDatabase methods. ... ok test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load) Make sure can't import records with same ID (in one go). ... ok test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load) Make sure can't import a single record twice (in one go). ... ok test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2) Make sure can't import a single record twice (in steps). ... ok test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading) Make sure all records are correctly loaded. ... ok test_reload (common_BioSQL.InDepthLoadTest.test_reload) Make sure can't reimport existing records. ... ok test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature) In depth check that SeqFeatures are transmitted through the db. ... ok test_transfer (common_BioSQL.InDepthLoadTest.test_transfer) Make sure can load record into another namespace. ... ok test_load_database (common_BioSQL.LoaderTest.test_load_database) Load SeqRecord objects into a BioSQL database. ... ok test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items) Test that valid ids can't be retrieved between namespaces. ... ok test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_server (common_BioSQL.MultiReadTest.test_server) Check BioSeqDatabase methods. ... ok test_get_db_items (common_BioSQL.ReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_lookup_items (common_BioSQL.ReadTest.test_lookup_items) Test retrieval of items using various ids. ... ok test_server (common_BioSQL.ReadTest.test_server) Check BioSeqDatabase methods. ... ok test_addition (common_BioSQL.SeqInterfaceTest.test_addition) Check can add Seq objects from BioSQL together. ... ok test_convert (common_BioSQL.SeqInterfaceTest.test_convert) Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication) Check can multiply Seq objects from BioSQL by integers. ... ok test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing) Check that slices of DBSeqRecord are retrieved properly. ... ok test_seq (common_BioSQL.SeqInterfaceTest.test_seq) Make sure Seqs from BioSQL implement the right interface. ... ok test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features) Check SeqFeatures of a sequence. ... ok test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record) Make sure SeqRecords from BioSQL implement the right interface. ... ok test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing) Check that slices of sequences are retrieved properly. ... ok test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location) Loaded uniprot-xml with ambiguous location in BioSQL. ... ok test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932) From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816) From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265) From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok test_arab1 (common_BioSQL.TransferTest.test_arab1) From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6) From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok test_no_ref (common_BioSQL.TransferTest.test_no_ref) From GenBank file to BioSQL, then again to a new namespace, noref. ... ok test_one_of (common_BioSQL.TransferTest.test_one_of) From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2) From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.207 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.087 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Blast_Record.py test_Blast_Record ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.029 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_CAPS.py test_CAPS ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test (test_CAPS.TestCAPS.test) ... ok testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok testNoCAPS_msa (test_CAPS.TestCAPS.testNoCAPS_msa) ... ok test_msa (test_CAPS.TestCAPS.test_msa) ... ok test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok test_trivial_msa (test_CAPS.TestCAPS.test_trivial_msa) ... ok test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Chi2.py test_Chi2 ... ok test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_ClustalOmega_tool.py test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Clustalw_tool.py test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Cluster.py test_Cluster ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok test_pca (test_Cluster.TestCluster.test_pca) ... ok test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok test_tree (test_Cluster.TestCluster.test_tree) ... ok test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_CodonTable.py test_CodonTable ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding) Check a few ambiguous codons for correct coding. ... ok test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons) Check if stop codons are properly extended. ... ok test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons) Test various ambiguous codons as start codon. ... ok test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons) Test various ambiguous codons as stop codon. ... ok test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables) Check if all IDs and all names are present in ambiguous tables. ... ok test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables) Check if all unambiguous codon tables have all entries. ... ok test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables) Check if we have the same number of tables for each type. ... ok test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table) Raise errors in AmbiguousForwardTable. ... ok test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins) Raise errors in list_possible proteins. ... ok test_print_table (test_CodonTable.PrintTable.test_print_table) Test output of __str__ function. ... ok test_table01 (test_CodonTable.SingleTableTests.test_table01) Check table 1: Standard. ... ok test_table02 (test_CodonTable.SingleTableTests.test_table02) Check table 2: Vertebrate Mitochondrial. ... ok test_table03 (test_CodonTable.SingleTableTests.test_table03) Check table 3: Yeast Mitochondrial. ... ok test_table04 (test_CodonTable.SingleTableTests.test_table04) Check table 4: Mold Mitochondrial and others. ... ok test_table05 (test_CodonTable.SingleTableTests.test_table05) Check table 5: Invertebrate Mitochondrial. ... ok test_table06 (test_CodonTable.SingleTableTests.test_table06) Check table 6: Ciliate and Other Nuclear. ... ok test_table09 (test_CodonTable.SingleTableTests.test_table09) Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok test_table10 (test_CodonTable.SingleTableTests.test_table10) Check table 10: Euplotid Nuclear. ... ok test_table11 (test_CodonTable.SingleTableTests.test_table11) Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok test_table12 (test_CodonTable.SingleTableTests.test_table12) Check table 12: Alternative Yeast Nuclear. ... ok test_table13 (test_CodonTable.SingleTableTests.test_table13) Check table 13: Ascidian Mitochondrial. ... ok test_table14 (test_CodonTable.SingleTableTests.test_table14) Check table 14: Alternative Flatworm Mitochondrial. ... ok test_table16 (test_CodonTable.SingleTableTests.test_table16) Check table 16: Chlorophycean Mitochondrial. ... ok test_table21 (test_CodonTable.SingleTableTests.test_table21) Check table 21: Trematode Mitochondrial. ... ok test_table22 (test_CodonTable.SingleTableTests.test_table22) Check table 22: Scenedesmus obliquus Mitochondrial. ... ok test_table23 (test_CodonTable.SingleTableTests.test_table23) Check table 9: Thraustochytrium Mitochondrial. ... ok test_table24 (test_CodonTable.SingleTableTests.test_table24) Check table 24: Pterobranchia Mitochondrial. ... ok test_table25 (test_CodonTable.SingleTableTests.test_table25) Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok test_table26 (test_CodonTable.SingleTableTests.test_table26) Check table 26: Pachysolen tannophilus Nuclear. ... ok test_table27 (test_CodonTable.SingleTableTests.test_table27) Check table 27: Karyorelict Nuclear. ... ok test_table28 (test_CodonTable.SingleTableTests.test_table28) Check table 28: Condylostoma Nuclear. ... ok test_table29 (test_CodonTable.SingleTableTests.test_table29) Check table 29: Mesodinium Nuclear. ... ok test_table30 (test_CodonTable.SingleTableTests.test_table30) Check table 30: Peritrich Nuclear. ... ok test_table31 (test_CodonTable.SingleTableTests.test_table31) Check table 31: Blastocrithidia Nuclear. ... ok test_table32 (test_CodonTable.SingleTableTests.test_table32) Check table 32: Balanophoraceae Plastid. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.030 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_ColorSpiral.py test_ColorSpiral ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_dict (test_ColorSpiral.DictTest.test_dict) get_color_dict() for classes A-D, no jitter. ... ok test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist) Get set of eight colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral) Get set of 16 colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral) Set of 625 colours, with jitter, using get_colors(). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Compass.py test_Compass ... ok testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Consensus.py test_Consensus ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok test_bootstrap_consensus_msa (test_Consensus.BootstrapTest.test_bootstrap_consensus_msa) ... ok test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok test_bootstrap_trees_msa (test_Consensus.BootstrapTest.test_bootstrap_trees_msa) ... ok test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.753 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Dialign_tool.py test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_EMBL_unittest.py test_EMBL_unittest ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line) Test SQ line with 0 length sequence. ... ok test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co) Test a ValueError is thrown by content after a CO line. ... ok test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords) Test sequence lines without coordinates. ... ok test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line) Test files with wrong DR lines. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.048 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Emboss.py test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss. ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_EmbossPhylipNew.py test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools. ---------------------------------------------------------------------- Ran 1 test in 0.040 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_EmbossPrimer.py test_EmbossPrimer ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse) Make sure we get info right from a single primer find. ... ok test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse) Make sure we get the data from normal primer3 files okay. ... ok test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse) Make sure we can parse an internal oligo file correctly. ... ok test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full) Test parsing multiple primer sets (NirK full). ... ok test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd) Test parsing multiple primer sets (NirK forward). ... ok test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse) Make sure that we can use all single target primer3 files. ... ok test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation) Make sure we can output primer information correctly. ... ok test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse) Make sure the output from a simple primersearch file is correct. ... ok test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse) Make sure that we can parse all primersearch files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez.py test_Entrez ... ok test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo) Test constructed url for request to Entrez. ... ok test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2) Commas: Link from protein to gene. ... ok test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3) Multiple ID entries: Find one-to-one links from protein to gene. ... ok test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok test_default_params (test_Entrez.TestURLConstruction.test_default_params) Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok test_email_warning (test_Entrez.TestURLConstruction.test_email_warning) Test issuing warning when user does not specify email address. ... ok test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key) Test checking whether a Request object specifies an API key. ... ok ---------------------------------------------------------------------- Ran 1 test in 4.146 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez_parser.py test_Entrez_parser ... ok test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas) Test parsing XML using Schemas. ... ok test_fasta (test_Entrez_parser.EFetchTest.test_fasta) Test error handling when presented with Fasta non-XML data. ... ok test_genbank (test_Entrez_parser.EFetchTest.test_genbank) Test error handling when presented with GenBank non-XML data. ... ok test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ... ok test_pmc (test_Entrez_parser.EFetchTest.test_pmc) Test parsing XML returned by EFetch from PubMed Central. ... ok test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ... ok test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ... ok test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ... ok test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html) Test error handling when presented with HTML (so XML-like) data. ... ok test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping) Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags) Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ... ok test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ... ok test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration) Test error handling for a missing XML declaration. ... ok test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition) Test error handling for a missing DTD or XML Schema. ... ok test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ... ok test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ... ok test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ... ok test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ... ok test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ... ok test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ... ok test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ... ok test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ... ok test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ... ok test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ... ok test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ... ok test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ... ok test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ... ok test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ... ok test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ... ok test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ... ok test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ... ok test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ... ok test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ... ok test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ... ok test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ... ok test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ... ok test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ... ok test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ... ok test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ... ok test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ... ok test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ... ok test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none) Test parsing ESummary XML where an Integer is not defined. ... ok test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ... ok test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ... ok test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ... ok test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ... ok test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ... ok test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ... ok test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ... ok test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ... ok test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO stream (bytes not string). ... ok test_closed_file (test_Entrez_parser.GeneralTests.test_closed_file) Test parsing closed file fails gracefully. ... ok test_parse_bytes_stream (test_Entrez_parser.GeneralTests.test_parse_bytes_stream) Test parsing a file opened in binary mode. ... ok test_parse_text_file (test_Entrez_parser.GeneralTests.test_parse_text_file) Test parsing a file opened in text mode. ... ok test_pickle (test_Entrez_parser.GeneralTests.test_pickle) Test if records created by the parser can be pickled. ... ok test_read_bytes_stream (test_Entrez_parser.GeneralTests.test_read_bytes_stream) Test reading a file opened in binary mode. ... ok test_read_text_file (test_Entrez_parser.GeneralTests.test_read_text_file) Test reading a file opened in text mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.305 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Enzyme.py test_Enzyme ... ok test_lactate (test_Enzyme.TestEnzyme.test_lactate) Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein) Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok test_parse_many (test_Enzyme.TestEnzyme.test_parse_many) Check parse function with multiple records. ... ok test_parse_one (test_Enzyme.TestEnzyme.test_parse_one) Check parse function with one record. ... ok test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok test_proline (test_Enzyme.TestEnzyme.test_proline) Parsing ENZYME record for proline racemase (5.1.1.4). ... ok test_valine (test_Enzyme.TestEnzyme.test_valine) Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_ExPASy.py test_ExPASy ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Fasttree_tool.py test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_File.py test_File ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object) Test as_handle with a custom path-like object. ... ok test_handle (test_File.AsHandleTestCase.test_handle) Test as_handle with a file-like object argument. ... ok test_path_object (test_File.AsHandleTestCase.test_path_object) Test as_handle with a pathlib.Path object. ... ok test_string_path (test_File.AsHandleTestCase.test_string_path) Test as_handle with a string path argument. ... ok test_stringio (test_File.AsHandleTestCase.test_stringio) Testing passing StringIO handles. ... ok test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok test_bgzf (test_File.RandomAccess.test_bgzf) Test BGZF compressed file. ... ok test_gzip (test_File.RandomAccess.test_gzip) Test gzip compressed file. ... ok test_plain (test_File.RandomAccess.test_plain) Test plain text file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GenBank.py test_GenBank ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction) Test EMBL CDS interaction, parse CDS features on embl files. ... ok test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction) Test EMBL Record interaction on embl files. ... ok test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction) Test CDS interaction, parse CDS features on gb(k) files. ... ok test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction) Test GenBank records interaction on gbk files. ... ok test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning) Feature line wrapping warning. ... ok test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location) Bad origin wrapping. ... ok test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix) Attempt to fix implied origin wrapping. ... ok test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning) Un-parsable feature location warning. ... ok test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap) Test the attempts to fix compound complex origin wrapping. ... ok test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb) Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl) Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok test_dblink (test_GenBank.GenBankTests.test_dblink) Parse GenBank record with old DBLINK project entry. ... ok test_dblink_two (test_GenBank.GenBankTests.test_dblink_two) Parse GenBank record with old and new DBLINK project entries. ... ok test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage) Missing taxonomy lineage. ... ok test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence) Tests if extremely long sequences can be read. ... ok test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap) Test features that wrap an origin, and have fuzzy location. ... ok test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing) Bad location wrapping. ... ok test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct) Check if user provided date is inserted correctly. ... ok test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime) Check if datetime objects are handled correctly. ... ok test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default) Check if default date is handled correctly. ... ok test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid) Check if invalid dates are treated as default. ... ok test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list) Check if date lists are handled correctly. ... ok test_genbank_read (test_GenBank.GenBankTests.test_genbank_read) GenBank.read(...) simple test. ... ok test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid) GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord) GenBank.read(...) error on multiple record input. ... ok test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end) GenBank.read(...) error on malformed file. ... ok test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate) Test that features wrapped around origin give expected data. ... ok test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error) Parsing invalid product line. ... ok test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly) Test if chromosome topology is conserved. ... ok test_long_names (test_GenBank.GenBankTests.test_long_names) Various GenBank names which push the column based LOCUS line. ... ok test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line) Check that we can read and write files with longer locus lines. ... ok test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing) Test malformed structured comment gives warning. ... ok test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing) Multiline structured comment parsing. ... ok test_negative_location (test_GenBank.GenBankTests.test_negative_location) Negative feature locations. ... ok test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read) Check qualifier escaping is preserved when parsing. ... ok test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write) Check qualifier escaping is preserved when writing. ... ok test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order) Check the qualifier order is preserved. ... ok test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing) Structured comment parsing. ... ok test_tsa (test_GenBank.GenBankTests.test_tsa) Test TSA annotation parsing. ... ok test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt) Check IMGT ID line parsing. ... ok test_topology_embl (test_GenBank.LineOneTests.test_topology_embl) Check EMBL ID line parsing. ... ok test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank) Check GenBank LOCUS line parsing. ... ok test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line) Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok test_mad_dots (test_GenBank.OutputTests.test_mad_dots) Writing and reading back accesssion.version variants. ... ok test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description) Read in file using SeqRecord default description. ... ok test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division) Make sure we don't kill the TSA data_file_division for TSA files. ... ok test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features) Test the ability to clean up feature values. ... ok test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus) Test the ENSEMBL locus line. ... ok test_write_format (test_GenBank.TestBasics.test_write_format) Test writing to the difference formats. ... ok test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin) Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.177 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GenomeDiagram.py test_GenomeDiagram ... ok test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions) Test color translations. ... ok test_add_track (test_GenomeDiagram.DiagramTest.test_add_track) Add track. ... ok test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error) Test adding unspecified track. ... ok test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level) Add track to occupied level. ... ok test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks) Delete track. ... ok test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf) Construct and draw PDF using method approach. ... ok test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf) Construct and draw PDF using object approach. ... ok test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks) Get track. ... ok test_move_track (test_GenomeDiagram.DiagramTest.test_move_track) Move a track. ... ok test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram) Construct and draw SVG and PDF for just part of a SeqRecord. ... ok test_renumber (test_GenomeDiagram.DiagramTest.test_renumber) Test renumbering tracks. ... ok test_str (test_GenomeDiagram.DiagramTest.test_str) Test diagram's info as string. ... ok test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments) Check how the write methods respond to output format arguments. ... ok test_limits (test_GenomeDiagram.GraphTest.test_limits) Check line graphs. ... ok test_slicing (test_GenomeDiagram.GraphTest.test_slicing) Check GraphData slicing. ... ok test_label_default (test_GenomeDiagram.LabelTest.test_label_default) Feature labels - default. ... ok test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils) All sigils. ... ok test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads) Feature arrow sigils, varying heads. ... ok test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts) Feature arrow sigils, varying shafts. ... ok test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts) Feature big-arrow sigils, varying shafts. ... ok test_labels (test_GenomeDiagram.SigilsTest.test_labels) Feature labels. ... ok test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads) Feature ARROW sigil heads within bounding box. ... ok test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads) Feature BIGARROW sigil heads within bounding box. ... ok test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy) Feature JAGGY sigil heads within bounding box. ... ok test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads) Feature OCTO sigil heads within bounding box. ... ok test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow) Feature arrow sigil heads within bounding box. ... ok test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow) Feature big-arrow sigil heads within bounding box. ... ok test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy) Feature arrow sigil heads within bounding box. ... ok test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo) Feature big-arrow sigil heads within bounding box. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.571 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsBitmaps.py test_GraphicsBitmaps ... skipping. Reportlab module rlPyCairo unavailable cannot import desired renderPM backend rlPyCairo Seek advice at the users list see https://pairlist2.pair.net/mailman/listinfo/reportlab-users ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsChromosome.py test_GraphicsChromosome ... ok test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count) Add counts to specific chromosome segments. ... ok test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label) Add labels to chromosome segments. ... ok test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count) Retrieve a color from a count number with the default color scheme. ... ok test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome) Test filling out the information on a chromosome. ... ok test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info) Test retrieval of segment information. ... ok test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale) Set the scale for a chromosome segment. ... ok test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism) Generate an organism with random chromosome info. ... ok test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism) Test the basic functionality of drawing an organism. ... ok test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf) Output a simple organism to a PDF file. ... ok test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps) Output a simple organism to a postscript file. ... ok test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg) Output a simple organism to an SVG file. ... ok test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget) Try widget derived functionality. ... ok test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures) Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples) Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.661 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsDistribution.py test_GraphicsDistribution ... ok test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page) Create a page with multiple distributions on it. ... ok test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page) Test displaying a page with single distribution. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsGeneral.py test_GraphicsGeneral ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1) Test creation of a simple ScatterPlot with one list. ... ok test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7) Test creation of a simple ScatterPlot with more lists. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.518 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_HMMCasino.py test_HMMCasino ... ok test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard) Standard Training with known states. ... ok test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without) Baum-Welch training without known state sequences. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_HMMGeneral.py test_HMMGeneral ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood) Calculate log likelihood. ... ok test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator) Test the maximum likelihood estimator for simple cases. ... ok test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition) Testing allow_transition. ... ok test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic) Non-ergodic model (meaning that some transitions are not allowed). ... ok test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm) Test a simple model with 2 states and 2 symbols. ... ok test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from) Testing the calculation of transitions_from. ... ok test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to) Testing the calculation of transitions_to. ... ok test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions) Testing allow_all_transitions. ... ok test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize) Making sure MarkovModelBuilder is initialized correctly. ... ok test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value) Testing the calculation of s values. ... ok test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.030 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG.py test_KEGG ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_irregular (test_KEGG.CompoundTests.test_irregular) compound.irregular tests. ... ok test_mass (test_KEGG.CompoundTests.test_mass) record.mass tests. ... ok test_sample (test_KEGG.CompoundTests.test_sample) compound.sample tests. ... ok test_4letter (test_KEGG.EnzymeTests.test_4letter) enzyme.4letter tests. ... ok test_exceptions (test_KEGG.EnzymeTests.test_exceptions) enzyme.exceptions tests. ... ok test_irregular (test_KEGG.EnzymeTests.test_irregular) enzyme.irregular tests. ... ok test_new (test_KEGG.EnzymeTests.test_new) enzyme.new tests. ... ok test_sample (test_KEGG.EnzymeTests.test_sample) enzyme.sample tests. ... ok test_map00950 (test_KEGG.MapTests.test_map00950) map00950.rea tests. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_graphics.py test_KGML_graphics ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic) Basic rendering of KGML: write to PDF without modification. ... ok test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify) Rendering of KGML to PDF, with modification. ... ok test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency) Rendering of KGML to PDF, with color alpha channel. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.906 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_graphics_online.py test_KGML_graphics_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.033 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_nographics.py test_KGML_nographics ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files) Read KGML from, and write KGML to, local files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.446 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KeyWList.py test_KeyWList ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_parse (test_KeyWList.KeyWListTest.test_parse) Test parsing keywlist.txt works. ... ok test_parse2 (test_KeyWList.KeyWListTest.test_parse2) Parsing keywlist2.txt (without header and footer). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.028 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_LogisticRegression.py test_LogisticRegression ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.026 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_MSAProbs_tool.py test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.046 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_MafIO_index.py test_MafIO_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary) Following issues 504 and 1086. ... ok test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length) Following issues 504 and 1086. ... ok test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3) Following issue 1083. ... ok test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1) Checking that spliced sequences are correct. ... ok test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2) Checking that spliced sequences are correct. ... ok test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.509 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Mafft_tool.py test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.032 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_MarkovModel.py test_MarkovModel ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.095 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Medline.py test_Medline ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok test_parse (test_Medline.TestMedline.test_parse) ... ok test_read (test_Medline.TestMedline.test_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Muscle_tool.py test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBIXML.py test_NCBIXML ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001) Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001) Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001) Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001) Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001) Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001) Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001) Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001) Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002) Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001) Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001) Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.385 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBI_BLAST_tools.py test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBI_qblast.py test_NCBI_qblast ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_blastp_nr_actin (test_NCBI_qblast.TestQblast.test_blastp_nr_actin) ... ok test_discomegablast (test_NCBI_qblast.TestQblast.test_discomegablast) ... ok test_error_conditions (test_NCBI_qblast.TestQblast.test_error_conditions) Test if exceptions were properly handled. ... ok test_orchid_est (test_NCBI_qblast.TestQblast.test_orchid_est) ... ok test_parse_qblast_ref_page (test_NCBI_qblast.TestQblast.test_parse_qblast_ref_page) ... ok test_pcr_primers (test_NCBI_qblast.TestQblast.test_pcr_primers) ... ok test_short_query (test_NCBI_qblast.TestQblast.test_short_query) Test SHORT_QUERY_ADJUST parameter. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NMR.py test_NMR ... ok test_noetools (test_NMR.NmrTests.test_noetools) Self test for NMR.NOEtools. ... ok test_xpktools (test_NMR.NmrTests.test_xpktools) Self test for NMR.xpktools. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NaiveBayes.py test_NaiveBayes ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_car_data (test_NaiveBayes.CarTest.test_car_data) Simple example using car data. ... ok test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Nexus.py test_Nexus ... ok test_NexusComments (test_Nexus.NexusTest1.test_NexusComments) Test the ability to parse nexus comments at internal and leaf nodes. ... ok test_NexusTest1 (test_Nexus.NexusTest1.test_NexusTest1) Test Nexus module. ... ok test_TreeTest1 (test_Nexus.NexusTest1.test_TreeTest1) Test Tree module. ... ok test_TreeTest2 (test_Nexus.NexusTest1.test_TreeTest2) Handle text labels on internal nodes. ... ok test_WriteToFileName (test_Nexus.NexusTest1.test_WriteToFileName) Test writing to a given filename. ... ok test_large_newick (test_Nexus.NexusTest1.test_large_newick) ... ok test_merge_with_support (test_Nexus.NexusTest1.test_merge_with_support) Test merge_with_support and consensus method. ... ok test_to_string (test_Nexus.NexusTest1.test_to_string) Test to_string method. ... ok test_write_alignment (test_Nexus.NexusTest1.test_write_alignment) ... ok test_write_alignment_msa (test_Nexus.NexusTest1.test_write_alignment_msa) ... ok test_write_with_dups (test_Nexus.NexusTest1.test_write_with_dups) ... ok test_data_and_codons_block (test_Nexus.OldSelfTests.test_data_and_codons_block) Simple sequence data file with DATA and CODONS block. ... ok test_data_sets_trees_unknown_block (test_Nexus.OldSelfTests.test_data_sets_trees_unknown_block) Sequence data file with DATA, SETS, TREES and an unknown block. ... ok test_taxa_and_characters_block (test_Nexus.OldSelfTests.test_taxa_and_characters_block) Taxa and characters multi-state block. ... ok test_taxa_and_characters_with_many_codings_one_without_state (test_Nexus.OldSelfTests.test_taxa_and_characters_with_many_codings_one_without_state) Taxa and chr blocks, over 9 codings, 1 character without states. ... ok test_taxa_and_characters_with_many_codings_two_without_state (test_Nexus.OldSelfTests.test_taxa_and_characters_with_many_codings_two_without_state) Taxa and chr blocks, over 9 codings, 2 character without states. ... ok test_trees_and_taxa_block (test_Nexus.OldSelfTests.test_trees_and_taxa_block) Basic tree file with TREES and TAXA block. ... ok test_empty_file_read (test_Nexus.TestSelf.test_empty_file_read) ... ok test_empty_file_read_msa (test_Nexus.TestSelf.test_empty_file_read_msa) ... ok test_multiple_output (test_Nexus.TestSelf.test_multiple_output) ... ok test_multiple_output_msa (test_Nexus.TestSelf.test_multiple_output_msa) ... ok test_repeated_names_no_taxa (test_Nexus.TestSelf.test_repeated_names_no_taxa) ... ok test_repeated_names_no_taxa_msa (test_Nexus.TestSelf.test_repeated_names_no_taxa_msa) ... ok test_repeated_names_with_taxa (test_Nexus.TestSelf.test_repeated_names_with_taxa) ... ok test_repeated_names_with_taxa_msa (test_Nexus.TestSelf.test_repeated_names_with_taxa_msa) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.500 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_baseml.py test_PAML_baseml ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_codeml.py test_PAML_codeml ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise) Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility) Test finding trees in the results. ... ok testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.475 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_tools.py test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_yn00.py test_PAML_yn00 ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDBList.py test_PDBList ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.037 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_CEAligner.py test_PDB_CEAligner ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner) Test aligning 7CFN on 6WQA. ... ok test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform) Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic) Test aligning 1LCD on 1LCD. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.317 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_DSSP.py test_PDB_DSSP ... ok test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA) Tests the usage of different ASA tables. ... ok test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file) Test parsing of pregenerated DSSP. ... ok test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds) Test parsing of DSSP hydrogen bond information. ... ok test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj) All elements correctly added to xtra attribute of input model object. ... ok test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file) Test parsing of pregenerated DSSP missing header information. ... ok setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.' ---------------------------------------------------------------------- Ran 1 test in 0.108 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Dice.py test_PDB_Dice ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_dice (test_PDB_Dice.DiceTests.test_dice) Self test for PDB.Dice module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Disordered.py test_PDB_Disordered ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered) Extract, save, and parse again disordered atoms. ... ok test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom) Copies disordered atoms and all their children. ... ok test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain) Copy propagates throughout SMCRA object. ... ok test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog) Calculate DisorderedAtom center of geometry. ... ok test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered) Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom) Remove altlocs from DisorderedAtom entities. ... ok test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue) Remove residues from DisorderedResidue entities. ... ok test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com) Calculate center of mass of structure including DisorderedAtoms. ... ok test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered) Transform propagates through disordered atoms. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Exposure.py test_PDB_Exposure ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN) HSExposureCN. ... ok test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA) HSExposureCA. ... ok test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB) HSExposureCB. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.181 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_FragmentMapper.py test_PDB_FragmentMapper ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper) Self test for FragmentMapper module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_KDTree.py test_PDB_KDTree ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual) Test all fixed radius neighbor search. ... ok test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple) Test all fixed radius neighbor search. ... ok test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search) Test searching all points within a certain radius of center. ... ok test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search) NeighborSearch: Find nearby randomly generated coordinates. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.876 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIF2Dict.py test_PDB_MMCIF2Dict ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments) Comments may begin outside of column 1 if preceded by whitespace. ... ok test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive) Comments may begin outside of column 1. ... ok test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline) Multi-line string followed by token on the same line. ... ok test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block) Verbatim blocks parsed correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIFIO.py test_PDB_MMCIFIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel) Write a multi-model, multi-chain mmCIF file. ... ok test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select) Write a selection of the structure using a Select subclass. ... ok test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict) Write an mmCIF dictionary out, read it in and compare them. ... ok test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue) Write a single residue using MMCIFIO. ... ok test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain) Write a single residue (chain id == X) using MMCIFIO. ... ok test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain) Write a single orphan residue using MMCIFIO. ... ok test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure) Write a full structure using MMCIFIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.135 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIFParser.py test_PDB_MMCIFParser ... ok test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion) Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering) Convert mmCIF to PDB and renumber atom serials. ... ok test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering) Convert mmCIF to PDB and preserve original serial numbering. ... ok testModels (test_PDB_MMCIFParser.ParseReal.testModels) Test file with multiple models. ... ok test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle) Test if the parser can handle file handle as well as filename. ... ok test_header (test_PDB_MMCIFParser.ParseReal.test_header) Test if the parser populates header data. ... ok test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions) Test file with residue insertion codes. ... ok test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers) Extract polypeptides from 1A80. ... ok test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast) Test if FastMMCIFParser can parse point mutations correctly. ... ok test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main) Test if MMCIFParser parse point mutations correctly. ... ok test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.682 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_NACCESS.py test_PDB_NACCESS ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS) Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.' test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file) Test parsing of pregenerated asa NACCESS file. ... ok test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file) Test parsing of pregenerated rsa NACCESS file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PDBIO.py test_PDB_PDBIO ... ok test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering) Preserve model serial numbers during I/O. ... ok test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy) Write PDB file with missing occupancy. ... ok test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits) Test raising error when structure cannot meet PDB format limits. ... ok test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select) Write a selection of the structure using a Select subclass. ... ok test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering) Test writing PDB and do not preserve atom numbering. ... ok test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering) Test writing PDB and preserve atom numbering. ... ok test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue) Write a single residue using PDBIO. ... ok test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain) Write a single residue (chain id == X) using PDBIO. ... ok test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain) Write a single orphan residue using PDBIO. ... ok test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure) Write a full structure using PDBIO. ... ok test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated) Test parsing of truncated lines. ... ok test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element) PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element) Write a structure with atomic element X with PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.138 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PDBParser.py test_PDB_PDBParser ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive) Parse a flawed PDB file in permissive mode: check warnings. ... ok test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict) Parse a flawed PDB file in permissive mode: check errors. ... ok test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive) Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict) Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive) Parse file with missing occupancy with PERMISSIVE=True. ... ok test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict) Parse file with missing occupancy with PERMISSIVE=False. ... ok test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details) Verify details of the parsed example PDB file. ... ok test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity) Verify the structure of the parsed example PDB file. ... ok test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict) Parse 1A8O.pdb file in strict mode. ... ok test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA) Walk down the structure hierarchy and test parser reliability. ... ok test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive) Catch exception on duplicated residue. ... ok test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict) Throw exception on duplicated residue. ... ok test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty) Parse an empty file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PSEA.py test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Polypeptide.py test_PDB_Polypeptide ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real) Test CaPPBuilder on real PDB file. ... ok test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd) Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau) Test tau angles calculated with CaPPBuilder. ... ok test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real) Test PPBuilder on real PDB file. ... ok test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd) Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion) Test phi/psi angles calculated with PPBuilder. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_QCPSuperimposer.py test_PDB_QCPSuperimposer ... ok test_compare_to_svd (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_compare_to_svd) Compare results of QCP to SVD. ... ok test_get_init_rms (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_get_init_rms) Test initial RMS calculation. ... ok test_get_transformed (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_get_transformed) Test transformation of coordinates after QCP. ... ok test_on_pdb (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_on_pdb) Align a PDB to itself. ... ok test_run (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_run) Test QCP on dummy data. ... ok test_set (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_set) Test setting of initial parameters. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.057 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_ResidueDepth.py test_PDB_ResidueDepth ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.' test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr) Test generation of xyzr (atomic radii) file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.046 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SASA.py test_PDB_SASA ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii) Run Shrake-Rupley with custom radii. ... ok test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm) Run Shrake-Rupley with default parameters. ... ok test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level) Raise exception on input Atom entity. ... ok test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type) Raise exception on unsupported entity type. ... ok test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1) Raise exception on invalid level parameter: X. ... ok test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2) Raise exception on invalid level parameter: S > C. ... ok test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity) Raise exception on invalid level parameter: S > C. ... ok test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points) Raise exception on bad n_points parameter. ... ok test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius) Raise exception on bad probe_radius parameter. ... ok test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution) Run Shrake-Rupley with 960 points per sphere. ... ok test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C) Run Shrake-Rupley with level C. ... ok test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R) Run Shrake-Rupley with level R. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.149 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SMCRA.py test_PDB_SMCRA ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element) Unknown element is assigned 'X'. ... ok test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment) Atom Element. ... ok test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok test_ions (test_PDB_SMCRA.Atom_Element.test_ions) Element for magnesium is assigned correctly. ... ok test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog) Calculate center of geometry of individual chains. ... ok test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure) Center of mass of empty structure raises ValueError. ... ok test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog) Calculate Structure center of geometry. ... ok test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com) Calculate Structure center of mass. ... ok test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id) Change the id of a model. ... ok test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self) Changing the id to itself does nothing (does not raise). ... ok test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id) Change the id of a model. ... ok test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises) Cannot change id to a value already in use by another child. ... ok test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id) Change the id of a residue. ... ok test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain) Invalidate cached full_ids if an id is changed. ... ok test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue) Invalidate cached full_ids if an id is changed. ... ok test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy) Make a copy of a residue. ... ok test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms) Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains) Yields chains from different models separately. ... ok test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues) Yields all residues from all models. ... ok test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities) Test comparing and sorting the several SMCRA objects. ... ok test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort) Test atoms are sorted correctly in residues. ... ok test_transform (test_PDB_SMCRA.TransformTests.test_transform) Transform entities (rotation and translation). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.212 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Selection.py test_PDB_Selection ... ok test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level) Unfold from lowest level to all levels. ... ok test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level) Unfold from chain level to all levels. ... ok test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level) Unfold from model to all levels. ... ok test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level) Unfold from chain level to all levels. ... ok test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level) Unfold from highest level to all levels. ... ok test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.046 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_StructureAlignment.py test_PDB_StructureAlignment ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign) Tests on module to align two proteins according to a FASTA alignment file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.155 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Superimposer.py test_PDB_Superimposer ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer) Test on module that superimpose two protein structures. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_internal_coords.py test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.057 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_parse_pdb_header.py test_PDB_parse_pdb_header ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_1 (test_PDB_parse_pdb_header.ParseReal.test_1) Parse the header of a known PDB file (1A8O). ... ok test_2 (test_PDB_parse_pdb_header.ParseReal.test_2) Parse the header of another PDB file (2BEG). ... ok test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line) Unit test for parsing and converting fields in HEADER record. ... ok test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title) Unit test for sensible result with no TITLE line. ... ok test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465) Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99) Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465) A UNIT-test for the private function _parse_remark_465. ... ok test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line) Unit test for correct parsing of multiline title records. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.064 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_vectors.py test_PDB_vectors ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_Vector (test_PDB_vectors.VectorTests.test_Vector) Test Vector object. ... ok test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles) Test Vector angles. ... ok test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) Confirm can generate coordinate space transform for 3 points. ... ok test_division (test_PDB_vectors.VectorTests.test_division) Confirm division works. ... ok test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates) Test spherical coordinates. ... ok test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0) Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180) Test 180 deg rotation. ... ok test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90) Test 90 deg rotation. ... ok test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space) Confirm multi_coord_space computes forward, reverse transforms. ... ok test_normalization (test_PDB_vectors.VectorTests.test_normalization) Test Vector normalization. ... ok test_refmat (test_PDB_vectors.VectorTests.test_refmat) Test refmat can mirror one matrix to another. ... ok test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0) Test rotmat when the rotation is 0 deg (singularity). ... ok test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180) Test rotmat when the rotation is 180 deg (singularity). ... ok test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90) Test regular 90 deg rotation. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.043 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PQR.py test_PQR ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge) Test if missing or malformed charge case is handled correctly. ... ok test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius) Test if missing, malformed or negative radius case is handled correctly. ... ok test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz) Test if bad coordinates exception is raised. ... ok test_single_input (test_PQR.ParseSimplePQR.test_single_input) Test if a single ATOM entry correctly parsed. ... ok test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure) Write a full structure using PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Pathway.py test_Pathway ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phd.py test_Phd ... ok test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO) Test phd_454 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO) Test phd1 using parser via SeqIO. ... ok test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser) Test phd1 file in detail. ... ok test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo.py test_Phylo ... ok test_convert (test_Phylo.IOTests.test_convert) Convert a tree between all supported formats. ... ok test_convert_phyloxml_binary (test_Phylo.IOTests.test_convert_phyloxml_binary) Try writing phyloxml to a binary handle; fail on Py3. ... ok test_convert_phyloxml_filename (test_Phylo.IOTests.test_convert_phyloxml_filename) Write phyloxml to a given filename. ... ok test_convert_phyloxml_text (test_Phylo.IOTests.test_convert_phyloxml_text) Write phyloxml to a text handle. ... ok test_format_branch_length (test_Phylo.IOTests.test_format_branch_length) Custom format string for Newick branch length serialization. ... ok test_int_labels (test_Phylo.IOTests.test_int_labels) Read newick formatted tree with numeric labels. ... ok test_newick_read_multiple (test_Phylo.IOTests.test_newick_read_multiple) Parse a Nexus file with multiple trees. ... ok test_newick_read_scinot (test_Phylo.IOTests.test_newick_read_scinot) Parse Newick branch lengths in scientific notation. ... ok test_newick_read_single1 (test_Phylo.IOTests.test_newick_read_single1) Read first Newick file with one tree. ... ok test_newick_read_single2 (test_Phylo.IOTests.test_newick_read_single2) Read second Newick file with one tree. ... ok test_newick_read_single3 (test_Phylo.IOTests.test_newick_read_single3) Read Nexus file with one tree. ... ok test_newick_write (test_Phylo.IOTests.test_newick_write) Parse a Nexus file with multiple trees. ... ok test_phylo_read_extra (test_Phylo.IOTests.test_phylo_read_extra) Additional tests to check correct parsing. ... ok test_unicode_exception (test_Phylo.IOTests.test_unicode_exception) Read a Newick file with a unicode byte order mark (BOM). ... ok test_collapse (test_Phylo.MixinTests.test_collapse) TreeMixin: collapse() method. ... ok test_collapse_all (test_Phylo.MixinTests.test_collapse_all) TreeMixin: collapse_all() method. ... ok test_common_ancestor (test_Phylo.MixinTests.test_common_ancestor) TreeMixin: common_ancestor() method. ... ok test_depths (test_Phylo.MixinTests.test_depths) TreeMixin: depths() method. ... ok test_distance (test_Phylo.MixinTests.test_distance) TreeMixin: distance() method. ... ok test_find_clades (test_Phylo.MixinTests.test_find_clades) TreeMixin: find_clades() method. ... ok test_find_elements (test_Phylo.MixinTests.test_find_elements) TreeMixin: find_elements() method. ... ok test_find_terminal (test_Phylo.MixinTests.test_find_terminal) TreeMixin: find_elements() with terminal argument. ... ok test_get_path (test_Phylo.MixinTests.test_get_path) TreeMixin: get_path() method. ... ok test_is_bifurcating (test_Phylo.MixinTests.test_is_bifurcating) TreeMixin: is_bifurcating() method. ... ok test_is_monophyletic (test_Phylo.MixinTests.test_is_monophyletic) TreeMixin: is_monophyletic() method. ... ok test_ladderize (test_Phylo.MixinTests.test_ladderize) TreeMixin: ladderize() method. ... ok test_prune (test_Phylo.MixinTests.test_prune) TreeMixin: prune() method. ... ok test_split (test_Phylo.MixinTests.test_split) TreeMixin: split() method. ... ok test_total_branch_length (test_Phylo.MixinTests.test_total_branch_length) TreeMixin: total_branch_length() method. ... ok test_trace (test_Phylo.MixinTests.test_trace) TreeMixin: trace() method. ... ok test_randomized (test_Phylo.TreeTests.test_randomized) Tree.randomized: generate a new randomized tree. ... ok test_root_at_midpoint (test_Phylo.TreeTests.test_root_at_midpoint) Tree.root_at_midpoint: reroot at the tree's midpoint. ... ok test_root_with_outgroup (test_Phylo.TreeTests.test_root_with_outgroup) Tree.root_with_outgroup: reroot at a given clade. ... ok test_str (test_Phylo.TreeTests.test_str) Tree.__str__: pretty-print to a string. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.288 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PhyloXML.py test_PhyloXML ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_alignment (test_PhyloXML.MethodTests.test_alignment) ... ok test_clade_getitem (test_PhyloXML.MethodTests.test_clade_getitem) Clade.__getitem__: get sub-clades by extended indexing. ... ok test_clade_to_phylogeny (test_PhyloXML.MethodTests.test_clade_to_phylogeny) Convert a Clade object to a new Phylogeny. ... ok test_color_hex (test_PhyloXML.MethodTests.test_color_hex) BranchColor: to_hex() method. ... ok test_events (test_PhyloXML.MethodTests.test_events) Events: Mapping-type behavior. ... ok test_phylogeny_to_phyloxml (test_PhyloXML.MethodTests.test_phylogeny_to_phyloxml) Convert a Phylogeny object to a new Phyloxml. ... ok test_phyloxml_getitem (test_PhyloXML.MethodTests.test_phyloxml_getitem) Phyloxml.__getitem__: get phylogenies by name or index. ... ok test_sequence_conversion (test_PhyloXML.MethodTests.test_sequence_conversion) ... ok test_singlular (test_PhyloXML.MethodTests.test_singlular) Clade, Phylogeny: Singular properties for plural attributes. ... ok test_to_alignment (test_PhyloXML.MethodTests.test_to_alignment) ... ok test_parse_apaf (test_PhyloXML.ParseTests.test_parse_apaf) Parse the phylogenies in apaf.xml. ... ok test_parse_bcl2 (test_PhyloXML.ParseTests.test_parse_bcl2) Parse the phylogenies in bcl_2.xml. ... ok test_parse_dollo (test_PhyloXML.ParseTests.test_parse_dollo) Parse the phylogenies in o_tol_332_d_dollo.xml. ... ok test_parse_made (test_PhyloXML.ParseTests.test_parse_made) Parse the phylogenies in made_up.xml. ... ok test_parse_phylo (test_PhyloXML.ParseTests.test_parse_phylo) Parse the phylogenies in phyloxml_examples.xml. ... ok test_read_apaf (test_PhyloXML.ParseTests.test_read_apaf) Read apaf.xml to produce a phyloXML object. ... ok test_read_bcl2 (test_PhyloXML.ParseTests.test_read_bcl2) Read bcl_2.xml to produce a phyloXML object. ... ok test_read_dollo (test_PhyloXML.ParseTests.test_read_dollo) Read o_tol_332_d_dollo.xml to produce a phyloXML object. ... ok test_read_made (test_PhyloXML.ParseTests.test_read_made) Read made_up.xml to produce a phyloXML object. ... ok test_read_phylo (test_PhyloXML.ParseTests.test_read_phylo) Read phyloxml_examples.xml to produce a phyloXML object. ... ok test_shape_apaf (test_PhyloXML.ParseTests.test_shape_apaf) Check the branching structure of apaf.xml. ... ok test_shape_bcl2 (test_PhyloXML.ParseTests.test_shape_bcl2) Check the branching structure of bcl_2.xml. ... ok test_shape_dollo (test_PhyloXML.ParseTests.test_shape_dollo) Check the branching structure of o_tol_332_d_dollo.xml. ... ok test_shape_phylo (test_PhyloXML.ParseTests.test_shape_phylo) Check the branching structure of phyloxml_examples.xml. ... ok test_Annotation (test_PhyloXML.TreeTests.test_Annotation) Instantiation of Annotation objects. ... ok test_BinaryCharacters (test_PhyloXML.TreeTests.test_BinaryCharacters) Instantiation of BinaryCharacters objects. ... ok test_Clade (test_PhyloXML.TreeTests.test_Clade) Instantiation of Clade objects. ... ok test_CladeRelation (test_PhyloXML.TreeTests.test_CladeRelation) Instantiation of CladeRelation objects. ... ok test_Confidence (test_PhyloXML.TreeTests.test_Confidence) Instantiation of Confidence objects. ... ok test_Date (test_PhyloXML.TreeTests.test_Date) Instantiation of Date objects. ... ok test_Distribution (test_PhyloXML.TreeTests.test_Distribution) Instantiation of Distribution objects. ... ok test_DomainArchitecture (test_PhyloXML.TreeTests.test_DomainArchitecture) Instantiation of DomainArchitecture objects. ... ok test_Events (test_PhyloXML.TreeTests.test_Events) Instantiation of Events objects. ... ok test_Other (test_PhyloXML.TreeTests.test_Other) Instantiation of Other objects. ... ok test_Phylogeny (test_PhyloXML.TreeTests.test_Phylogeny) Instantiation of Phylogeny objects. ... ok test_Phyloxml (test_PhyloXML.TreeTests.test_Phyloxml) Instantiation of Phyloxml objects. ... ok test_Polygon (test_PhyloXML.TreeTests.test_Polygon) Instantiation of Polygon objects. ... ok test_Property (test_PhyloXML.TreeTests.test_Property) Instantiation of Property objects. ... ok test_Reference (test_PhyloXML.TreeTests.test_Reference) Instantiation of Reference objects. ... ok test_Sequence (test_PhyloXML.TreeTests.test_Sequence) Instantiation of Sequence objects. ... ok test_SequenceRelation (test_PhyloXML.TreeTests.test_SequenceRelation) Instantiation of SequenceRelation objects. ... ok test_Taxonomy (test_PhyloXML.TreeTests.test_Taxonomy) Instantiation of Taxonomy objects. ... ok test_Uri (test_PhyloXML.TreeTests.test_Uri) Instantiation of Uri objects. ... ok test_apaf (test_PhyloXML.WriterTests.test_apaf) Round-trip parsing and serialization of apaf.xml. ... ok test_bcl2 (test_PhyloXML.WriterTests.test_bcl2) Round-trip parsing and serialization of bcl_2.xml. ... ok test_dollo (test_PhyloXML.WriterTests.test_dollo) Round-trip parsing and serialization of o_tol_332_d_dollo.xml. ... ok test_made (test_PhyloXML.WriterTests.test_made) Round-trip parsing and serialization of made_up.xml. ... ok test_phylo (test_PhyloXML.WriterTests.test_phylo) Round-trip parsing and serialization of phyloxml_examples.xml. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.249 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_CDAO.py test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format. ---------------------------------------------------------------------- Ran 1 test in 0.043 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_NeXML.py test_Phylo_NeXML ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_parse (test_Phylo_NeXML.ParseTests.test_parse) Extract and count phylogenetic trees using Phylo.parse. ... ok test_write (test_Phylo_NeXML.WriterTests.test_write) Test for serialization of objects to NeXML format. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_matplotlib.py test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils. ---------------------------------------------------------------------- Ran 1 test in 0.043 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_networkx.py test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.042 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop.py test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop_nodepend.py test_PopGen_GenePop_nodepend ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser) Basic operation of the File Record Parser. ... ok test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features) Testing the ability to remove population/loci via class methods. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser) Basic operation of the Record Parser. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic) Basic test on Record. ... ok test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils) Basic operation of GenePop Utils. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Prank_tool.py test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Probcons_tool.py test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_ProtParam.py test_ProtParam ... ok test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity) Calculate protein aromaticity. ... ok test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH) Test charge_at_pH function. ... ok test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids) Calculate amino acid counts. ... ok test_flexibility (test_ProtParam.ProtParamTest.test_flexibility) Calculate protein flexibility. ... ok test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent) Calculate amino acid percentages. ... ok test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight) Calculate protein molecular weight. ... ok test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight) Calculate monoisotopic molecular weight. ... ok test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_gravy (test_ProtParam.ProtParamTest.test_gravy) Calculate gravy. Tests all pre-defined scales. ... ok test_instability_index (test_ProtParam.ProtParamTest.test_instability_index) Calculate protein instability index. ... ok test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point) Calculate the isoelectric point. ... ok test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient) Molar extinction coefficient. ... ok test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale) Calculate the Kite Doolittle scale. ... ok test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction) Calculate secondary structure fractions. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_RCSBFormats.py test_RCSBFormats ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains) Compare parsed chains. ... ok test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models) Compared parsed models. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.278 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Restriction.py test_Restriction ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers) Test to be sure isochizomer and neoschizomers are as expected. ... ok test_comparisons (test_Restriction.EnzymeComparison.test_comparisons) Test comparison operators between different enzymes. ... ok test_change (test_Restriction.RestrictionBatchPrintTest.test_change) Test that change() changes something. ... ok test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3) Test that print_as('map'); print_that() correctly wraps round. ... ok test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions) Test Fancier restriction analysis. ... ok test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis) Sequence analysis with a restriction batch. ... ok test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch) Creating and modifying a restriction batch. ... ok test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches) Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches) Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq) Test several methods of FormattedSeq. ... ok test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters) Test if non-IUPAC letters raise a TypeError. ... ok test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object) Test if sequence must be a Seq or MutableSeq object. ... ok test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences) Deal with cutting circular sequences. ... ok test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions) Check if cutting after first and penultimate position works. ... ok test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting) Test basic cutting with EarI (ambiguous overhang). ... ok test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting) Test basic cutting with EcoRI (5'overhang). ... ok test_init (test_Restriction.SimpleEnzyme.test_init) Check for error during __init__. ... ok test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting) Test basic cutting with KpnI (3'overhang). ... ok test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites) Check if overlapping recognition sites are properly handled. ... ok test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands) Check if recognition sites on both strands are properly handled. ... ok test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts) Check if '/' and '//' work as '.search' and '.catalyse'. ... ok test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting) Test basic cutting with SmaI (blunt cutter). ... ok test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting) Test basic cutting with SnaI (unknown). ... ok test_print_that (test_Restriction.TestPrintOutputs.test_print_that) Test print_that function. ... ok test_str_method (test_Restriction.TestPrintOutputs.test_str_method) Test __str__ and __repr__ outputs. ... ok test_supplier (test_Restriction.TestPrintOutputs.test_supplier) Test output of supplier list for different enzyme types. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Astral.py test_SCOP_Astral ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Cla.py test_SCOP_Cla ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testError (test_SCOP_Cla.ClaTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testIndex (test_SCOP_Cla.ClaTests.testIndex) Test CLA file indexing. ... ok testParse (test_SCOP_Cla.ClaTests.testParse) Test if all records in a CLA file are being read. ... ok testRecord (test_SCOP_Cla.ClaTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Cla.ClaTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Des.py test_SCOP_Des ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testError (test_SCOP_Des.DesTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Des.DesTests.testParse) Test if all records in a DES file are being read. ... ok testRecord (test_SCOP_Des.DesTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Des.DesTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Dom.py test_SCOP_Dom ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testError (test_SCOP_Dom.DomTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Dom.DomTests.testParse) Test if all records in a DOM file are being read. ... ok testRecord (test_SCOP_Dom.DomTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Dom.DomTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Hie.py test_SCOP_Hie ... ok testError (test_SCOP_Hie.HieTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Hie.HieTests.testParse) Test if all records in a HIE file are being read. ... ok testStr (test_SCOP_Hie.HieTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Raf.py test_SCOP_Raf ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testParse (test_SCOP_Raf.RafTests.testParse) Parse a RAF record. ... ok testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Residues.py test_SCOP_Residues ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse) Test if we can parse residue subsets enclosed in brackets. ... ok testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Scop.py test_SCOP_Scop ... ok testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok testParse (test_SCOP_Scop.ScopTests.testParse) ... ok testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents) Test getDescendents method. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.048 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.043 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SVDSuperimposer.py test_SVDSuperimposer ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab.py test_SearchIO_blast_tab ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_tab_2226_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_001) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_001). ... ok test_tab_2226_tblastn_002 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_002) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_002). ... ok test_tab_2226_tblastn_003 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_003) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_003). ... ok test_tab_2226_tblastn_004 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_004) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_004). ... ok test_tab_2226_tblastn_005 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_005) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005). ... ok test_tab_2226_tblastn_005_comments_false (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_005_comments_false) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005). ... ok test_tab_2226_tblastn_006 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_006) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_006). ... ok test_tab_2226_tblastn_007 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_007) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_007). ... ok test_tab_2226_tblastn_008 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_008) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_008). ... ok test_tab_2226_tblastn_009 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_009) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_009). ... ok test_tab_2226_tblastn_010 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_010) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_010). ... ok test_tab_2226_tblastn_011 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_011) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_011). ... ok test_tab_2226_tblastn_012 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_012) Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_012). ... ok test_tab_2226_tblastn_013 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_013) Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_013). ... ok test_tab_2228_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2228_tblastn_001) Test parsing TBLASTN 2.2.28+ tabular output (tab_2228_tblastn_001). ... ok test_tab_2228_tblastx_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2228_tblastx_001) Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab_index.py test_SearchIO_blast_tab_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_blasttab_2226_tblastn_001 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_001) Test blast-tab indexing, BLAST 2.2.26+, multiple queries. ... ok test_blasttab_2226_tblastn_002 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_002) Test blast-tab indexing, BLAST 2.2.26+, single query, no hits. ... ok test_blasttab_2226_tblastn_004 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_004) Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits. ... ok test_blasttab_2226_tblastn_005 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_005) Test blast-tab indexing, BLAST 2.2.26+, multiple queries, commented. ... ok test_blasttab_2226_tblastn_006 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_006) Test blast-tab indexing, BLAST 2.2.26+, single query, no hits, commented. ... ok test_blasttab_2226_tblastn_009 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_009) Test blast-tab indexing, BLAST 2.2.26+, custom columns. ... ok test_blasttab_2226_tblastn_010 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_010) Test blast-tab indexing, BLAST 2.2.26+, custom columns, commented. ... ok test_blasttab_2226_tblastn_011 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_011) Test blast-tab indexing, BLAST 2.2.26+, all columns, commented. ... ok test_blasttab_comment_sing (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_comment_sing) Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits, commented. ... ok test_blasttab_2226_multiple_first (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_first) Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first (tab_2226_tblastn_001.txt). ... ok test_blasttab_2226_multiple_first_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_first_commented) Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first, commented (tab_2226_tblastn_005.txt). ... ok test_blasttab_2226_multiple_last (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_last) Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last (tab_2226_tblastn_001.txt). ... ok test_blasttab_2226_multiple_last_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_last_commented) Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last, commented (tab_2226_tblastn_005.txt). ... ok test_blasttab_2226_multiple_middle_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_middle_commented) Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, middle, commented (tab_2226_tblastn_005.txt). ... ok test_blasttab_2226_single (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_single) Test blast-tab raw string retrieval, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok test_blasttab_2226_single_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_single_commented) Test blast-tab raw string retrieval, BLAST 2.2.26+, single query, commented (tab_2226_tblastn_008.txt). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml.py test_SearchIO_blast_xml ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_xml_2226_blastn_006 (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006) ... ok test_xml_2226_blastn_006_use_raw_hit_ids (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006_use_raw_hit_ids) ... ok test_xml_2226_blastn_006_use_raw_query_ids (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006_use_raw_query_ids) ... ok test_xml_2212L_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2212L_blastn_001) ... ok test_xml_2226_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_001) ... ok test_xml_2226_blastn_002 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_002) ... ok test_xml_2226_blastn_003 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_003) ... ok test_xml_2226_blastn_004 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_004) ... ok test_xml_2226_blastn_005 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_005) ... ok test_xml_2212L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2212L_blastp_001) ... ok test_xml_2218L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218L_blastp_001) ... ok test_xml_2218_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218_blastp_001) ... ok test_xml_2218_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218_blastp_002) ... ok test_xml_2222_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2222_blastp_001) ... ok test_xml_2226_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_001) ... ok test_xml_2226_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_002) ... ok test_xml_2226_blastp_003 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_003) ... ok test_xml_2226_blastp_004 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_004) ... ok test_xml_2226_blastp_005 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_005) ... ok test_xml_2212L_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2212L_blastx_001) ... ok test_xml_2222_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2222_blastx_001) ... ok test_xml_2226_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_001) ... ok test_xml_2226_blastx_002 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_002) ... ok test_xml_2226_blastx_003 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_003) ... ok test_xml_2226_blastx_004 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_004) ... ok test_xml_2212L_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2212L_tblastn_001) ... ok test_xml_2226_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_001) ... ok test_xml_2226_tblastn_002 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_002) ... ok test_xml_2226_tblastn_003 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_003) ... ok test_xml_2226_tblastn_004 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_004) ... ok test_xml_2226_tblastn_005 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_005) ... ok test_xml_2212L_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2212L_tblastx_001) ... ok test_xml_2226_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_001) ... ok test_xml_2226_tblastx_002 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_002) ... ok test_xml_2226_tblastx_003 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_003) ... ok test_xml_2226_tblastx_004 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_004) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.124 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml_index.py test_SearchIO_blast_xml_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_blastxml_2212L_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2212L_blastp_001) Test blast-xml indexing, BLAST 2.2.12. ... ok test_blastxml_2218_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2218_blastp_001) Test blast-xml indexing, BLAST 2.2.18+. ... ok test_blastxml_2222_blastx_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2222_blastx_001) Test blast-xml indexing, BLAST 2.2.22+. ... ok test_blastxml_2226_tblastn_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_001) Test blast-xml indexing, BLAST 2.2.26+, multiple queries. ... ok test_blastxml_2226_tblastn_002 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_002) Test blast-xml indexing, BlAST 2.2.26+, single query, no hits. ... ok test_blastxml_2226_tblastn_004 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_004) Test blast-xml indexing, BLAST 2.2.26+, single query, multiple hits. ... ok test_blastxml_2226_multiple_first (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_first) Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, first (xml_2226_blastp_001.xml). ... ok test_blastxml_2226_multiple_last (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_last) Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, last (xml_2226_blastp_001.xml). ... ok test_blastxml_2226_multiple_middle (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_middle) Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, middle (xml_2226_blastp_001.xml). ... ok test_blastxml_2226_single (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_single) Test blast-xml raw string retrieval, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.917 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl.py test_SearchIO_blat_psl ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001) Test parsing blat output (pslx_34_001.pslx). ... ok test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002) Test parsing blat output (pslx_34_002.pslx). ... ok test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003) Test parsing blat output (pslx_34_003.pslx). ... ok test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004) Test parsing blat output (pslx_34_004.pslx). ... ok test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005) Test parsing blat output (pslx_34_005.pslx). ... ok test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002) Test parsing blat output (pslx_35_002.pslx). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001) Test blat-psl indexing, multiple queries. ... ok test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002) Test blat-psl indexing, single query, no hits. ... ok test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003) Test blat-psl indexing, single query, single hit. ... ok test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004) Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005) Test blat-psl indexing, multiple queries, no header. ... ok test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006) Test blat-pslx indexing, multiple queries. ... ok test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007) Test blat-pslx indexing, single query, no hits. ... ok test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008) Test blat-pslx indexing, single query, single hit. ... ok test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009) Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010) Test blat-pslx indexing, multiple queries, no header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate.py test_SearchIO_exonerate ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar) Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c) Compares vulgar-text coordinate parsing for the coding2coding model. ... ok test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g) Compares vulgar-text coordinate parsing for the genome2genome model. ... ok test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d) Compares vulgar-text coordinate parsing for the protein2dna model. ... ok test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local) Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome) Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding) Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts) Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome) Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein) Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome) Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome) Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner) Test parsing exonerate output (exn_22_m_ner.exn). ... ok test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts) Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome) Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped) Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans) Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple) Test parsing exonerate output (exn_22_q_multiple.exn). ... ok test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts) Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron) Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar) Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts) Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_text_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome) Test exonerate-text indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple) Test exonerate-text indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_vulgar_index.py test_SearchIO_exonerate_vulgar_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome) Test exonerate-vulgar indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple) Test exonerate-vulgar indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.040 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10 ... ok test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002) Test parsing fasta34 output (output002.m10). ... ok test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003) Test parsing fasta34 output (output003.m10). ... ok test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001) Test parsing fasta35 output (output001.m10). ... ok test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004) Test parsing fasta35 output (output004.m10). ... ok test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005) Test parsing ssearch35 output (output005.m10). ... ok test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006) Test parsing fasta35 output (output006.m10). ... ok test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007) Test parsing fasta36 output (output007.m10). ... ok test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008) Test parsing tfastx36 output (output008.m10). ... ok test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009) Test parsing fasta36 output (output009.m10). ... ok test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010) Test parsing fasta36 output (output010.m10). ... ok test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011) Test parsing fasta36 output (output011.m10). ... ok test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012) Test parsing fasta36 output (output012.m10). ... ok test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013) Test parsing fasta36 output (output013.m10). ... ok test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014) Test parsing fasta36 output (output014.m10). ... ok test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015) Test parsing fasta36 output (output015.m10). ... ok test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016) Test parsing fasta36 output (output016.m10). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_fasta_m10_index.py test_SearchIO_fasta_m10_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001) Test fasta-m10 indexing, fasta35, multiple queries. ... ok test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002) Test fasta-m10 indexing, fasta34, multiple queries. ... ok test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005) Test fasta-m10 indexing, ssearch35, multiple queries. ... ok test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008) Test fasta-m10 indexing, tfastx36, multiple queries. ... ok test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009) Test fasta-m10 indexing, fasta36, multiple queries. ... ok test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010) Test fasta-m10 indexing, fasta36, single query, no hits. ... ok test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011) Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012) Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hhsuite2_text.py test_SearchIO_hhsuite2_text ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo) Parsing 2uvo. ... ok test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable) Parsing 4uvo with empty results table. ... ok test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader) Parsing 4uvo with only header present. ... ok test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79) Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm) Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198) Parsing hhpred_9590198.hhr file. ... ok test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx) Parsing allx.hhr file. ... ok test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1) Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21) Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22) Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq) Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24) Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20) Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22) Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer2_text_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.1. ... ok test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.3. ... ok test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.4. ... ok test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam) Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch) Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.070 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab ... ok test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002) Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.039 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_domtab_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_001) Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002) Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003) Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004) Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001) Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_last) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_middle) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_single) Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.046 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002) Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003) Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004) Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001) Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.036 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_tab_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_001) Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002) Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003) Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004) Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_last) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_middle) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_single) Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.041 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text ... ok test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001) Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002) Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003) Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004) Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005) Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001) Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001) Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001) Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002) Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003) Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004) Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005) Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006) Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007) Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008) Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009) Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010) Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok test_30_hmmscan_011 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_011) Parsing hmmscan 3.0 (text_30_hmmscan_011). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001) Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001) Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_text_index.py test_SearchIO_hmmer3_text_index ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002) Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_006) Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_007) Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_008) Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmsearch_005) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_last) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_middle) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_single) Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.035 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_model.py test_SearchIO_model ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters) Test HSPFragment query and hit coordinate-related setters and getters. ... ok test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly) Test HSPFragment query and hit coordinate-related read-only getters. ... ok test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs) Test HSPFragment attributes' default values. ... ok test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error) Test HSPFragment query and hit frame setters, invalid values. ... ok test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok) Test HSPFragment query and hit frame setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem) Test HSPFragment.__getitem__. ... ok test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot) Test HSPFragment.__getitem__, with alignment annotation. ... ok test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs) Test HSPFragment.__getitem__, with attributes. ... ok test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set) Test HSPFragment query and hit id and description setters. ... ok test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord) Test HSPFragment.__init__, with SeqRecord. ... ok test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes) Test HSPFragment.__init__, wrong sequence argument types. ... ok test_len (test_SearchIO_model.HSPFragmentCases.test_len) Test HSPFragment.__len__. ... ok test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq) Test HSPFragment molecule_type property, query and hit sequences not present. ... ok test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq) Test HSPFragment molecule_type property, query or hit sequences present. ... ok test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle) Test pickling and unpickling of HSPFragment. ... ok test_repr (test_SearchIO_model.HSPFragmentCases.test_repr) Test HSPFragment.__repr__. ... ok test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len) Test HSPFragment sequence setter with unequal hit and query lengths. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel) Test HSPFragment sequence attribute types and default values. ... ok test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error) Test HSPFragment query and hit strand setters, invalid values. ... ok test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame) Test HSPFragment query and hit strand getters, from minus frame. ... ok test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame) Test HSPFragment query and hit strand getters, from plus frame. ... ok test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame) Test HSPFragment query and hit strand getters, from zero frame. ... ok test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok) Test HSPFragment query and hit strand setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem) Test HSPFragment.__getitem__, no alignments. ... ok test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit) Test HSPFragment.__getitem__, only hit. ... ok test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query) Test HSPFragment.__getitem__, only query. ... ok test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init) Test HSPFragment.__init__ attributes. ... ok test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter) Test HSP.__iter__, no alignments. ... ok test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len) Test HSPFragment.__len__, no alignments. ... ok test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr) Test HSPFragment.__repr__, no alignments. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel) Test HSPFragment sequence attributes, no alignments. ... ok test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains) Test HSP.__contains__. ... ok test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem) Test HSP.__delitem__. ... ok test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments) Test HSP.fragments property. ... ok test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem) Test HSP.__getitem__. ... ok test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set) Test HSP query and hit id and description setters. ... ok test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len) Test HSP.__len__. ... ok test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type) Test HSP.molecule_type getter. ... ok test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set) Test HSP.molecule_type setter. ... ok test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle) Test pickling and unpickling of HSP. ... ok test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range) Test HSP range properties. ... ok test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges) Test HSP ranges properties. ... ok test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs) Test HSP sequence properties. ... ok test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple) Test HSP.__setitem__, multiple items. ... ok test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single) Test HSP.__setitem__, single item. ... ok test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span) Test HSP span properties. ... ok test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment) Test HSP.alignment property. ... ok test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span) Test HSP.aln_span property. ... ok test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment) Test HSP.fragment property. ... ok test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment) Test HSP.__init__ without fragments. ... ok test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len) Test HSP.__len__. ... ok test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range) Test HSP range properties. ... ok test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq) Test HSP sequence properties. ... ok test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span) Test HSP span properties. ... ok test_append (test_SearchIO_model.HitCases.test_append) Test Hit.append. ... ok test_bool (test_SearchIO_model.HitCases.test_bool) Test Hit.__bool__. ... ok test_delitem (test_SearchIO_model.HitCases.test_delitem) Test Hit.__delitem__. ... ok test_desc_set (test_SearchIO_model.HitCases.test_desc_set) Test Hit.description setter. ... ok test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord) Test Hit.description setter, without HSP SeqRecords. ... ok test_filter (test_SearchIO_model.HitCases.test_filter) Test Hit.filter. ... ok test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered) Test Hit.hit_filter, all hits filtered out. ... ok test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func) Test Hit.filter, without arguments. ... ok test_fragments (test_SearchIO_model.HitCases.test_fragments) Test Hit.fragments. ... ok test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple) Test Hit.__getitem__, multiple items. ... ok test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single) Test Hit.__getitem__, single item. ... ok test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func) Test Hit.map, without arguments. ... ok test_hsps (test_SearchIO_model.HitCases.test_hsps) Test Hit.hsps. ... ok test_id_set (test_SearchIO_model.HitCases.test_id_set) Test Hit.id setter. ... ok test_index (test_SearchIO_model.HitCases.test_index) Test Hit.index. ... ok test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present) Test Hit.index, when index is not present. ... ok test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only) Test Hit.__init__, with hsps only. ... ok test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only) Test Hit.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.HitCases.test_init_none) Test Hit.__init__, no arguments. ... ok test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple) Test Hit.__setitem__, multiple items. ... ok test_iter (test_SearchIO_model.HitCases.test_iter) Test Hit.__iter__. ... ok test_len (test_SearchIO_model.HitCases.test_len) Test Hit.__len__. ... ok test_map (test_SearchIO_model.HitCases.test_map) Test Hit.hsp_map. ... ok test_pickle (test_SearchIO_model.HitCases.test_pickle) Test pickling and unpickling of Hit. ... ok test_pop (test_SearchIO_model.HitCases.test_pop) Test Hit.pop. ... ok test_repr (test_SearchIO_model.HitCases.test_repr) Test Hit.__repr__. ... ok test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single) Test Hit.__setitem__, single item. ... ok test_sort (test_SearchIO_model.HitCases.test_sort) Test Hit.sort. ... ok test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place) Test Hit.sort, not in place. ... ok test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok) Test Hit._validate_hsp. ... ok test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id) Test Hit._validate_hsp, wrong hit ID. ... ok test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id) Test Hit._validate_hsp, wrong query ID. ... ok test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type) Test Hit._validate_hsp, wrong type. ... ok test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist) Test QueryResult.absorb, hit does not exist. ... ok test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists) Test QueryResult.absorb, hit with the same ID exists. ... ok test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists) Test QueryResult.append, when alt ID exists. ... ok test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt) Test QueryResult.append, when alt ID exists as primary. ... ok test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok) Test QueryResult.append, with custom hit key function. ... ok test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists) Test QueryResult.append, when ID exists. ... ok test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok) Test QueryResult.append. ... ok test_bool (test_SearchIO_model.QueryResultCases.test_bool) Test QueryResult.__bool__. ... ok test_contains (test_SearchIO_model.QueryResultCases.test_contains) Test QueryResult.__contains__. ... ok test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt) Test QueryResult.__contains__, with alternative IDs. ... ok test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok) Test QueryResult.__delitem__, with alt ID. ... ok test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok) Test QueryResult.__delitem__. ... ok test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok) Test QueryResult.__delitem__, with slice. ... ok test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok) Test QueryResult.__getitem__, with string. ... ok test_description_set (test_SearchIO_model.QueryResultCases.test_description_set) Test QueryResult.description setter. ... ok test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord) Test QueryResult.description setter, without HSP SeqRecords. ... ok test_fragments (test_SearchIO_model.QueryResultCases.test_fragments) Test QueryResult.fragments. ... ok test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok) Test QueryResult.__getitem__, single item with alternative ID. ... ok test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok) Test QueryResult.__getitem__. ... ok test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok) Test QueryResult.__getitem__, with integer. ... ok test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok) Test QueryResult.__getitem__, with slice. ... ok test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok) Test QueryResult.__getitem__, with slice and alt IDs. ... ok test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter) Test QueryResult.hit_filter. ... ok test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered) Test QueryResult.hit_filter, all hits filtered out. ... ok test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func) Test QueryResult.hit_filter, without arguments. ... ok test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys) Test QueryResult.hit_keys. ... ok test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map) Test QueryResult.hit_map. ... ok test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func) Test QueryResult.hit_map, without arguments. ... ok test_hits (test_SearchIO_model.QueryResultCases.test_hits) Test QueryResult.hits. ... ok test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter) Test QueryResult.hsp_filter. ... ok test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered) Test QueryResult.hsp_filter, all hits filtered out. ... ok test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func) Test QueryResult.hsp_filter, no arguments. ... ok test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map) Test QueryResult.hsp_map. ... ok test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func) Test QueryResult.hsp_map, without arguments. ... ok test_hsps (test_SearchIO_model.QueryResultCases.test_hsps) Test QueryResult.hsps. ... ok test_id_set (test_SearchIO_model.QueryResultCases.test_id_set) Test QueryResult.id setter. ... ok test_index (test_SearchIO_model.QueryResultCases.test_index) Test QueryResult.index. ... ok test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt) Test QueryResult.index, with alt ID. ... ok test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present) Test QueryResult.index, when index is not present. ... ok test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only) Test QueryResult.__init__, with hits only. ... ok test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only) Test QueryResult.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.QueryResultCases.test_init_none) Test QueryResult.__init__, no arguments. ... ok test_items (test_SearchIO_model.QueryResultCases.test_items) Test QueryResult.items. ... ok test_iter (test_SearchIO_model.QueryResultCases.test_iter) Test QueryResult.__iter__. ... ok test_len (test_SearchIO_model.QueryResultCases.test_len) Test QueryResult.__len__. ... ok test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok test_pickle (test_SearchIO_model.QueryResultCases.test_pickle) Test pickling and unpickling of QueryResult. ... ok test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok) Test QueryResult.pop, with integer index. ... ok test_pop_nonexistent_key (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_key) Test QueryResult.pop with default for nonexistent key. ... ok test_pop_nonexistent_with_default (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_with_default) Test QueryResult.pop with default for nonexistent key. ... ok test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok) Test QueryResult.pop. ... ok test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok) Test QueryResult.pop, with alternative ID. ... ok test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok) Test QueryResult.pop, with string index. ... ok test_repr (test_SearchIO_model.QueryResultCases.test_repr) Test QueryResult.__repr__. ... ok test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty) Test QueryResult.__setitem__, from empty container. ... ok test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok) Test QueryResult.__setitem__. ... ok test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt) Test QueryResult.__setitem__, checking alt hit IDs. ... ok test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing) Test QueryResult.__setitem__, existing key. ... ok test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote) Test QueryResult.__setitem__, previously alt ID. ... ok test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type) Test QueryResult.__setitem__, wrong key type. ... ok test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id) Test QueryResult.__setitem__, wrong query ID. ... ok test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type) Test QueryResult.__setitem__, wrong type. ... ok test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok) Test QueryResult.sort, with custom key, not in place. ... ok test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok) Test QueryResult.sort, with custom key. ... ok test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok) Test QueryResult.sort, not in place. ... ok test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok) Test QueryResult.sort. ... ok test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok) Test QueryResult.sort, reverse, not in place. ... ok test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok) Test QueryResult.sort, reverse. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_write.py test_SearchIO_write ... ok test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields) Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl) Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx) Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl) Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query) Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx) Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query) Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab) Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.145 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqFeature.py test_SeqFeature ... /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior. warnings.warn( ok test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_origin_spanning_location (test_SeqFeature.TestExtract.test_origin_spanning_location) Test location spanning origin. ... ok test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record) Test compound location with reference to another record. ... ok test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence) Test compound location with reference to another sequence. ... ok test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record) Test location with reference to another record. ... ok test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence) Test location with reference to another sequence. ... ok test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy) Test fuzzy representations. ... ok test_pickle (test_SeqFeature.TestPositions.test_pickle) Test pickle behaviour of position instances. ... ok test_eq_identical (test_SeqFeature.TestReference.test_eq_identical) Test two identical references eq() to True. ... ok test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok test_location_aliases (test_SeqFeature.TestSeqFeature.test_location_aliases) ... ok test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds) Test that a CDS feature is subject to respective checks. ... ok test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets) Test adding and subtracting integer offsets. ... ok test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO.py test_SeqIO ... ok test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type) Convert Clustal to NEXUS with molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type) Convert Clustal to NEXUS without molecule type. ... ok test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok test_embl13 (test_SeqIO.TestSeqIO.test_embl13) Test parsing embl file with wrapped locations and unspecified type. ... ok test_embl14 (test_SeqIO.TestSeqIO.test_embl14) Test parsing file with features over-indented for EMBL. ... ok test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok test_empty_file (test_SeqIO.TestSeqIO.test_empty_file) Check parsers can cope with an empty file. ... ok test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type) Convert FASTA to SeqXML with molecule type. ... ok test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type) Convert FASTA to SeqXML without molecule type. ... ok test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16) Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20) Test parsing GenPept file with nasty bond locations. ... ok test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22) Test that genbank format write doesn't destroy db_source in annotations. ... ok test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23) Test that peptide genbank files can be written with long names. ... ok test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok test_ig3 (test_SeqIO.TestSeqIO.test_ig3) Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1) Test parsing file with features over-indented for EMBL. ... ok test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok test_uniprot_xml_namespace (test_SeqIO.TestSeqIO.test_uniprot_xml_namespace) ... ok test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta) Testing FASTA with gzip. ... ok test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq) Testing FASTQ with gzip. ... ok test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank) Testing GenBank with gzip. ... ok ---------------------------------------------------------------------- Ran 1 test in 9.037 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_AbiIO.py test_SeqIO_AbiIO ... ok test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type) Test if filetype is ABIF. ... ok test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1) Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok test_raw (test_SeqIO_AbiIO.TestAbi.test_raw) Test access to raw ABIF tags. ... ok test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord) Test if the extracted seqrecords data are equal to expected values. ... ok test_trim (test_SeqIO_AbiIO.TestAbi.test_trim) Test if trim works. ... ok test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type) Test if error is raised if filetype is not ABIF. ... ok test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag) Test that we can handle non-ascii tags. ... ok test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode) Test if exception is raised if file is not opened in 'rb' mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.188 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_FastaIO.py test_SeqIO_FastaIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser) Test FastaTwoLineParser edge-cases. ... ok test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser) Test SimpleFastaParser edge-cases. ... ok test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser) Test FastaTwoLineParser exceptions. ... ok test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser) Test regular FastaTwoLineParser cases. ... ok test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser) Test regular SimpleFastaParser cases. ... ok test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name) Test FASTA record with no identifier. ... ok test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files) Test Fasta files containing a single nucleotide sequence. ... ok test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files) Test Fasta files containing a single protein sequence. ... ok test_fails (test_SeqIO_FastaIO.Wrapping.test_fails) Test case which should fail. ... ok test_passes (test_SeqIO_FastaIO.Wrapping.test_passes) Test case which should pass. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Gck.py test_SeqIO_Gck ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths) Read a file with incorrect length. ... ok test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read) Read an artificial sample file. ... ok test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read) Read a file with an incomplete header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.048 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Insdc.py test_SeqIO_Insdc ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion) Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1) Check parsing of annotation from EMBL files (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2) Check parsing of annotation from EMBL files (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3) Check parsing of annotation from EMBL files (3). ... ok test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4) Check parsing of annotation from EMBL files (4). ... ok test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1) Check writing-and-parsing EMBL file (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2) Check writing-and-parsing EMBL file (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3) Check writing-and-parsing EMBL file (3). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_NibIO.py test_SeqIO_NibIO ... ok test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_PdbIO.py test_SeqIO_PdbIO ... ok test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader) Read a single-chain CIF without a header by ATOM entries. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader) Parse a PDB with no HEADER line. ... ok test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader) Read a single-chain PDB without a header by ATOM entries. ... ok test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion) Read a PDB with residue insertion code. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.194 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_QualityIO.py test_SeqIO_QualityIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger) Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa) Mapping check for function phred_quality_from_solexa. ... ok test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina) Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa) Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred) Mapping check for function solexa_quality_from_phred. ... ok test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger) Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta) Check FASTQ parsing matches FASTA parsing. ... ok test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out) Check FASTQ to FASTA output. ... ok test_paired (test_SeqIO_QualityIO.TestQual.test_paired) Check FASTQ parsing matches FASTA+QUAL parsing. ... ok test_qual (test_SeqIO_QualityIO.TestQual.test_qual) Check FASTQ parsing matches QUAL parsing. ... ok test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative) Check QUAL negative scores mapped to PHRED zero. ... ok test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out) Check FASTQ to QUAL output. ... ok test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000) Read and write back simple example with mixed case 1000bp read. ... ok test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000) Read and write back simple example with upper case 2000bp read. ... ok test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna) Read and write back simple example with ambiguous DNA. ... ok test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna) Read and write back simple example with ambiguous RNA. ... ok test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end) Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start) Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle) Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end) Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start) Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest) Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original) Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02) Write and read back E3MFGYR02_random_10_reads.sff. ... ok test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end) Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start) Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle) Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start) Write and read back E3MFGYR02_index_at_start.sff. ... ok test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle) Write and read back E3MFGYR02_index_in_middle.sff. ... ok test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest) Write and read back E3MFGYR02_no_manifest.sff. ... ok test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed) Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta) Write and read back example.fasta. ... ok test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq) Write and read back example.fastq. ... ok test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual) Write and read back example.qual. ... ok test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated) Write and read back odd SeqRecord objects. ... ok test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff) Write and read back greek.sff. ... ok test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked) Write and read back illumina_faked.fastq. ... ok test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff) Write and read back paired.sff. ... ok test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93) Write and read back sanger_93.fastq. ... ok test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked) Write and read back sanger_faked.fastq. ... ok test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example) Write and read back solexa_example.fastq. ... ok test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked) Write and read back solexa_faked.fastq. ... ok test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky) Write and read back tricky.fastq. ... ok test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.267 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_SeqXML.py test_SeqIO_SeqXML ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref) Read multiple cross references to a single source. ... ok test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property) Read property with multiple values. ... ok test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description) Check empty description. ... ok test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read) Read full characters set for each type. ... ok test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species) Check global species. ... ok test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition) Check local source. ... ok test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species) Check local species. ... ok test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required) Check minimal record. ... ok test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc) Read special XML characters in description. ... ok test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc) Test special unicode characters in the description. ... ok test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna) Read and write DNA. ... ok test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies) Read and write global species. ... ok test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein) Read and write protein. ... ok test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna) Read and write RNA. ... ok test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species) Test writing species from annotation tags. ... ok test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors) Handling of corrupt files. ... ok test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header) Check if the header information is parsed. ... ok test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header) Check if the header information is parsed. ... ok test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header) Check if the header information is parsed. ... ok test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header) Check if the header information is parsed. ... ok test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO) Files readable using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.057 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_SnapGene.py test_SeqIO_SnapGene ... ok test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna) Read a file with supernumerary DNA packet. ... ok test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie) Read a file with missing or invalid cookie packet. ... ok test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna) Read a file without a DNA packet. ... ok test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet) Read a file with incomplete packet. ... ok test_read (test_SeqIO_SnapGene.TestSnapGene.test_read) Read sample files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_TwoBitIO.py test_SeqIO_TwoBitIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.451 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Xdna.py test_SeqIO_Xdna ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length) Read a file with incorrect length. ... ok test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type) Read a file with an unknown sequence type. ... ok test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features) Read a file with an incorrect number of features. ... ok test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version) Read a file with unexpected version number. ... ok test_read (test_SeqIO_Xdna.TestXdna.test_read) Read sample files. ... ok test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss) Emit warnings when dropping data on write. ... ok test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type) Write correct sequence type. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_after (test_SeqIO_features.FeatureWriting.test_after) Features: write/read simple after locations. ... ok test_before (test_SeqIO_features.FeatureWriting.test_before) Features: write/read simple before locations. ... ok test_between (test_SeqIO_features.FeatureWriting.test_between) GenBank/EMBL write/read simple between locations. ... ok test_exact (test_SeqIO_features.FeatureWriting.test_exact) GenBank/EMBL write/read simple exact locations. ... ok test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join) Features: write/read fuzzy join locations. ... ok test_join (test_SeqIO_features.FeatureWriting.test_join) GenBank/EMBL write/read simple join locations. ... ok test_oneof (test_SeqIO_features.FeatureWriting.test_oneof) Features: write/read simple one-of locations. ... ok test_unknown (test_SeqIO_features.FeatureWriting.test_unknown) GenBank/EMBL write/read with unknown end points. ... ok test_within (test_SeqIO_features.FeatureWriting.test_within) Features: write/read simple within locations. ... ok test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok test_CDS (test_SeqIO_features.NC_000932.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_CDS (test_SeqIO_features.NC_005816.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_Features (test_SeqIO_features.NC_005816.test_Features) Checking GenBank features sequences vs FASTA ffn file. ... ok test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok test_Genome (test_SeqIO_features.NC_005816.test_Genome) Checking GenBank sequence vs FASTA fna file. ... ok test_Translations (test_SeqIO_features.NC_005816.test_Translations) Checking translation of FASTA features (faa vs ffn). ... ok test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers) Pass in qualifiers to SeqFeatures. ... ok test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join) Feature on DNA (join, mixed strand). ... ok test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join) Feature on DNA (multi-join, mixed strand). ... ok test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between) Feature on protein (between location, zero length). ... ok test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join) Feature on protein (join). ... ok test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy) Feature on protein (fuzzy join). ... ok test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join) Feature on protein (multi-join). ... ok test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof) Feature on protein (one-of positions). ... ok test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple) Feature on protein (simple). ... ok test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna) Feature on DNA (simple, default strand). ... ok test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join) Feature on DNA (join, strand +1). ... ok test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after) Feature on DNA (join, strand -1, after position). ... ok test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before) Feature on DNA (join, strand -1, before position). ... ok test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus) Feature on DNA (join, strand -1). ... ok test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0) Feature on DNA (simple, strand 0). ... ok test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1) Feature on DNA (simple, strand +1). ... ok test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus) Feature on DNA (simple, strand -1). ... ok test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none) Feature on DNA (simple, strand None). ... ok test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna) Feature on RNA (simple, default strand). ... ok test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna) Feature on DNA (single letter, default strand). ... ok test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna) Feature on DNA (between location, zero length, default strand). ... ok test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end) Feature on DNA (between location at end, zero length, default strand). ... ok test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323) Write and read back AAA03323.embl. ... ok test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046) Write and read back AE017046.embl. ... ok test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited) Write and read back DD231055_edited.embl. ... ok test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs) Write and read back Human_contigs.embl. ... ok test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932) Write and read back NC_000932.gb. ... ok test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816) Write and read back NC_005816.gb. ... ok test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265) Write and read back NT_019265.gb. ... ok test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5) Write and read back SC10H5.embl. ... ok test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361) Write and read back TRBG361.embl. ... ok test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107) Write and read back U87107.embl. ... ok test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1) Write and read back arab1.gb. ... ok test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq) Write and read back blank_seq.gb. ... ok test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6) Write and read back cor6_6.gb. ... ok test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap) Write and read back dbsource_wrap.gb. ... ok test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords) Write and read back extra_keywords.gb. ... ok test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start) Write and read back gbvrl1_start.seq. ... ok test_noref (test_SeqIO_features.TestWriteRead.test_noref) Write and read back noref.gb. ... ok test_one_of (test_SeqIO_features.TestWriteRead.test_one_of) Write and read back of_one.gb. ... ok test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line) Write and read back origin_line.gb. ... ok test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1) Write and read back pri1.gb. ... ok test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq) Write and read back protein_refseq.gb. ... ok test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2) Write and read back protein_refseq2.gb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.347 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_index.py test_SeqIO_index ... ok test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails) Reject alphabet argument in Bio.SeqIO.index(). ... ok test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db) Reject alphabet argument in Bio.SeqIO.index_db(). ... ok test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index) Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db) Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict) Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok test_key_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_key_checks_with_pathobj) ... ok test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok test_raw_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_raw_checks_with_pathobj) ... ok test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok test_simple_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_simple_checks_with_pathobj) ... ok test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db) Check index_db preserves order in multiple indexed files. ... ok test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index) Check index preserves order in indexed file. ... ok test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db) Check index_db preserves ordering indexed file. ... ok test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict) Check to_dict preserves order in indexed file. ... ok test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel) Check relative links to child folder. ... ok test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder) Check relative links in same folder. ... ok test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs) Check absolute filenames in index. ... ok test_old (test_SeqIO_index.OldIndexTest.test_old) Load existing index with no options (from parent directory). ... ok test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread) Setting check_same_thread to False doesn't raise an exception. ... ok test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents) Check actual filenames in existing indexes. ... ok test_old_files (test_SeqIO_index.OldIndexTest.test_old_files) Load existing index with correct files (from parent directory). ... ok test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir) Load existing index with correct files (from same directory). ... ok test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong) Load existing index with wrong files. ... ok test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2) Load existing index with wrong number of files. ... ok test_old_format (test_SeqIO_index.OldIndexTest.test_old_format) Load existing index with correct format. ... ok test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong) Load existing index with wrong format. ... ok test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel) Load existing index (with relative paths) with no options (from parent directory). ... ok test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir) Load existing index with no options (from same directory). ... ok test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel) Load existing index (with relative paths) with no options (from same directory). ... ok test_pathobj (test_SeqIO_index.OldIndexTest.test_pathobj) Load existing index from a pathlib.Path object. ... ok ---------------------------------------------------------------------- Ran 1 test in 8.612 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_online.py test_SeqIO_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.043 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_write.py test_SeqIO_write ... ok test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqRecord.py test_SeqRecord ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations) Pass in annotations to SeqRecords. ... ok test_deprecated_string_seq (test_SeqRecord.SeqRecordCreation.test_deprecated_string_seq) ... ok test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations) Pass in letter annotations to SeqRecords. ... ok test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq) Replacing .seq if .letter_annotation present. ... ok test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq) Simple addition of Seq or string. ... ok test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left) Simple left addition of Seq or string. ... ok test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord) Simple left addition of SeqRecord from genbank file. ... ok test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple) Simple addition. ... ok test_bytes (test_SeqRecord.SeqRecordMethods.test_bytes) ... ok test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift) Simple slice and add to shift. ... ok test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple) Simple slice and add. ... ok test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple) Simple slice. ... ok test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants) Simple slices using different start/end values. ... ok test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero) Zero slice. ... ok test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqUtils.py test_SeqUtils ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation) Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization) Test Codon Adaptation Index (CAI) initialization from sequences. ... ok test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction) Tests gc_fraction function. ... ok test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.058 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Seq_objs.py test_Seq_objs ... ok test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok test_le (test_Seq_objs.ComparisonTests.test_le) ... ok test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq) Test if feature extraction works properly for unknown sequences. ... ok test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend) Check extending a MutableSeq object. ... ok test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error) Check MutableSeq __init__ raises the appropriate exceptions. ... ok test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem) Check setting sequence contents of a MutableSeq object. ... ok test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error) Check Seq __init__ raises the appropriate exceptions. ... ok test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap) Check count_overlap exception matches python string count method. ... ok test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG) Check our count_overlap method using GG with variable ends and starts. ... ok test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN) Check our count_overlap method using NN with variable ends and starts. ... ok test_equality (test_Seq_objs.StringMethodTests.test_equality) Test equality when mixing types. ... ok test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq) Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed) Check MutableSeq objects can be joined. ... ok test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file) Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq) Checks if Seq join correctly concatenates sequence with the spacer. ... ok test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file) Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok test_search (test_Seq_objs.StringMethodTests.test_search) Check the search method of Seq objects. ... ok test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok test_str_count (test_Seq_objs.StringMethodTests.test_str_count) Check matches the python string count method. ... ok test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG) Check our count_overlap method using GG. ... ok test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN) Check our count_overlap method using NN. ... ok test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode) Check matches the python string encode method. ... ok test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith) Check matches the python string endswith method. ... ok test_str_find (test_Seq_objs.StringMethodTests.test_str_find) Check matches the python string find method. ... ok test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem) Check slicing and indexing works like a string. ... ok test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok test_str_index (test_Seq_objs.StringMethodTests.test_str_index) Check matches the python string index method. ... ok test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower) Check matches the python string islower method. ... ok test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper) Check matches the python string isupper method. ... ok test_str_length (test_Seq_objs.StringMethodTests.test_str_length) Check matches the python string __len__ method. ... ok test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower) Check matches the python string lower method. ... ok test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip) Check matches the python string lstrip method. ... ok test_str_removeprefix (test_Seq_objs.StringMethodTests.test_str_removeprefix) Check matches the python string removeprefix method. ... ok test_str_removesuffix (test_Seq_objs.StringMethodTests.test_str_removesuffix) Check matches the python string removesuffix method. ... ok test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace) Check matches the python string replace method. ... ok test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind) Check matches the python string rfind method. ... ok test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex) Check matches the python string rindex method. ... ok test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit) Check matches the python string rsplit method. ... ok test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip) Check matches the python string rstrip method. ... ok test_str_split (test_Seq_objs.StringMethodTests.test_str_split) Check matches the python string split method. ... ok test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith) Check matches the python string startswith method. ... ok test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip) Check matches the python string strip method. ... ok test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper) Check matches the python string upper method. ... ok test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription) Check obj.back_transcribe() method. ... ok test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement) Check obj.complement() method. ... ok test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement) Check obj.reverse_complement() method. ... ok test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription) Check obj.transcribe() method. ... ok test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate) Check obj.translate() method. ... ok test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons) Check obj.translate() method with ambiguous codons. ... ok test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons) Check obj.translate() method with invalid codons. ... ok test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops) Check obj.translate() method with stop codons. ... ok test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable) Check creating a MutableSeq object. ... ok test_toseq (test_Seq_objs.StringMethodTests.test_toseq) Check creating a Seq object. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.785 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SffIO.py test_SffIO ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok test_empty (test_SffIO.TestErrors.test_empty) ... ok test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok test_no_index (test_SffIO.TestErrors.test_no_index) ... ok test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok test_manifest (test_SffIO.TestIndex.test_manifest) ... ok test_index (test_SffIO.TestSelf.test_index) ... ok test_read (test_SffIO.TestSelf.test_read) ... ok test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok test_write (test_SffIO.TestSelf.test_write) ... ok test_coords (test_SffIO.TestUAN.test_coords) ... ok test_region (test_SffIO.TestUAN.test_region) ... ok test_time (test_SffIO.TestUAN.test_time) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SwissProt.py test_SwissProt ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_O23729 (test_SwissProt.TestSwissProt.test_O23729) Parsing SwissProt file O23729.txt. ... ok test_O95832 (test_SwissProt.TestSwissProt.test_O95832) Parsing SwissProt file O95832.txt. ... ok test_P04439 (test_SwissProt.TestSwissProt.test_P04439) Parsing SwissProt file P04439.txt. ... ok test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186) Parsing SwissProt file P0A186.txt. ... ok test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95) Parsing SwissProt file P0CK95.txt. ... ok test_P16235 (test_SwissProt.TestSwissProt.test_P16235) Parsing SwissProt file P16235.txt. ... ok test_P39896 (test_SwissProt.TestSwissProt.test_P39896) Parsing SwissProt file P39896.txt. ... ok test_P60137 (test_SwissProt.TestSwissProt.test_P60137) Parsing SwissProt file P60137.txt. ... ok test_P60904 (test_SwissProt.TestSwissProt.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P62258 (test_SwissProt.TestSwissProt.test_P62258) Parsing SwissProt file P62258. ... ok test_P68308 (test_SwissProt.TestSwissProt.test_P68308) Parsing SwissProt file P68308.txt. ... ok test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454) Parsing SwissProt file Q13454.txt. ... ok test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639) Parsing SwissProt file Q13639. ... ok test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739) Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok test_ft_line (test_SwissProt.TestSwissProt.test_ft_line) Parsing SwissProt file O23729, which has a new-style FT line. ... ok test_sp012 (test_SwissProt.TestSwissProt.test_sp012) Parsing SwissProt file sp012. ... ok test_sp013 (test_SwissProt.TestSwissProt.test_sp013) Parsing SwissProt file sp013. ... ok test_sp015 (test_SwissProt.TestSwissProt.test_sp015) Parsing SwissProt file sp015. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_TCoffee_tool.py test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_TogoWS.py test_TogoWS ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_TreeConstruction.py test_TreeConstruction ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok test_known_matrices_msa (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices_msa) ... ok test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok test_nonmatching_seqs_msa (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs_msa) ... ok test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok test_built_tree_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree_msa) ... ok test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok test_nj_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_nj_msa) ... ok test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok test_upgma_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma_msa) ... ok test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok test_get_score_msa (test_TreeConstruction.ParsimonyScorerTest.test_get_score_msa) ... ok test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok test_build_tree_msa (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree_msa) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.260 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_UniGene.py test_UniGene ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_parse (test_UniGene.TestUniGene.test_parse) ... ok test_read (test_UniGene.TestUniGene.test_read) ... ok test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.020 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_UniProt_GOA.py test_UniProt_GOA ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator) Test GOA GAF file iterator. ... ok test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator) Test GOA GPA file iterator. ... ok test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator) Test GOA GPI file iterator, gpi-version: 1.1. ... ok test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two) Test GOA GPI file iterator, gpi-version: 1.2. ... ok test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing) Test record_has, and writerec. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Uniprot.py test_Uniprot ... ok test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6) Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8) Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok test_P60904 (test_Uniprot.TestUniprot.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P84001 (test_Uniprot.TestUniprot.test_P84001) Parse mass spec structured comment with unknown loc. ... ok test_Q13639 (test_Uniprot.TestUniprot.test_Q13639) Compare SwissProt text and uniprot XML versions of Q13639. ... ok test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex) Compare SwissProt text and uniprot XML versions of several examples. ... ok test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index) Index SwissProt text and uniprot XML versions of several examples. ... ok test_sp016 (test_Uniprot.TestUniprot.test_sp016) Parsing SwissProt file sp016. ... ok test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed) Checks if parser supports new XML Element (submittedName). ... ok test_uni001 (test_Uniprot.TestUniprot.test_uni001) Parsing Uniprot file uni001. ... ok test_uni003 (test_Uniprot.TestUniprot.test_uni003) Parsing Uniprot file uni003. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.135 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_XXmotif_tool.py test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.047 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_align.py test_align ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_basic_alignment (test_align.TestBasics.test_basic_alignment) Basic tests on a simple alignment of three sequences. ... ok test_empty_alignment (test_align.TestBasics.test_empty_alignment) Very simple tests on an empty alignment. ... ok test_read_clustal1 (test_align.TestReading.test_read_clustal1) Parse an alignment file and get an alignment object. ... ok test_read_clustal2 (test_align.TestReading.test_read_clustal2) Parse an alignment file and get an alignment object. ... ok test_read_fasta (test_align.TestReading.test_read_fasta) ... ok test_read_write_clustal (test_align.TestReading.test_read_write_clustal) Test the base alignment stuff. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_align_substitution_matrices.py test_align_substitution_matrices ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix) Test basic matrix operations. ... ok test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector) Test basic vector operations. ... ok test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq) Test nucleotide frequency calculations. ... ok test_pickling (test_align_substitution_matrices.TestBasics.test_pickling) Test pickling a substitution matrix. ... ok test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq) Test amino acid frequency calculations. ... ok test_read_write (test_align_substitution_matrices.TestBasics.test_read_write) Test reading and writing substitution matrices. ... ok test_loading (test_align_substitution_matrices.TestLoading.test_loading) Confirm that all provided substitution matrices can be loaded. ... ok test_reading (test_align_substitution_matrices.TestLoading.test_reading) Confirm matrix reading works with filename or handle. ... ok test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies) Test calculating substitution frequencies. ... ok test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities) Test calculating substitution probabilities. ... ok test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities) Test symmetrizing substitution probabilities. ... ok test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities) Test calculating expected amino acid probabilities. ... ok test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities) Test calculating expected amino acid substitution probabilities. ... ok test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores) Test calculating amino acid substitution log-ratios. ... ok test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident) Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.247 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_bgzf.py test_bgzf ... ok test_BgzfBlocks_TypeError (test_bgzf.BgzfTests.test_BgzfBlocks_TypeError) Check get expected TypeError from BgzfBlocks. ... ok test_append_mode (test_bgzf.BgzfTests.test_append_mode) ... ok test_bam_ex1 (test_bgzf.BgzfTests.test_bam_ex1) Reproduce BGZF compression for BAM file. ... ok test_double_flush (test_bgzf.BgzfTests.test_double_flush) ... ok test_example_cor6 (test_bgzf.BgzfTests.test_example_cor6) Reproduce BGZF compression for cor6_6.gb GenBank file. ... ok test_example_fastq (test_bgzf.BgzfTests.test_example_fastq) Reproduce BGZF compression for a FASTQ file. ... ok test_example_gb (test_bgzf.BgzfTests.test_example_gb) Reproduce BGZF compression for NC_000932 GenBank file. ... ok test_example_wnts_xml (test_bgzf.BgzfTests.test_example_wnts_xml) Reproduce BGZF compression for wnts.xml BLAST file. ... ok test_iter_bam_ex1 (test_bgzf.BgzfTests.test_iter_bam_ex1) Check iteration over SamBam/ex1.bam. ... ok test_iter_example_cor6 (test_bgzf.BgzfTests.test_iter_example_cor6) Check iteration over GenBank/cor6_6.gb.bgz. ... ok test_iter_example_fastq (test_bgzf.BgzfTests.test_iter_example_fastq) Check iteration over Quality/example.fastq.bgz. ... ok test_iter_example_gb (test_bgzf.BgzfTests.test_iter_example_gb) Check iteration over GenBank/NC_000932.gb.bgz. ... ok test_iter_wnts_xml (test_bgzf.BgzfTests.test_iter_wnts_xml) Check iteration over Blast/wnts.xml.bgz. ... ok test_many_blocks_in_single_read (test_bgzf.BgzfTests.test_many_blocks_in_single_read) ... ok test_random_bam_ex1 (test_bgzf.BgzfTests.test_random_bam_ex1) Check random access to SamBam/ex1.bam. ... ok test_random_bam_ex1_header (test_bgzf.BgzfTests.test_random_bam_ex1_header) Check random access to SamBam/ex1_header.bam. ... ok test_random_bam_ex1_refresh (test_bgzf.BgzfTests.test_random_bam_ex1_refresh) Check random access to SamBam/ex1_refresh.bam. ... ok test_random_example_cor6 (test_bgzf.BgzfTests.test_random_example_cor6) Check random access to GenBank/cor6_6.gb.bgz. ... ok test_random_example_dos_fastq (test_bgzf.BgzfTests.test_random_example_dos_fastq) Check random access to Quality/example_dos.fastq.bgz (DOS newlines). ... ok test_random_example_fastq (test_bgzf.BgzfTests.test_random_example_fastq) Check random access to Quality/example.fastq.bgz (Unix newlines). ... ok test_random_wnts_xml (test_bgzf.BgzfTests.test_random_wnts_xml) Check random access to Blast/wnts.xml.bgz. ... ok test_reader_with_binary_fileobj (test_bgzf.BgzfTests.test_reader_with_binary_fileobj) A BgzfReader must accept a binary mode file object. ... ok test_reader_with_non_binary_fileobj (test_bgzf.BgzfTests.test_reader_with_non_binary_fileobj) A BgzfReader must raise ValueError on a non-binary file object. ... ok test_text_example_fastq (test_bgzf.BgzfTests.test_text_example_fastq) Check text mode access to Quality/example.fastq.bgz. ... ok test_text_wnts_xml (test_bgzf.BgzfTests.test_text_wnts_xml) Check text mode access to Blast/wnts.xml.bgz. ... ok test_write_tell (test_bgzf.BgzfTests.test_write_tell) Check offset works during BGZF writing. ... ok test_writer_with_binary_fileobj (test_bgzf.BgzfTests.test_writer_with_binary_fileobj) A BgzfWriter must accept a binary mode file object. ... ok test_writer_with_non_binary_fileobj (test_bgzf.BgzfTests.test_writer_with_non_binary_fileobj) A BgzfWriter must raise ValueError on a non-binary file object. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.211 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_cellosaurus.py test_cellosaurus ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test__str__ (test_cellosaurus.TestCellosaurus.test__str__) Test string function. ... ok test_parse (test_cellosaurus.TestCellosaurus.test_parse) Test parsing function. ... ok test_read (test_cellosaurus.TestCellosaurus.test_read) Test read function. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_codonalign.py test_codonalign ... ok test_TypeError (test_codonalign.TestAddition.test_TypeError) Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok test_ValueError (test_codonalign.TestAddition.test_ValueError) Check that ValueError is thrown for Alignments of different lengths. ... ok test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment) Check addition of CodonAlignment and CodonAlignment. ... ok test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment) Check addition of CodonAlignment and MultipleSeqAlignment. ... ok test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok test_align (test_codonalign.TestCodonAlignment.test_align) ... ok test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok test_mk (test_codonalign.Test_MK.test_mk) ... ok test_build (test_codonalign.Test_build.test_build) ... ok test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok ---------------------------------------------------------------------- Ran 1 test in 2.551 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_geo.py test_geo ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok test_record_str (test_geo.TestGeo.test_record_str) ... ok test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_kNN.py test_kNN ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok test_classify (test_kNN.TestKNN.test_classify) ... ok test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_mmtf.py test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_mmtf_online.py test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.038 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs.py test_motifs ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok test_simple (test_motifs.MotifTestPWM.test_simple) Test if Bio.motifs PWM scoring works. ... ok test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char) Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case) Test if Bio.motifs PWM scoring works with mixed case. ... ok test_alignace_parsing (test_motifs.TestAlignAce.test_alignace_parsing) Test if Bio.motifs can parse AlignAce output files. ... ok test_format (test_motifs.TestBasic.test_format) ... ok test_relative_entropy (test_motifs.TestBasic.test_relative_entropy) ... ok test_reverse_complement (test_motifs.TestBasic.test_reverse_complement) Test if motifs can be reverse-complemented. ... ok test_clusterbuster_parsing_and_output (test_motifs.TestClusterBuster.test_clusterbuster_parsing_and_output) Test if Bio.motifs can parse and output Cluster-Buster PFM files. ... ok test_pfm_four_columns_parsing (test_motifs.TestJASPAR.test_pfm_four_columns_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok test_pfm_four_rows_parsing (test_motifs.TestJASPAR.test_pfm_four_rows_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok test_pfm_parsing (test_motifs.TestJASPAR.test_pfm_parsing) Test if Bio.motifs can parse JASPAR-style pfm files. ... ok test_sites_parsing (test_motifs.TestJASPAR.test_sites_parsing) Test if Bio.motifs can parse JASPAR-style sites files. ... ok test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1) Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2) Parse motifs/mast.adh.de.oops.html.xml file. ... ok test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3) Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1) Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2) Parsing motifs/meme.adh.classic.oops.xml file. ... ok test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3) Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna) Test if Bio.motifs can parse MEME output files using RNA. ... ok test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser) Parse motifs/minimal_test.meme file. ... ok test_TFoutput (test_motifs.TestTransfac.test_TFoutput) Ensure that we can write proper TransFac output files. ... ok test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser) Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser) Parse motifs/transfac.dat file. ... ok test_xms_parsing (test_motifs.TestXMS.test_xms_parsing) Test if Bio.motifs can parse and output xms PFM files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.182 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs_online.py test_motifs_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.029 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2.py test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2_no_C.py test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise_aligner.py test_pairwise_aligner ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_str_seq_seqrecord (test_pairwise_aligner.TestAlignerInput.test_str_seq_seqrecord) Test aligning sequences provided as str, Seq, or SeqRecord objects. ... ok test_three_letter_amino_acids_global (test_pairwise_aligner.TestAlignerInput.test_three_letter_amino_acids_global) Test aligning sequences provided as lists of three-letter amino acids. ... ok test_three_letter_amino_acids_local (test_pairwise_aligner.TestAlignerInput.test_three_letter_amino_acids_local) ... ok test_pickle_aligner_match_mismatch (test_pairwise_aligner.TestAlignerPickling.test_pickle_aligner_match_mismatch) ... ok test_pickle_aligner_substitution_matrix (test_pairwise_aligner.TestAlignerPickling.test_pickle_aligner_substitution_matrix) ... ok test_aligner_nonexisting_property (test_pairwise_aligner.TestAlignerProperties.test_aligner_nonexisting_property) ... ok test_aligner_property_epsilon (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_epsilon) ... ok test_aligner_property_gapscores (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_gapscores) ... ok test_aligner_property_match_mismatch (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_match_mismatch) ... ok test_aligner_property_mode (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_mode) ... ok test_alignment_end_gap (test_pairwise_aligner.TestAlignmentFormat.test_alignment_end_gap) ... ok test_alignment_simple (test_pairwise_aligner.TestAlignmentFormat.test_alignment_simple) ... ok test_alignment_wildcard (test_pairwise_aligner.TestAlignmentFormat.test_alignment_wildcard) ... ok test_aligner_array_errors (test_pairwise_aligner.TestArgumentErrors.test_aligner_array_errors) ... ok test_aligner_string_errors (test_pairwise_aligner.TestArgumentErrors.test_aligner_string_errors) ... ok test_confusing_arguments (test_pairwise_aligner.TestKeywordArgumentsConstructor.test_confusing_arguments) ... ok test_align_overflow_error (test_pairwise_aligner.TestOverflowError.test_align_overflow_error) ... ok test_extend_penalty1 (test_pairwise_aligner.TestPairwiseExtendPenalty.test_extend_penalty1) ... ok test_extend_penalty2 (test_pairwise_aligner.TestPairwiseExtendPenalty.test_extend_penalty2) ... ok test_align_affine1_score (test_pairwise_aligner.TestPairwiseGlobal.test_align_affine1_score) ... ok test_needlemanwunsch_simple1 (test_pairwise_aligner.TestPairwiseGlobal.test_needlemanwunsch_simple1) ... ok test_gotoh_local (test_pairwise_aligner.TestPairwiseLocal.test_gotoh_local) ... ok test_smithwaterman (test_pairwise_aligner.TestPairwiseLocal.test_smithwaterman) ... ok test_match_dictionary1 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary1) ... ok test_match_dictionary2 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary2) ... ok test_match_dictionary3 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary3) ... ok test_match_dictionary4 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary4) ... ok test_match_dictionary5 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary5) ... ok test_match_dictionary6 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary6) ... ok test_align_one_char1 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char1) ... ok test_align_one_char2 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char2) ... ok test_align_one_char3 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char3) ... ok test_align_one_char_score3 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char_score3) ... ok test_match_score_open_penalty1 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty1) ... ok test_match_score_open_penalty2 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty2) ... ok test_match_score_open_penalty3 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty3) ... ok test_match_score_open_penalty4 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty4) ... ok test_penalize_end_gaps (test_pairwise_aligner.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) ... ok test_penalize_extend_when_opening (test_pairwise_aligner.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) ... ok test_separate_gap_penalties1 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) ... ok test_separate_gap_penalties2 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) ... ok test_separate_gap_penalties_with_extension (test_pairwise_aligner.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) ... ok test_broken_gap_function (test_pairwise_aligner.TestPerSiteGapPenalties.test_broken_gap_function) ... ok test_gap_here_only_1 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_1) ... ok test_gap_here_only_2 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_2) ... ok test_gap_here_only_3 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_3) ... ok test_gap_here_only_local_1 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_1) ... ok test_gap_here_only_local_2 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_2) ... ok test_gap_here_only_local_3 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_3) ... ok test_blastn (test_pairwise_aligner.TestPredefinedScoringSchemes.test_blastn) ... ok test_blastp (test_pairwise_aligner.TestPredefinedScoringSchemes.test_blastp) ... ok test_megablast (test_pairwise_aligner.TestPredefinedScoringSchemes.test_megablast) ... ok test_align_affine1_score (test_pairwise_aligner.TestUnicodeStrings.test_align_affine1_score) ... ok test_gotoh_local (test_pairwise_aligner.TestUnicodeStrings.test_gotoh_local) ... ok test_needlemanwunsch_simple1 (test_pairwise_aligner.TestUnicodeStrings.test_needlemanwunsch_simple1) ... ok test_smithwaterman (test_pairwise_aligner.TestUnicodeStrings.test_smithwaterman) ... ok test_needlemanwunsch_simple1 (test_pairwise_aligner.TestUnknownCharacter.test_needlemanwunsch_simple1) ... ok test_needlemanwunsch_simple2 (test_pairwise_aligner.TestUnknownCharacter.test_needlemanwunsch_simple2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.181 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise_alignment_map.py test_pairwise_alignment_map ... ok test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok test_chimp (test_pairwise_alignment_map.TestLiftOver.test_chimp) ... ok test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok test1 (test_pairwise_alignment_map.TestZeroGaps.test1) ... ok test2 (test_pairwise_alignment_map.TestZeroGaps.test2) ... ok test3 (test_pairwise_alignment_map.TestZeroGaps.test3) ... ok test4 (test_pairwise_alignment_map.TestZeroGaps.test4) ... ok test5 (test_pairwise_alignment_map.TestZeroGaps.test5) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.150 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_phenotype.py test_phenotype ... ok test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator) Test basic functionalities of CsvIterator file parser. ... ok test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator) Test basic functionalities of JsonIterator file parser. ... ok test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord) Test basic functionalities of PlateRecord objects. ... ok test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors) Test bad arguments with PlateRecord objects. ... ok test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord) Test basic functionalities of WellRecord objects. ... ok test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args) Test error handling of the fit method. ... ok test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO) Test basic functionalities of phenotype IO methods. ... ok test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors) Test bad arguments to phenotype IO methods. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.694 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_phenotype_fit.py test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_phyml_tool.py test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_prodoc.py test_prodoc ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc) Parsing an excerpt of prosite.doc. ... ok test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100) Reading Prodoc record PDOC00100. ... ok test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113) Reading Prodoc record PDOC00113. ... ok test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144) Reading Prodoc record PDOC00144. ... ok test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149) Reading Prodoc record PDOC00149. ... ok test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340) Reading Prodoc record PDOC00340. ... ok test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424) Reading Prodoc record PDOC00424. ... ok test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472) Reading Prodoc record PDOC00472. ... ok test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640) Reading Prodoc record PDOC00640. ... ok test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787) Reading Prodoc record PDOC00787. ... ok test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933) Reading Prodoc record PDOC00933. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_prosite.py test_prosite ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_read1 (test_prosite.TestPrositeRead.test_read1) Parsing Prosite record ps00107.txt. ... ok test_read2 (test_prosite.TestPrositeRead.test_read2) Parsing Prosite record ps00159.txt. ... ok test_read3 (test_prosite.TestPrositeRead.test_read3) Parsing Prosite record ps00165.txt. ... ok test_read4 (test_prosite.TestPrositeRead.test_read4) Parsing Prosite record ps00432.txt. ... ok test_read5 (test_prosite.TestPrositeRead.test_read5) Parsing Prosite record ps00488.txt. ... ok test_read6 (test_prosite.TestPrositeRead.test_read6) Parsing Prosite record ps00546.txt. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_raxml_tool.py test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_samtools_tool.py test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_seq.py test_seq ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values) Test that other tests do not introduce characters to our values. ... ok test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok test_seq (test_seq.TestAttributes.test_seq) ... ok test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok test_immutable (test_seq.TestComplement.test_immutable) ... ok test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements) Test double reverse complement preserves the sequence. ... ok test_add_method (test_seq.TestMutableSeq.test_add_method) Test adding wrong type to MutableSeq. ... ok test_appending (test_seq.TestMutableSeq.test_appending) ... ok test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok test_complement (test_seq.TestMutableSeq.test_complement) ... ok test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok test_count (test_seq.TestMutableSeq.test_count) ... ok test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison) Test __eq__ comparison method. ... ok test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok test_index (test_seq.TestMutableSeq.test_index) ... ok test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok test_length (test_seq.TestMutableSeq.test_length) ... ok test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction) Test MutableSeq object initialization. ... ok test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison) Test __ne__ comparison method. ... ok test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok test_repr (test_seq.TestMutableSeq.test_repr) ... ok test_reverse (test_seq.TestMutableSeq.test_reverse) Test using reverse method. ... ok test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride) Test reverse using -1 stride. ... ok test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n) Test setting wobble codon to N (set slice with stride 3). ... ok test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok test_as_string (test_seq.TestSeq.test_as_string) Test converting Seq to string. ... ok test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide) Test getting first nucleotide of Seq. ... ok test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide) Test getting last nucleotide of Seq. ... ok test_length (test_seq.TestSeq.test_length) Test len method on Seq object. ... ok test_replace (test_seq.TestSeq.test_replace) ... ok test_repr (test_seq.TestSeq.test_repr) Test representation of Seq object. ... ok test_reverse (test_seq.TestSeq.test_reverse) Test reverse using -1 stride. ... ok test_seq_construction (test_seq.TestSeq.test_seq_construction) Test Seq object initialization. ... ok test_slicing (test_seq.TestSeq.test_slicing) Test slicing of Seq. ... ok test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok test_defined (test_seq.TestSeqDefined.test_defined) ... ok test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok test_imul_method (test_seq.TestSeqMultiplication.test_imul_method) Test imul method; relies on addition and mull methods. ... ok test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions) Test imul method exceptions. ... ok test_mul_method (test_seq.TestSeqMultiplication.test_mul_method) Test mul method; relies on addition method. ... ok test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions) Test mul method exceptions. ... ok test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method) Test rmul method; relies on addition method. ... ok test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions) Test rmul method exceptions. ... ok test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types) Test incompatible types __gt__ comparison method. ... ok test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types) Test incompatible types __ge__ comparison method. ... ok test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types) Test incompatible types __lt__ comparison method. ... ok test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types) Test incompatible types __le__ comparison method. ... ok test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion) Test __ne__ comparison method. ... ok test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok test_stops (test_seq.TestStopCodons.test_stops) ... ok test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok test_translation (test_seq.TestTranslating.test_translation) ... ok test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins) Check translation fails on a protein. ... ok test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons) Check for error and warning messages. ... ok test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type) Test translation table cannot be CodonTable. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.046 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=4 + /usr/bin/python3 run_tests.py --offline --verbose -v test_translate.py test_translate ... ok Skipping any tests requiring internet access Python version: 3.12.3 (main, Apr 17 2024, 00:00:00) [GCC 14.0.1 20240411 (Red Hat 14.0.1-0)] Operating system: posix linux test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.027 seconds + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-biopython-1.83-6.fc41.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.sBXR90 + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/share/doc/python3-biopython + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/biopython-1.83/Doc /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/biopython-1.83/Scripts /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.83-6.fc41 python3-biopython = 1.83-6.fc41 python3-biopython(x86-64) = 1.83-6.fc41 python3.12-biopython = 1.83-6.fc41 python3.12dist(biopython) = 1.83 python3dist(biopython) = 1.83 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) python(abi) = 3.12 python3.12dist(numpy) rtld(GNU_HASH) Processing files: python-biopython-debugsource-1.83-6.fc41.x86_64 Provides: python-biopython-debugsource = 1.83-6.fc41 python-biopython-debugsource(x86-64) = 1.83-6.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.83-6.fc41.x86_64 Provides: debuginfo(build-id) = 0767f8174281e76ecb943a4e0e421ddfee7b17e1 debuginfo(build-id) = 0fbc94a3f79cb438f8a705689b9571df95b9203d debuginfo(build-id) = 1d50c211f8e2a9152155a41b39d1c7e08f91b20e debuginfo(build-id) = 1da938ebca181247d6ec86213260eced2e491fb7 debuginfo(build-id) = 46552c1cd89f71bae98678a23b7c9adb70a59474 debuginfo(build-id) = 65e4baad355abf948af0d9cc102245f0142db673 debuginfo(build-id) = 69510fb3a7f62be60bda42bae5988dc5a2c2e900 debuginfo(build-id) = cb9e2d8e690a817270ce72037aac046928051433 debuginfo(build-id) = e16f3b8e86d52b77c5c4c7064a3101cb4b307728 python-biopython-debuginfo = 1.83-6.fc41 python3-biopython-debuginfo = 1.83-6.fc41 python3-biopython-debuginfo(x86-64) = 1.83-6.fc41 python3.12-biopython-debuginfo = 1.83-6.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(x86-64) = 1.83-6.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 Wrote: /builddir/build/SRPMS/python-biopython-1.83-6.fc41.src.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.83-6.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.83-6.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.83-6.fc41.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.p8zBle + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-6.fc41.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.oq98jE + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/biopython-1.83-SPECPARTS + rm -rf biopython-1.83 biopython-1.83.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-biopython-1.83-6.fc41.src.rpm Finish: build phase for python-biopython-1.83-6.fc41.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1713531086.045918/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.83-6.fc41.src.rpm) Config(child) 2 minutes 34 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python-biopython", "epoch": null, "version": "1.83", "release": "6.fc41", "arch": "src" }, { "name": "python-biopython-debugsource", "epoch": null, "version": "1.83", "release": "6.fc41", "arch": "x86_64" }, { "name": "python3-biopython-debuginfo", "epoch": null, "version": "1.83", "release": "6.fc41", "arch": "x86_64" }, { "name": "python3-biopython", "epoch": null, "version": "1.83", "release": "6.fc41", "arch": "x86_64" } ] } RPMResults finished