Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c10a' (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/7305856-fedora-38-x86_64 --chroot fedora-38-x86_64 Version: 0.72 PID: 6568 Logging PID: 6569 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 7305856, 'buildroot_pkgs': [], 'chroot': 'fedora-38-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '5eae85f56c3eaaf4d51942df3de5ade29dd4aa60', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes:pr:8/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.83-5', 'project_dirname': 'automatic-obsoletes:pr:8', 'project_name': 'automatic-obsoletes', 'project_owner': 'torsava', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/torsava/automatic-obsoletes/fedora-38-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'torsava/automatic-obsoletes--https://src.fedoraproject.org/user/music', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'https://src.fedoraproject.org/user/music', 'tags': [], 'task_id': '7305856-fedora-38-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes:pr:8/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/torsava/automatic-obsoletes:pr:8/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython'... Running: git checkout 5eae85f56c3eaaf4d51942df3de5ade29dd4aa60 -- cmd: ['git', 'checkout', '5eae85f56c3eaaf4d51942df3de5ade29dd4aa60', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython rc: 0 stdout: stderr: Note: switching to '5eae85f56c3eaaf4d51942df3de5ade29dd4aa60'. 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 5eae85f automatic import of python-biopython Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading biopython-1.83.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o biopython-1.83.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/torsava/automatic-obsoletes:pr:8/python-biopython/biopython-1.83.tar.gz/md5/fa95c92de7cfbb153b070e3da5aaf14a/biopython-1.83.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 18.5M 100 18.5M 0 0 73.7M 0 --:--:-- --:--:-- --:--:-- 73.5M 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-y9fh2ob9/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713011165.797942 -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-y9fh2ob9/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713011165.797942 -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-y9fh2ob9/python-biopython/python-biopython.spec) Config(fedora-38-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-38-x86_64-bootstrap-1713011165.797942/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:38 INFO: Pulling image: registry.fedoraproject.org/fedora:38 INFO: Copy content of container registry.fedoraproject.org/fedora:38 to /var/lib/mock/fedora-38-x86_64-bootstrap-1713011165.797942/root INFO: Checking that registry.fedoraproject.org/fedora:38 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:38 with podman image mount INFO: image registry.fedoraproject.org/fedora:38 as /var/lib/containers/storage/overlay/c12fdfa4ea5b7d6efc14a116bd49660835bd9a960dd1e256962eb1d88359408e/merged INFO: umounting image registry.fedoraproject.org/fedora:38 (/var/lib/containers/storage/overlay/c12fdfa4ea5b7d6efc14a116bd49660835bd9a960dd1e256962eb1d88359408e/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 22 MB/s | 14 MB 00:00 fedora 13 MB/s | 83 MB 00:06 updates 13 MB/s | 41 MB 00:03 Last metadata expiration check: 0:00:03 ago on Sat Apr 13 12:26:42 2024. Package python3-dnf-4.18.2-1.fc38.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.6.0-1.fc38 updates 323 k Upgrading: dnf noarch 4.19.2-1.fc38 updates 504 k dnf-data noarch 4.19.2-1.fc38 updates 39 k libdnf x86_64 0.73.1-1.fc38 copr_base 672 k libmodulemd x86_64 2.15.0-9.fc38 copr_base 232 k libsolv x86_64 0.7.28-1.fc38 copr_base 426 k python3-dnf noarch 4.19.2-1.fc38 updates 609 k python3-hawkey x86_64 0.73.1-1.fc38 copr_base 108 k python3-libdnf x86_64 0.73.1-1.fc38 copr_base 853 k python3-rpm x86_64 4.18.91-3.fc38 copr_base 67 k rpm x86_64 4.18.91-3.fc38 copr_base 501 k rpm-build-libs x86_64 4.18.91-3.fc38 copr_base 96 k rpm-libs x86_64 4.18.91-3.fc38 copr_base 309 k rpm-sign-libs x86_64 4.18.91-3.fc38 copr_base 26 k yum noarch 4.19.2-1.fc38 updates 36 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc38 updates 156 k python3-dateutil noarch 1:2.8.2-6.fc38 copr_base 349 k python3-dbus x86_64 1.3.2-6.fc38 copr_base 147 k python3-distro noarch 1.9.0-3.fc38 copr_base 47 k python3-six noarch 1.16.0-20.fc38 copr_base 42 k python3-systemd x86_64 235-3.fc38 copr_base 102 k Transaction Summary ================================================================================ Install 7 Packages Upgrade 14 Packages Total download size: 5.5 M Downloading Packages: (1/21): python3-distro-1.9.0-3.fc38.noarch.rpm 744 kB/s | 47 kB 00:00 (2/21): python3-dbus-1.3.2-6.fc38.x86_64.rpm 2.1 MB/s | 147 kB 00:00 (3/21): python3-dateutil-2.8.2-6.fc38.noarch.rp 3.8 MB/s | 349 kB 00:00 (4/21): python3-systemd-235-3.fc38.x86_64.rpm 4.0 MB/s | 102 kB 00:00 (5/21): dbus-libs-1.14.10-1.fc38.x86_64.rpm 3.2 MB/s | 156 kB 00:00 (6/21): python3-dnf-plugins-core-4.6.0-1.fc38.n 5.3 MB/s | 323 kB 00:00 (7/21): libdnf-0.73.1-1.fc38.x86_64.rpm 33 MB/s | 672 kB 00:00 (8/21): python3-six-1.16.0-20.fc38.noarch.rpm 428 kB/s | 42 kB 00:00 (9/21): libmodulemd-2.15.0-9.fc38.x86_64.rpm 18 MB/s | 232 kB 00:00 (10/21): libsolv-0.7.28-1.fc38.x86_64.rpm 28 MB/s | 426 kB 00:00 (11/21): python3-hawkey-0.73.1-1.fc38.x86_64.rp 8.6 MB/s | 108 kB 00:00 (12/21): python3-libdnf-0.73.1-1.fc38.x86_64.rp 41 MB/s | 853 kB 00:00 (13/21): python3-rpm-4.18.91-3.fc38.x86_64.rpm 4.0 MB/s | 67 kB 00:00 (14/21): rpm-4.18.91-3.fc38.x86_64.rpm 30 MB/s | 501 kB 00:00 (15/21): rpm-build-libs-4.18.91-3.fc38.x86_64.r 9.2 MB/s | 96 kB 00:00 (16/21): rpm-libs-4.18.91-3.fc38.x86_64.rpm 22 MB/s | 309 kB 00:00 (17/21): rpm-sign-libs-4.18.91-3.fc38.x86_64.rp 2.1 MB/s | 26 kB 00:00 (18/21): dnf-data-4.19.2-1.fc38.noarch.rpm 4.5 MB/s | 39 kB 00:00 (19/21): dnf-4.19.2-1.fc38.noarch.rpm 19 MB/s | 504 kB 00:00 (20/21): yum-4.19.2-1.fc38.noarch.rpm 3.9 MB/s | 36 kB 00:00 (21/21): python3-dnf-4.19.2-1.fc38.noarch.rpm 9.4 MB/s | 609 kB 00:00 -------------------------------------------------------------------------------- Total 11 MB/s | 5.5 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : rpm-libs-4.18.91-3.fc38.x86_64 1/35 Upgrading : libmodulemd-2.15.0-9.fc38.x86_64 2/35 Upgrading : libsolv-0.7.28-1.fc38.x86_64 3/35 Upgrading : libdnf-0.73.1-1.fc38.x86_64 4/35 Upgrading : python3-libdnf-0.73.1-1.fc38.x86_64 5/35 Upgrading : python3-hawkey-0.73.1-1.fc38.x86_64 6/35 Upgrading : rpm-build-libs-4.18.91-3.fc38.x86_64 7/35 Upgrading : rpm-sign-libs-4.18.91-3.fc38.x86_64 8/35 Upgrading : python3-rpm-4.18.91-3.fc38.x86_64 9/35 Upgrading : dnf-data-4.19.2-1.fc38.noarch 10/35 Upgrading : python3-dnf-4.19.2-1.fc38.noarch 11/35 Upgrading : dnf-4.19.2-1.fc38.noarch 12/35 Running scriptlet: dnf-4.19.2-1.fc38.noarch 12/35 Installing : dbus-libs-1:1.14.10-1.fc38.x86_64 13/35 Installing : python3-dbus-1.3.2-6.fc38.x86_64 14/35 Installing : python3-systemd-235-3.fc38.x86_64 15/35 Installing : python3-six-1.16.0-20.fc38.noarch 16/35 Installing : python3-dateutil-1:2.8.2-6.fc38.noarch 17/35 Installing : python3-distro-1.9.0-3.fc38.noarch 18/35 Installing : python3-dnf-plugins-core-4.6.0-1.fc38.noarch 19/35 Upgrading : yum-4.19.2-1.fc38.noarch 20/35 Running scriptlet: rpm-4.18.91-3.fc38.x86_64 21/35 Upgrading : rpm-4.18.91-3.fc38.x86_64 21/35 Cleanup : rpm-4.18.2-1.fc38.x86_64 22/35 Cleanup : yum-4.18.2-1.fc38.noarch 23/35 Running scriptlet: dnf-4.18.2-1.fc38.noarch 24/35 Cleanup : dnf-4.18.2-1.fc38.noarch 24/35 Running scriptlet: dnf-4.18.2-1.fc38.noarch 24/35 Cleanup : python3-dnf-4.18.2-1.fc38.noarch 25/35 Cleanup : python3-hawkey-0.72.0-1.fc38.x86_64 26/35 Cleanup : python3-rpm-4.18.2-1.fc38.x86_64 27/35 Cleanup : dnf-data-4.18.2-1.fc38.noarch 28/35 Cleanup : rpm-build-libs-4.18.2-1.fc38.x86_64 29/35 Cleanup : rpm-sign-libs-4.18.2-1.fc38.x86_64 30/35 Cleanup : python3-libdnf-0.72.0-1.fc38.x86_64 31/35 Cleanup : libdnf-0.72.0-1.fc38.x86_64 32/35 Cleanup : libsolv-0.7.27-1.fc38.x86_64 33/35 Cleanup : libmodulemd-2.15.0-2.fc38.x86_64 34/35 Cleanup : rpm-libs-4.18.2-1.fc38.x86_64 35/35 Running scriptlet: rpm-4.18.91-3.fc38.x86_64 35/35 Running scriptlet: rpm-libs-4.18.2-1.fc38.x86_64 35/35 Verifying : python3-dateutil-1:2.8.2-6.fc38.noarch 1/35 Verifying : python3-dbus-1.3.2-6.fc38.x86_64 2/35 Verifying : python3-distro-1.9.0-3.fc38.noarch 3/35 Verifying : python3-six-1.16.0-20.fc38.noarch 4/35 Verifying : python3-systemd-235-3.fc38.x86_64 5/35 Verifying : dbus-libs-1:1.14.10-1.fc38.x86_64 6/35 Verifying : python3-dnf-plugins-core-4.6.0-1.fc38.noarch 7/35 Verifying : libdnf-0.73.1-1.fc38.x86_64 8/35 Verifying : libdnf-0.72.0-1.fc38.x86_64 9/35 Verifying : libmodulemd-2.15.0-9.fc38.x86_64 10/35 Verifying : libmodulemd-2.15.0-2.fc38.x86_64 11/35 Verifying : libsolv-0.7.28-1.fc38.x86_64 12/35 Verifying : libsolv-0.7.27-1.fc38.x86_64 13/35 Verifying : python3-hawkey-0.73.1-1.fc38.x86_64 14/35 Verifying : python3-hawkey-0.72.0-1.fc38.x86_64 15/35 Verifying : python3-libdnf-0.73.1-1.fc38.x86_64 16/35 Verifying : python3-libdnf-0.72.0-1.fc38.x86_64 17/35 Verifying : python3-rpm-4.18.91-3.fc38.x86_64 18/35 Verifying : python3-rpm-4.18.2-1.fc38.x86_64 19/35 Verifying : rpm-4.18.91-3.fc38.x86_64 20/35 Verifying : rpm-4.18.2-1.fc38.x86_64 21/35 Verifying : rpm-build-libs-4.18.91-3.fc38.x86_64 22/35 Verifying : rpm-build-libs-4.18.2-1.fc38.x86_64 23/35 Verifying : rpm-libs-4.18.91-3.fc38.x86_64 24/35 Verifying : rpm-libs-4.18.2-1.fc38.x86_64 25/35 Verifying : rpm-sign-libs-4.18.91-3.fc38.x86_64 26/35 Verifying : rpm-sign-libs-4.18.2-1.fc38.x86_64 27/35 Verifying : dnf-4.19.2-1.fc38.noarch 28/35 Verifying : dnf-4.18.2-1.fc38.noarch 29/35 Verifying : dnf-data-4.19.2-1.fc38.noarch 30/35 Verifying : dnf-data-4.18.2-1.fc38.noarch 31/35 Verifying : python3-dnf-4.19.2-1.fc38.noarch 32/35 Verifying : python3-dnf-4.18.2-1.fc38.noarch 33/35 Verifying : yum-4.19.2-1.fc38.noarch 34/35 Verifying : yum-4.18.2-1.fc38.noarch 35/35 Upgraded: dnf-4.19.2-1.fc38.noarch dnf-data-4.19.2-1.fc38.noarch libdnf-0.73.1-1.fc38.x86_64 libmodulemd-2.15.0-9.fc38.x86_64 libsolv-0.7.28-1.fc38.x86_64 python3-dnf-4.19.2-1.fc38.noarch python3-hawkey-0.73.1-1.fc38.x86_64 python3-libdnf-0.73.1-1.fc38.x86_64 python3-rpm-4.18.91-3.fc38.x86_64 rpm-4.18.91-3.fc38.x86_64 rpm-build-libs-4.18.91-3.fc38.x86_64 rpm-libs-4.18.91-3.fc38.x86_64 rpm-sign-libs-4.18.91-3.fc38.x86_64 yum-4.19.2-1.fc38.noarch Installed: dbus-libs-1:1.14.10-1.fc38.x86_64 python3-dateutil-1:2.8.2-6.fc38.noarch python3-dbus-1.3.2-6.fc38.x86_64 python3-distro-1.9.0-3.fc38.noarch python3-dnf-plugins-core-4.6.0-1.fc38.noarch python3-six-1.16.0-20.fc38.noarch python3-systemd-235-3.fc38.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-38-x86_64-1713011165.797942/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-4.18.91-3.fc38.x86_64 rpm-sequoia-1.5.0-2.fc38.x86_64 python3-dnf-4.19.2-1.fc38.noarch python3-dnf-plugins-core-4.6.0-1.fc38.noarch yum-4.19.2-1.fc38.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 19 MB/s | 3.9 MB 00:00 fedora 7.2 MB/s | 33 MB 00:04 updates 6.5 MB/s | 10 MB 00:01 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.26-1.fc38 updates 1.8 M bzip2 x86_64 1.0.8-13.fc38 fedora 52 k coreutils x86_64 9.1-12.fc38 updates 1.1 M cpio x86_64 2.13-14.fc38 fedora 276 k diffutils x86_64 3.10-1.fc38 updates 398 k fedora-release-common noarch 38-36 updates 22 k findutils x86_64 1:4.9.0-3.fc38 fedora 492 k gawk x86_64 5.1.1-5.fc38 fedora 1.0 M glibc-minimal-langpack x86_64 2.37-18.fc38 updates 41 k grep x86_64 3.8-3.fc38 fedora 293 k gzip x86_64 1.12-3.fc38 fedora 166 k info x86_64 7.0.2-2.fc38 fedora 181 k patch x86_64 2.7.6-19.fc38 fedora 126 k redhat-rpm-config noarch 257-1.fc38 updates 76 k rpm-build x86_64 4.18.91-3.fc38 copr_base 69 k sed x86_64 4.8-12.fc38 fedora 306 k shadow-utils x86_64 2:4.13-6.fc38 fedora 1.3 M tar x86_64 2:1.34-8.fc38 fedora 889 k unzip x86_64 6.0-60.fc38 fedora 184 k util-linux x86_64 2.39.1-2.fc38 copr_base 1.1 M which x86_64 2.21-39.fc38 fedora 42 k xz x86_64 5.4.1-1.fc38 fedora 419 k Installing dependencies: alternatives x86_64 1.26-1.fc38 updates 39 k ansible-srpm-macros noarch 1-12.fc38 updates 21 k audit-libs x86_64 3.1.2-8.fc38 updates 117 k authselect x86_64 1.4.3-1.fc38 updates 149 k authselect-libs x86_64 1.4.3-1.fc38 updates 249 k basesystem noarch 11-15.fc38 fedora 7.0 k binutils x86_64 2.39-16.fc38 updates 5.4 M binutils-gold x86_64 2.39-16.fc38 updates 795 k bzip2-libs x86_64 1.0.8-13.fc38 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-1.0.fc38 updates 837 k coreutils-common x86_64 9.1-12.fc38 updates 2.0 M cracklib x86_64 2.9.11-1.fc38 updates 93 k crypto-policies noarch 20230301-1.gita12f7b2.fc38 fedora 93 k curl x86_64 8.0.1-7.fc38 updates 348 k cyrus-sasl-lib x86_64 2.1.28-9.fc38 fedora 794 k debugedit x86_64 5.0-9.fc38 updates 78 k dwz x86_64 0.15-2.fc38 fedora 135 k ed x86_64 1.19-2.fc38 fedora 78 k efi-srpm-macros noarch 5-7.fc38 fedora 22 k elfutils x86_64 0.191-1.fc38 updates 557 k elfutils-debuginfod-client x86_64 0.191-1.fc38 updates 37 k elfutils-default-yama-scope noarch 0.191-1.fc38 updates 12 k elfutils-libelf x86_64 0.191-1.fc38 updates 208 k elfutils-libs x86_64 0.191-1.fc38 updates 263 k fedora-gpg-keys noarch 38-1 fedora 126 k fedora-release noarch 38-36 updates 12 k fedora-release-identity-basic noarch 38-36 updates 13 k fedora-repos noarch 38-1 fedora 9.1 k file x86_64 5.45-5.fc38 copr_base 50 k file-libs x86_64 5.45-5.fc38 copr_base 764 k filesystem x86_64 3.18-3.fc38 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-11.fc38 fedora 26 k forge-srpm-macros noarch 0.2.0-3.fc38 updates 19 k fpc-srpm-macros noarch 1.3-7.fc38 fedora 7.8 k gdb-minimal x86_64 14.1-3.fc38 updates 4.3 M gdbm-libs x86_64 1:1.23-3.fc38 fedora 56 k ghc-srpm-macros noarch 1.6.1-1.fc38 fedora 8.0 k glibc x86_64 2.37-18.fc38 updates 2.1 M glibc-common x86_64 2.37-18.fc38 updates 320 k glibc-gconv-extra x86_64 2.37-18.fc38 updates 1.6 M gmp x86_64 1:6.2.1-4.fc38 fedora 313 k gnat-srpm-macros noarch 6-2.fc38 fedora 8.8 k go-srpm-macros noarch 3.5.0-1.fc38 updates 27 k jansson x86_64 2.13.1-6.fc38 fedora 44 k kernel-srpm-macros noarch 1.0-19.fc38 updates 10 k keyutils-libs x86_64 1.6.3-1.fc38 updates 31 k krb5-libs x86_64 1.21-3.fc38 updates 764 k libacl x86_64 2.3.1-7.fc38 updates 23 k libarchive x86_64 3.6.1-4.fc38 fedora 400 k libattr x86_64 2.5.1-6.fc38 fedora 18 k libblkid x86_64 2.39.1-2.fc38 copr_base 117 k libbrotli x86_64 1.1.0-3.fc38 copr_base 336 k libcap x86_64 2.48-8.fc38 updates 68 k libcap-ng x86_64 0.8.5-1.fc38 copr_base 33 k libcom_err x86_64 1.46.5-4.fc38 fedora 26 k libcurl x86_64 8.0.1-7.fc38 updates 315 k libdb x86_64 5.3.28-55.fc38 fedora 758 k libeconf x86_64 0.5.2-1.fc38 updates 30 k libevent x86_64 2.1.12-8.fc38 fedora 257 k libfdisk x86_64 2.39.1-2.fc38 copr_base 163 k libffi x86_64 3.4.4-2.fc38 fedora 38 k libgcc x86_64 13.2.1-7.fc38 updates 115 k libgomp x86_64 13.2.1-7.fc38 updates 324 k libidn2 x86_64 2.3.7-1.fc38 updates 119 k libmount x86_64 2.39.1-2.fc38 copr_base 155 k libnghttp2 x86_64 1.52.0-2.fc38 updates 75 k libnsl2 x86_64 2.0.0-5.fc38 fedora 30 k libpkgconf x86_64 1.8.0-6.fc38 fedora 35 k libpsl x86_64 0.21.2-2.fc38 fedora 65 k libpwquality x86_64 1.4.5-9.fc38 copr_base 109 k libselinux x86_64 3.5-4.fc38 copr_base 87 k libsemanage x86_64 3.5-4.fc38 copr_base 120 k libsepol x86_64 3.5-1.fc38 fedora 324 k libsigsegv x86_64 2.14-4.fc38 fedora 27 k libsmartcols x86_64 2.39.1-2.fc38 copr_base 68 k libssh x86_64 0.10.6-2.fc38 updates 212 k libssh-config noarch 0.10.6-2.fc38 updates 9.0 k libstdc++ x86_64 13.2.1-7.fc38 updates 870 k libtasn1 x86_64 4.19.0-2.fc38 fedora 74 k libtirpc x86_64 1.3.4-1.rc3.fc38 updates 93 k libunistring x86_64 1.1-3.fc38 fedora 545 k libunistring1.0 x86_64 1.0-1.fc38 fedora 539 k libutempter x86_64 1.2.1-8.fc38 fedora 26 k libuuid x86_64 2.39.1-2.fc38 copr_base 29 k libverto x86_64 0.3.2-5.fc38 fedora 21 k libxcrypt x86_64 4.4.36-1.fc38 updates 119 k libxml2 x86_64 2.12.6-1.fc38 copr_base 694 k libzstd x86_64 1.5.5-1.fc38 updates 308 k lua-libs x86_64 5.4.4-9.fc38 fedora 133 k lua-srpm-macros noarch 1-13.fc38 updates 8.7 k lz4-libs x86_64 1.9.4-2.fc38 fedora 67 k mpfr x86_64 4.1.1-3.fc38 fedora 600 k ncurses-base noarch 6.4-7.20230520.fc38.1 updates 88 k ncurses-libs x86_64 6.4-7.20230520.fc38.1 updates 336 k ocaml-srpm-macros noarch 7-3.fc38 fedora 13 k openblas-srpm-macros noarch 2-13.fc38 fedora 7.5 k openldap x86_64 2.6.6-1.fc38 updates 254 k openssl-libs x86_64 1:3.0.9-2.fc38 updates 2.1 M p11-kit x86_64 0.25.3-1.fc38 updates 521 k p11-kit-trust x86_64 0.25.3-1.fc38 updates 142 k package-notes-srpm-macros noarch 0.5-8.fc38 updates 11 k pam x86_64 1.5.2-16.fc38 fedora 560 k pam-libs x86_64 1.5.2-16.fc38 fedora 58 k pcre2 x86_64 10.42-1.fc38.1 fedora 234 k pcre2-syntax noarch 10.42-1.fc38.1 fedora 144 k perl-srpm-macros noarch 1-48.fc38 fedora 8.4 k pkgconf x86_64 1.8.0-6.fc38 fedora 41 k pkgconf-m4 noarch 1.8.0-6.fc38 fedora 14 k pkgconf-pkg-config x86_64 1.8.0-6.fc38 fedora 9.6 k popt x86_64 1.19-2.fc38 fedora 67 k publicsuffix-list-dafsa noarch 20240107-1.fc38 updates 58 k pyproject-srpm-macros noarch 1.12.0-1.fc38 updates 14 k python-srpm-macros noarch 3.11-10.fc38 fedora 26 k qt5-srpm-macros noarch 5.15.12-1.fc38 updates 8.3 k qt6-srpm-macros noarch 6.6.0-1.fc38 updates 8.6 k readline x86_64 8.2-4.fc38 updates 212 k rpm x86_64 4.18.91-3.fc38 copr_base 501 k rpm-build-libs x86_64 4.18.91-3.fc38 copr_base 96 k rpm-libs x86_64 4.18.91-3.fc38 copr_base 309 k rpm-sequoia x86_64 1.6.0-1.fc38 updates 872 k rpmautospec-rpm-macros noarch 0.6.3-1.fc38 updates 10 k rust-srpm-macros noarch 26.2-1.fc38 copr_base 13 k setup noarch 2.14.3-2.fc38 fedora 152 k sqlite-libs x86_64 3.40.1-2.fc38 fedora 666 k systemd-libs x86_64 253.17-1.fc38 updates 649 k tzdata noarch 2024a-1.fc38 updates 715 k util-linux-core x86_64 2.39.1-2.fc38 copr_base 470 k xxhash-libs x86_64 0.8.2-1.fc38 updates 37 k xz-libs x86_64 5.4.1-1.fc38 fedora 108 k zip x86_64 3.0-37.fc38 updates 265 k zlib x86_64 1.2.13-3.fc38 fedora 95 k zstd x86_64 1.5.5-1.fc38 updates 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 154 Packages Total download size: 53 M Installed size: 180 M Downloading Packages: (1/154): libblkid-2.39.1-2.fc38.x86_64.rpm 1.3 MB/s | 117 kB 00:00 (2/154): file-libs-5.45-5.fc38.x86_64.rpm 7.3 MB/s | 764 kB 00:00 (3/154): libcap-ng-0.8.5-1.fc38.x86_64.rpm 1.9 MB/s | 33 kB 00:00 (4/154): libfdisk-2.39.1-2.fc38.x86_64.rpm 5.4 MB/s | 163 kB 00:00 (5/154): libmount-2.39.1-2.fc38.x86_64.rpm 901 kB/s | 155 kB 00:00 (6/154): libbrotli-1.1.0-3.fc38.x86_64.rpm 1.3 MB/s | 336 kB 00:00 (7/154): libselinux-3.5-4.fc38.x86_64.rpm 8.5 MB/s | 87 kB 00:00 (8/154): file-5.45-5.fc38.x86_64.rpm 143 kB/s | 50 kB 00:00 (9/154): libsemanage-3.5-4.fc38.x86_64.rpm 11 MB/s | 120 kB 00:00 (10/154): libpwquality-1.4.5-9.fc38.x86_64.rpm 3.1 MB/s | 109 kB 00:00 (11/154): libsmartcols-2.39.1-2.fc38.x86_64.rpm 6.4 MB/s | 68 kB 00:00 (12/154): libuuid-2.39.1-2.fc38.x86_64.rpm 2.8 MB/s | 29 kB 00:00 (13/154): libxml2-2.12.6-1.fc38.x86_64.rpm 37 MB/s | 694 kB 00:00 (14/154): rpm-4.18.91-3.fc38.x86_64.rpm 22 MB/s | 501 kB 00:00 (15/154): rpm-build-4.18.91-3.fc38.x86_64.rpm 4.5 MB/s | 69 kB 00:00 (16/154): rpm-build-libs-4.18.91-3.fc38.x86_64. 6.6 MB/s | 96 kB 00:00 (17/154): rust-srpm-macros-26.2-1.fc38.noarch.r 1.4 MB/s | 13 kB 00:00 (18/154): rpm-libs-4.18.91-3.fc38.x86_64.rpm 14 MB/s | 309 kB 00:00 (19/154): util-linux-2.39.1-2.fc38.x86_64.rpm 49 MB/s | 1.1 MB 00:00 (20/154): util-linux-core-2.39.1-2.fc38.x86_64. 17 MB/s | 470 kB 00:00 (21/154): basesystem-11-15.fc38.noarch.rpm 23 kB/s | 7.0 kB 00:00 (22/154): bzip2-libs-1.0.8-13.fc38.x86_64.rpm 122 kB/s | 41 kB 00:00 (23/154): bzip2-1.0.8-13.fc38.x86_64.rpm 151 kB/s | 52 kB 00:00 (24/154): crypto-policies-20230301-1.gita12f7b2 1.3 MB/s | 93 kB 00:00 (25/154): cpio-2.13-14.fc38.x86_64.rpm 1.9 MB/s | 276 kB 00:00 (26/154): cyrus-sasl-lib-2.1.28-9.fc38.x86_64.r 6.0 MB/s | 794 kB 00:00 (27/154): ed-1.19-2.fc38.x86_64.rpm 1.9 MB/s | 78 kB 00:00 (28/154): dwz-0.15-2.fc38.x86_64.rpm 1.9 MB/s | 135 kB 00:00 (29/154): efi-srpm-macros-5-7.fc38.noarch.rpm 536 kB/s | 22 kB 00:00 (30/154): fedora-repos-38-1.noarch.rpm 132 kB/s | 9.1 kB 00:00 (31/154): fedora-gpg-keys-38-1.noarch.rpm 1.6 MB/s | 126 kB 00:00 (32/154): fonts-srpm-macros-2.0.5-11.fc38.noarc 733 kB/s | 26 kB 00:00 (33/154): filesystem-3.18-3.fc38.x86_64.rpm 14 MB/s | 1.1 MB 00:00 (34/154): findutils-4.9.0-3.fc38.x86_64.rpm 6.9 MB/s | 492 kB 00:00 (35/154): fpc-srpm-macros-1.3-7.fc38.noarch.rpm 264 kB/s | 7.8 kB 00:00 (36/154): gawk-5.1.1-5.fc38.x86_64.rpm 20 MB/s | 1.0 MB 00:00 (37/154): gdbm-libs-1.23-3.fc38.x86_64.rpm 1.9 MB/s | 56 kB 00:00 (38/154): ghc-srpm-macros-1.6.1-1.fc38.noarch.r 248 kB/s | 8.0 kB 00:00 (39/154): gmp-6.2.1-4.fc38.x86_64.rpm 8.3 MB/s | 313 kB 00:00 (40/154): gnat-srpm-macros-6-2.fc38.noarch.rpm 230 kB/s | 8.8 kB 00:00 (41/154): grep-3.8-3.fc38.x86_64.rpm 5.4 MB/s | 293 kB 00:00 (42/154): gzip-1.12-3.fc38.x86_64.rpm 5.1 MB/s | 166 kB 00:00 (43/154): info-7.0.2-2.fc38.x86_64.rpm 4.0 MB/s | 181 kB 00:00 (44/154): jansson-2.13.1-6.fc38.x86_64.rpm 1.2 MB/s | 44 kB 00:00 (45/154): libarchive-3.6.1-4.fc38.x86_64.rpm 7.2 MB/s | 400 kB 00:00 (46/154): libattr-2.5.1-6.fc38.x86_64.rpm 426 kB/s | 18 kB 00:00 (47/154): libcom_err-1.46.5-4.fc38.x86_64.rpm 719 kB/s | 26 kB 00:00 (48/154): libdb-5.3.28-55.fc38.x86_64.rpm 19 MB/s | 758 kB 00:00 (49/154): libffi-3.4.4-2.fc38.x86_64.rpm 1.0 MB/s | 38 kB 00:00 (50/154): libevent-2.1.12-8.fc38.x86_64.rpm 5.0 MB/s | 257 kB 00:00 (51/154): libnsl2-2.0.0-5.fc38.x86_64.rpm 874 kB/s | 30 kB 00:00 (52/154): libpkgconf-1.8.0-6.fc38.x86_64.rpm 953 kB/s | 35 kB 00:00 (53/154): libpsl-0.21.2-2.fc38.x86_64.rpm 1.6 MB/s | 65 kB 00:00 (54/154): libsepol-3.5-1.fc38.x86_64.rpm 7.2 MB/s | 324 kB 00:00 (55/154): libsigsegv-2.14-4.fc38.x86_64.rpm 405 kB/s | 27 kB 00:00 (56/154): libtasn1-4.19.0-2.fc38.x86_64.rpm 1.2 MB/s | 74 kB 00:00 (57/154): libunistring-1.1-3.fc38.x86_64.rpm 8.0 MB/s | 545 kB 00:00 (58/154): libutempter-1.2.1-8.fc38.x86_64.rpm 496 kB/s | 26 kB 00:00 (59/154): libverto-0.3.2-5.fc38.x86_64.rpm 558 kB/s | 21 kB 00:00 (60/154): libunistring1.0-1.0-1.fc38.x86_64.rpm 7.2 MB/s | 539 kB 00:00 (61/154): lua-libs-5.4.4-9.fc38.x86_64.rpm 3.3 MB/s | 133 kB 00:00 (62/154): lz4-libs-1.9.4-2.fc38.x86_64.rpm 1.8 MB/s | 67 kB 00:00 (63/154): mpfr-4.1.1-3.fc38.x86_64.rpm 11 MB/s | 600 kB 00:00 (64/154): ocaml-srpm-macros-7-3.fc38.noarch.rpm 344 kB/s | 13 kB 00:00 (65/154): openblas-srpm-macros-2-13.fc38.noarch 188 kB/s | 7.5 kB 00:00 (66/154): pam-libs-1.5.2-16.fc38.x86_64.rpm 1.6 MB/s | 58 kB 00:00 (67/154): pam-1.5.2-16.fc38.x86_64.rpm 11 MB/s | 560 kB 00:00 (68/154): patch-2.7.6-19.fc38.x86_64.rpm 3.8 MB/s | 126 kB 00:00 (69/154): pcre2-syntax-10.42-1.fc38.1.noarch.rp 3.5 MB/s | 144 kB 00:00 (70/154): pcre2-10.42-1.fc38.1.x86_64.rpm 5.2 MB/s | 234 kB 00:00 (71/154): perl-srpm-macros-1-48.fc38.noarch.rpm 197 kB/s | 8.4 kB 00:00 (72/154): pkgconf-1.8.0-6.fc38.x86_64.rpm 1.0 MB/s | 41 kB 00:00 (73/154): pkgconf-m4-1.8.0-6.fc38.noarch.rpm 279 kB/s | 14 kB 00:00 (74/154): pkgconf-pkg-config-1.8.0-6.fc38.x86_6 162 kB/s | 9.6 kB 00:00 (75/154): popt-1.19-2.fc38.x86_64.rpm 1.3 MB/s | 67 kB 00:00 (76/154): python-srpm-macros-3.11-10.fc38.noarc 527 kB/s | 26 kB 00:00 (77/154): sed-4.8-12.fc38.x86_64.rpm 4.8 MB/s | 306 kB 00:00 (78/154): setup-2.14.3-2.fc38.noarch.rpm 3.4 MB/s | 152 kB 00:00 (79/154): sqlite-libs-3.40.1-2.fc38.x86_64.rpm 12 MB/s | 666 kB 00:00 (80/154): shadow-utils-4.13-6.fc38.x86_64.rpm 12 MB/s | 1.3 MB 00:00 (81/154): tar-1.34-8.fc38.x86_64.rpm 13 MB/s | 889 kB 00:00 (82/154): unzip-6.0-60.fc38.x86_64.rpm 4.6 MB/s | 184 kB 00:00 (83/154): which-2.21-39.fc38.x86_64.rpm 868 kB/s | 42 kB 00:00 (84/154): xz-5.4.1-1.fc38.x86_64.rpm 8.0 MB/s | 419 kB 00:00 (85/154): xz-libs-5.4.1-1.fc38.x86_64.rpm 2.1 MB/s | 108 kB 00:00 (86/154): zlib-1.2.13-3.fc38.x86_64.rpm 2.5 MB/s | 95 kB 00:00 (87/154): alternatives-1.26-1.fc38.x86_64.rpm 126 kB/s | 39 kB 00:00 (88/154): ansible-srpm-macros-1-12.fc38.noarch. 69 kB/s | 21 kB 00:00 (89/154): authselect-1.4.3-1.fc38.x86_64.rpm 886 kB/s | 149 kB 00:00 (90/154): audit-libs-3.1.2-8.fc38.x86_64.rpm 219 kB/s | 117 kB 00:00 (91/154): authselect-libs-1.4.3-1.fc38.x86_64.r 572 kB/s | 249 kB 00:00 (92/154): binutils-gold-2.39-16.fc38.x86_64.rpm 892 kB/s | 795 kB 00:00 (93/154): ca-certificates-2023.2.60_v7.0.306-1. 1.0 MB/s | 837 kB 00:00 (94/154): bash-5.2.26-1.fc38.x86_64.rpm 767 kB/s | 1.8 MB 00:02 (95/154): coreutils-9.1-12.fc38.x86_64.rpm 786 kB/s | 1.1 MB 00:01 (96/154): cracklib-2.9.11-1.fc38.x86_64.rpm 559 kB/s | 93 kB 00:00 (97/154): curl-8.0.1-7.fc38.x86_64.rpm 837 kB/s | 348 kB 00:00 (98/154): debugedit-5.0-9.fc38.x86_64.rpm 927 kB/s | 78 kB 00:00 (99/154): diffutils-3.10-1.fc38.x86_64.rpm 800 kB/s | 398 kB 00:00 (100/154): coreutils-common-9.1-12.fc38.x86_64. 786 kB/s | 2.0 MB 00:02 (101/154): elfutils-debuginfod-client-0.191-1.f 447 kB/s | 37 kB 00:00 (102/154): elfutils-0.191-1.fc38.x86_64.rpm 959 kB/s | 557 kB 00:00 (103/154): elfutils-default-yama-scope-0.191-1. 150 kB/s | 12 kB 00:00 (104/154): elfutils-libelf-0.191-1.fc38.x86_64. 836 kB/s | 208 kB 00:00 (105/154): fedora-release-38-36.noarch.rpm 146 kB/s | 12 kB 00:00 (106/154): elfutils-libs-0.191-1.fc38.x86_64.rp 792 kB/s | 263 kB 00:00 (107/154): fedora-release-common-38-36.noarch.r 266 kB/s | 22 kB 00:00 (108/154): fedora-release-identity-basic-38-36. 155 kB/s | 13 kB 00:00 (109/154): forge-srpm-macros-0.2.0-3.fc38.noarc 224 kB/s | 19 kB 00:00 (110/154): glibc-2.37-18.fc38.x86_64.rpm 1.1 MB/s | 2.1 MB 00:01 (111/154): glibc-common-2.37-18.fc38.x86_64.rpm 964 kB/s | 320 kB 00:00 (112/154): binutils-2.39-16.fc38.x86_64.rpm 634 kB/s | 5.4 MB 00:08 (113/154): glibc-minimal-langpack-2.37-18.fc38. 478 kB/s | 41 kB 00:00 (114/154): go-srpm-macros-3.5.0-1.fc38.noarch.r 326 kB/s | 27 kB 00:00 (115/154): kernel-srpm-macros-1.0-19.fc38.noarc 124 kB/s | 10 kB 00:00 (116/154): glibc-gconv-extra-2.37-18.fc38.x86_6 1.3 MB/s | 1.6 MB 00:01 (117/154): keyutils-libs-1.6.3-1.fc38.x86_64.rp 370 kB/s | 31 kB 00:00 (118/154): libacl-2.3.1-7.fc38.x86_64.rpm 276 kB/s | 23 kB 00:00 (119/154): libcap-2.48-8.fc38.x86_64.rpm 803 kB/s | 68 kB 00:00 (120/154): gdb-minimal-14.1-3.fc38.x86_64.rpm 1.1 MB/s | 4.3 MB 00:03 (121/154): libcurl-8.0.1-7.fc38.x86_64.rpm 1.2 MB/s | 315 kB 00:00 (122/154): libeconf-0.5.2-1.fc38.x86_64.rpm 121 kB/s | 30 kB 00:00 (123/154): krb5-libs-1.21-3.fc38.x86_64.rpm 1.3 MB/s | 764 kB 00:00 (124/154): libidn2-2.3.7-1.fc38.x86_64.rpm 1.4 MB/s | 119 kB 00:00 (125/154): libnghttp2-1.52.0-2.fc38.x86_64.rpm 886 kB/s | 75 kB 00:00 (126/154): libgcc-13.2.1-7.fc38.x86_64.rpm 276 kB/s | 115 kB 00:00 (127/154): libssh-0.10.6-2.fc38.x86_64.rpm 1.2 MB/s | 212 kB 00:00 (128/154): libssh-config-0.10.6-2.fc38.noarch.r 108 kB/s | 9.0 kB 00:00 (129/154): libgomp-13.2.1-7.fc38.x86_64.rpm 649 kB/s | 324 kB 00:00 (130/154): libtirpc-1.3.4-1.rc3.fc38.x86_64.rpm 557 kB/s | 93 kB 00:00 (131/154): libxcrypt-4.4.36-1.fc38.x86_64.rpm 717 kB/s | 119 kB 00:00 (132/154): lua-srpm-macros-1-13.fc38.noarch.rpm 104 kB/s | 8.7 kB 00:00 (133/154): libzstd-1.5.5-1.fc38.x86_64.rpm 920 kB/s | 308 kB 00:00 (134/154): ncurses-base-6.4-7.20230520.fc38.1.n 531 kB/s | 88 kB 00:00 (135/154): libstdc++-13.2.1-7.fc38.x86_64.rpm 1.5 MB/s | 870 kB 00:00 (136/154): openldap-2.6.6-1.fc38.x86_64.rpm 874 kB/s | 254 kB 00:00 (137/154): ncurses-libs-6.4-7.20230520.fc38.1.x 1.0 MB/s | 336 kB 00:00 (138/154): p11-kit-trust-0.25.3-1.fc38.x86_64.r 850 kB/s | 142 kB 00:00 (139/154): package-notes-srpm-macros-0.5-8.fc38 132 kB/s | 11 kB 00:00 (140/154): publicsuffix-list-dafsa-20240107-1.f 693 kB/s | 58 kB 00:00 (141/154): pyproject-srpm-macros-1.12.0-1.fc38. 163 kB/s | 14 kB 00:00 (142/154): p11-kit-0.25.3-1.fc38.x86_64.rpm 1.0 MB/s | 521 kB 00:00 (143/154): qt5-srpm-macros-5.15.12-1.fc38.noarc 100 kB/s | 8.3 kB 00:00 (144/154): qt6-srpm-macros-6.6.0-1.fc38.noarch. 104 kB/s | 8.6 kB 00:00 (145/154): redhat-rpm-config-257-1.fc38.noarch. 902 kB/s | 76 kB 00:00 (146/154): readline-8.2-4.fc38.x86_64.rpm 1.2 MB/s | 212 kB 00:00 (147/154): rpmautospec-rpm-macros-0.6.3-1.fc38. 120 kB/s | 10 kB 00:00 (148/154): openssl-libs-3.0.9-2.fc38.x86_64.rpm 1.6 MB/s | 2.1 MB 00:01 (149/154): systemd-libs-253.17-1.fc38.x86_64.rp 1.5 MB/s | 649 kB 00:00 (150/154): rpm-sequoia-1.6.0-1.fc38.x86_64.rpm 1.5 MB/s | 872 kB 00:00 (151/154): xxhash-libs-0.8.2-1.fc38.x86_64.rpm 447 kB/s | 37 kB 00:00 (152/154): zip-3.0-37.fc38.x86_64.rpm 1.6 MB/s | 265 kB 00:00 (153/154): tzdata-2024a-1.fc38.noarch.rpm 1.7 MB/s | 715 kB 00:00 (154/154): zstd-1.5.5-1.fc38.x86_64.rpm 1.9 MB/s | 482 kB 00:00 -------------------------------------------------------------------------------- Total 3.4 MB/s | 53 MB 00:15 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-3.fc38.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-7.fc38.x86_64 1/154 Running scriptlet: libgcc-13.2.1-7.fc38.x86_64 1/154 Installing : crypto-policies-20230301-1.gita12f7b2.fc38.noarc 2/154 Running scriptlet: crypto-policies-20230301-1.gita12f7b2.fc38.noarc 2/154 Installing : tzdata-2024a-1.fc38.noarch 3/154 Installing : fedora-release-identity-basic-38-36.noarch 4/154 Installing : qt6-srpm-macros-6.6.0-1.fc38.noarch 5/154 Installing : qt5-srpm-macros-5.15.12-1.fc38.noarch 6/154 Installing : publicsuffix-list-dafsa-20240107-1.fc38.noarch 7/154 Installing : package-notes-srpm-macros-0.5-8.fc38.noarch 8/154 Installing : ncurses-base-6.4-7.20230520.fc38.1.noarch 9/154 Installing : libssh-config-0.10.6-2.fc38.noarch 10/154 Installing : kernel-srpm-macros-1.0-19.fc38.noarch 11/154 Installing : coreutils-common-9.1-12.fc38.x86_64 12/154 Installing : ansible-srpm-macros-1-12.fc38.noarch 13/154 Installing : pkgconf-m4-1.8.0-6.fc38.noarch 14/154 Installing : perl-srpm-macros-1-48.fc38.noarch 15/154 Installing : pcre2-syntax-10.42-1.fc38.1.noarch 16/154 Installing : openblas-srpm-macros-2-13.fc38.noarch 17/154 Installing : ocaml-srpm-macros-7-3.fc38.noarch 18/154 Installing : gnat-srpm-macros-6-2.fc38.noarch 19/154 Installing : ghc-srpm-macros-1.6.1-1.fc38.noarch 20/154 Installing : fpc-srpm-macros-1.3-7.fc38.noarch 21/154 Installing : fedora-gpg-keys-38-1.noarch 22/154 Installing : fedora-release-38-36.noarch 23/154 Installing : fedora-repos-38-1.noarch 24/154 Installing : fedora-release-common-38-36.noarch 25/154 Installing : setup-2.14.3-2.fc38.noarch 26/154 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.3-2.fc38.noarch 26/154 Installing : filesystem-3.18-3.fc38.x86_64 27/154 Installing : basesystem-11-15.fc38.noarch 28/154 Installing : glibc-gconv-extra-2.37-18.fc38.x86_64 29/154 Running scriptlet: glibc-gconv-extra-2.37-18.fc38.x86_64 29/154 Installing : glibc-minimal-langpack-2.37-18.fc38.x86_64 30/154 Installing : glibc-common-2.37-18.fc38.x86_64 31/154 Running scriptlet: glibc-2.37-18.fc38.x86_64 32/154 Installing : glibc-2.37-18.fc38.x86_64 32/154 Running scriptlet: glibc-2.37-18.fc38.x86_64 32/154 Installing : ncurses-libs-6.4-7.20230520.fc38.1.x86_64 33/154 Installing : bash-5.2.26-1.fc38.x86_64 34/154 Running scriptlet: bash-5.2.26-1.fc38.x86_64 34/154 Installing : zlib-1.2.13-3.fc38.x86_64 35/154 Installing : xz-libs-5.4.1-1.fc38.x86_64 36/154 Installing : bzip2-libs-1.0.8-13.fc38.x86_64 37/154 Installing : libzstd-1.5.5-1.fc38.x86_64 38/154 Installing : elfutils-libelf-0.191-1.fc38.x86_64 39/154 Installing : libuuid-2.39.1-2.fc38.x86_64 40/154 Installing : popt-1.19-2.fc38.x86_64 41/154 Installing : libstdc++-13.2.1-7.fc38.x86_64 42/154 Installing : libblkid-2.39.1-2.fc38.x86_64 43/154 Installing : readline-8.2-4.fc38.x86_64 44/154 Installing : gmp-1:6.2.1-4.fc38.x86_64 45/154 Installing : libattr-2.5.1-6.fc38.x86_64 46/154 Installing : libacl-2.3.1-7.fc38.x86_64 47/154 Installing : libcap-2.48-8.fc38.x86_64 48/154 Installing : libxcrypt-4.4.36-1.fc38.x86_64 49/154 Installing : lz4-libs-1.9.4-2.fc38.x86_64 50/154 Installing : libeconf-0.5.2-1.fc38.x86_64 51/154 Installing : systemd-libs-253.17-1.fc38.x86_64 52/154 Installing : mpfr-4.1.1-3.fc38.x86_64 53/154 Installing : dwz-0.15-2.fc38.x86_64 54/154 Installing : unzip-6.0-60.fc38.x86_64 55/154 Installing : file-libs-5.45-5.fc38.x86_64 56/154 Installing : file-5.45-5.fc38.x86_64 57/154 Installing : libcap-ng-0.8.5-1.fc38.x86_64 58/154 Installing : audit-libs-3.1.2-8.fc38.x86_64 59/154 Installing : pam-libs-1.5.2-16.fc38.x86_64 60/154 Installing : libsmartcols-2.39.1-2.fc38.x86_64 61/154 Installing : libcom_err-1.46.5-4.fc38.x86_64 62/154 Installing : libsepol-3.5-1.fc38.x86_64 63/154 Installing : libtasn1-4.19.0-2.fc38.x86_64 64/154 Installing : lua-libs-5.4.4-9.fc38.x86_64 65/154 Installing : pcre2-10.42-1.fc38.1.x86_64 66/154 Installing : libselinux-3.5-4.fc38.x86_64 67/154 Installing : sed-4.8-12.fc38.x86_64 68/154 Installing : grep-3.8-3.fc38.x86_64 69/154 Installing : findutils-1:4.9.0-3.fc38.x86_64 70/154 Installing : xz-5.4.1-1.fc38.x86_64 71/154 Installing : libmount-2.39.1-2.fc38.x86_64 72/154 Installing : alternatives-1.26-1.fc38.x86_64 73/154 Installing : util-linux-core-2.39.1-2.fc38.x86_64 74/154 Installing : libsemanage-3.5-4.fc38.x86_64 75/154 Installing : shadow-utils-2:4.13-6.fc38.x86_64 76/154 Running scriptlet: libutempter-1.2.1-8.fc38.x86_64 77/154 Installing : libutempter-1.2.1-8.fc38.x86_64 77/154 Installing : tar-2:1.34-8.fc38.x86_64 78/154 Installing : zip-3.0-37.fc38.x86_64 79/154 Installing : zstd-1.5.5-1.fc38.x86_64 80/154 Installing : libfdisk-2.39.1-2.fc38.x86_64 81/154 Installing : bzip2-1.0.8-13.fc38.x86_64 82/154 Installing : libxml2-2.12.6-1.fc38.x86_64 83/154 Installing : sqlite-libs-3.40.1-2.fc38.x86_64 84/154 Installing : ed-1.19-2.fc38.x86_64 85/154 Installing : patch-2.7.6-19.fc38.x86_64 86/154 Installing : elfutils-default-yama-scope-0.191-1.fc38.noarch 87/154 Running scriptlet: elfutils-default-yama-scope-0.191-1.fc38.noarch 87/154 Installing : libbrotli-1.1.0-3.fc38.x86_64 88/154 Installing : cpio-2.13-14.fc38.x86_64 89/154 Installing : gdbm-libs-1:1.23-3.fc38.x86_64 90/154 Installing : cyrus-sasl-lib-2.1.28-9.fc38.x86_64 91/154 Installing : jansson-2.13.1-6.fc38.x86_64 92/154 Installing : libdb-5.3.28-55.fc38.x86_64 93/154 Installing : libffi-3.4.4-2.fc38.x86_64 94/154 Installing : p11-kit-0.25.3-1.fc38.x86_64 95/154 Installing : p11-kit-trust-0.25.3-1.fc38.x86_64 96/154 Running scriptlet: p11-kit-trust-0.25.3-1.fc38.x86_64 96/154 Installing : openssl-libs-1:3.0.9-2.fc38.x86_64 97/154 Installing : coreutils-9.1-12.fc38.x86_64 98/154 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noar 99/154 Installing : ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noar 99/154 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noar 99/154 Installing : gzip-1.12-3.fc38.x86_64 100/154 Running scriptlet: authselect-libs-1.4.3-1.fc38.x86_64 101/154 Installing : authselect-libs-1.4.3-1.fc38.x86_64 101/154 Installing : libarchive-3.6.1-4.fc38.x86_64 102/154 Installing : authselect-1.4.3-1.fc38.x86_64 103/154 Installing : cracklib-2.9.11-1.fc38.x86_64 104/154 Installing : libpwquality-1.4.5-9.fc38.x86_64 105/154 Installing : libevent-2.1.12-8.fc38.x86_64 106/154 Installing : openldap-2.6.6-1.fc38.x86_64 107/154 Installing : rpm-sequoia-1.6.0-1.fc38.x86_64 108/154 Installing : rpm-libs-4.18.91-3.fc38.x86_64 109/154 Installing : libpkgconf-1.8.0-6.fc38.x86_64 110/154 Installing : pkgconf-1.8.0-6.fc38.x86_64 111/154 Installing : pkgconf-pkg-config-1.8.0-6.fc38.x86_64 112/154 Installing : libsigsegv-2.14-4.fc38.x86_64 113/154 Installing : gawk-5.1.1-5.fc38.x86_64 114/154 Installing : libunistring-1.1-3.fc38.x86_64 115/154 Installing : libidn2-2.3.7-1.fc38.x86_64 116/154 Installing : libunistring1.0-1.0-1.fc38.x86_64 117/154 Installing : libpsl-0.21.2-2.fc38.x86_64 118/154 Installing : libverto-0.3.2-5.fc38.x86_64 119/154 Installing : diffutils-3.10-1.fc38.x86_64 120/154 Installing : keyutils-libs-1.6.3-1.fc38.x86_64 121/154 Installing : krb5-libs-1.21-3.fc38.x86_64 122/154 Installing : libtirpc-1.3.4-1.rc3.fc38.x86_64 123/154 Installing : libnsl2-2.0.0-5.fc38.x86_64 124/154 Installing : pam-1.5.2-16.fc38.x86_64 125/154 Installing : libssh-0.10.6-2.fc38.x86_64 126/154 Installing : libgomp-13.2.1-7.fc38.x86_64 127/154 Installing : libnghttp2-1.52.0-2.fc38.x86_64 128/154 Installing : libcurl-8.0.1-7.fc38.x86_64 129/154 Installing : elfutils-libs-0.191-1.fc38.x86_64 130/154 Installing : elfutils-debuginfod-client-0.191-1.fc38.x86_64 131/154 Installing : binutils-gold-2.39-16.fc38.x86_64 132/154 Installing : binutils-2.39-16.fc38.x86_64 133/154 Running scriptlet: binutils-2.39-16.fc38.x86_64 133/154 Installing : elfutils-0.191-1.fc38.x86_64 134/154 Installing : rpm-build-libs-4.18.91-3.fc38.x86_64 135/154 Installing : curl-8.0.1-7.fc38.x86_64 136/154 Running scriptlet: rpm-4.18.91-3.fc38.x86_64 137/154 Installing : rpm-4.18.91-3.fc38.x86_64 137/154 Installing : efi-srpm-macros-5-7.fc38.noarch 138/154 Installing : lua-srpm-macros-1-13.fc38.noarch 139/154 Installing : rpmautospec-rpm-macros-0.6.3-1.fc38.noarch 140/154 Installing : xxhash-libs-0.8.2-1.fc38.x86_64 141/154 Installing : gdb-minimal-14.1-3.fc38.x86_64 142/154 Installing : debugedit-5.0-9.fc38.x86_64 143/154 Installing : rust-srpm-macros-26.2-1.fc38.noarch 144/154 Installing : pyproject-srpm-macros-1.12.0-1.fc38.noarch 145/154 Installing : rpm-build-4.18.91-3.fc38.x86_64 146/154 Installing : fonts-srpm-macros-1:2.0.5-11.fc38.noarch 147/154 Installing : python-srpm-macros-3.11-10.fc38.noarch 148/154 Installing : forge-srpm-macros-0.2.0-3.fc38.noarch 149/154 Installing : go-srpm-macros-3.5.0-1.fc38.noarch 150/154 Installing : redhat-rpm-config-257-1.fc38.noarch 151/154 Installing : util-linux-2.39.1-2.fc38.x86_64 152/154 Installing : which-2.21-39.fc38.x86_64 153/154 Installing : info-7.0.2-2.fc38.x86_64 154/154 Running scriptlet: filesystem-3.18-3.fc38.x86_64 154/154 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noar 154/154 Running scriptlet: authselect-libs-1.4.3-1.fc38.x86_64 154/154 Running scriptlet: rpm-4.18.91-3.fc38.x86_64 154/154 Running scriptlet: info-7.0.2-2.fc38.x86_64 154/154 Verifying : file-5.45-5.fc38.x86_64 1/154 Verifying : file-libs-5.45-5.fc38.x86_64 2/154 Verifying : libblkid-2.39.1-2.fc38.x86_64 3/154 Verifying : libbrotli-1.1.0-3.fc38.x86_64 4/154 Verifying : libcap-ng-0.8.5-1.fc38.x86_64 5/154 Verifying : libfdisk-2.39.1-2.fc38.x86_64 6/154 Verifying : libmount-2.39.1-2.fc38.x86_64 7/154 Verifying : libpwquality-1.4.5-9.fc38.x86_64 8/154 Verifying : libselinux-3.5-4.fc38.x86_64 9/154 Verifying : libsemanage-3.5-4.fc38.x86_64 10/154 Verifying : libsmartcols-2.39.1-2.fc38.x86_64 11/154 Verifying : libuuid-2.39.1-2.fc38.x86_64 12/154 Verifying : libxml2-2.12.6-1.fc38.x86_64 13/154 Verifying : rpm-4.18.91-3.fc38.x86_64 14/154 Verifying : rpm-build-4.18.91-3.fc38.x86_64 15/154 Verifying : rpm-build-libs-4.18.91-3.fc38.x86_64 16/154 Verifying : rpm-libs-4.18.91-3.fc38.x86_64 17/154 Verifying : rust-srpm-macros-26.2-1.fc38.noarch 18/154 Verifying : util-linux-2.39.1-2.fc38.x86_64 19/154 Verifying : util-linux-core-2.39.1-2.fc38.x86_64 20/154 Verifying : basesystem-11-15.fc38.noarch 21/154 Verifying : bzip2-1.0.8-13.fc38.x86_64 22/154 Verifying : bzip2-libs-1.0.8-13.fc38.x86_64 23/154 Verifying : cpio-2.13-14.fc38.x86_64 24/154 Verifying : crypto-policies-20230301-1.gita12f7b2.fc38.noarc 25/154 Verifying : cyrus-sasl-lib-2.1.28-9.fc38.x86_64 26/154 Verifying : dwz-0.15-2.fc38.x86_64 27/154 Verifying : ed-1.19-2.fc38.x86_64 28/154 Verifying : efi-srpm-macros-5-7.fc38.noarch 29/154 Verifying : fedora-gpg-keys-38-1.noarch 30/154 Verifying : fedora-repos-38-1.noarch 31/154 Verifying : filesystem-3.18-3.fc38.x86_64 32/154 Verifying : findutils-1:4.9.0-3.fc38.x86_64 33/154 Verifying : fonts-srpm-macros-1:2.0.5-11.fc38.noarch 34/154 Verifying : fpc-srpm-macros-1.3-7.fc38.noarch 35/154 Verifying : gawk-5.1.1-5.fc38.x86_64 36/154 Verifying : gdbm-libs-1:1.23-3.fc38.x86_64 37/154 Verifying : ghc-srpm-macros-1.6.1-1.fc38.noarch 38/154 Verifying : gmp-1:6.2.1-4.fc38.x86_64 39/154 Verifying : gnat-srpm-macros-6-2.fc38.noarch 40/154 Verifying : grep-3.8-3.fc38.x86_64 41/154 Verifying : gzip-1.12-3.fc38.x86_64 42/154 Verifying : info-7.0.2-2.fc38.x86_64 43/154 Verifying : jansson-2.13.1-6.fc38.x86_64 44/154 Verifying : libarchive-3.6.1-4.fc38.x86_64 45/154 Verifying : libattr-2.5.1-6.fc38.x86_64 46/154 Verifying : libcom_err-1.46.5-4.fc38.x86_64 47/154 Verifying : libdb-5.3.28-55.fc38.x86_64 48/154 Verifying : libevent-2.1.12-8.fc38.x86_64 49/154 Verifying : libffi-3.4.4-2.fc38.x86_64 50/154 Verifying : libnsl2-2.0.0-5.fc38.x86_64 51/154 Verifying : libpkgconf-1.8.0-6.fc38.x86_64 52/154 Verifying : libpsl-0.21.2-2.fc38.x86_64 53/154 Verifying : libsepol-3.5-1.fc38.x86_64 54/154 Verifying : libsigsegv-2.14-4.fc38.x86_64 55/154 Verifying : libtasn1-4.19.0-2.fc38.x86_64 56/154 Verifying : libunistring-1.1-3.fc38.x86_64 57/154 Verifying : libunistring1.0-1.0-1.fc38.x86_64 58/154 Verifying : libutempter-1.2.1-8.fc38.x86_64 59/154 Verifying : libverto-0.3.2-5.fc38.x86_64 60/154 Verifying : lua-libs-5.4.4-9.fc38.x86_64 61/154 Verifying : lz4-libs-1.9.4-2.fc38.x86_64 62/154 Verifying : mpfr-4.1.1-3.fc38.x86_64 63/154 Verifying : ocaml-srpm-macros-7-3.fc38.noarch 64/154 Verifying : openblas-srpm-macros-2-13.fc38.noarch 65/154 Verifying : pam-1.5.2-16.fc38.x86_64 66/154 Verifying : pam-libs-1.5.2-16.fc38.x86_64 67/154 Verifying : patch-2.7.6-19.fc38.x86_64 68/154 Verifying : pcre2-10.42-1.fc38.1.x86_64 69/154 Verifying : pcre2-syntax-10.42-1.fc38.1.noarch 70/154 Verifying : perl-srpm-macros-1-48.fc38.noarch 71/154 Verifying : pkgconf-1.8.0-6.fc38.x86_64 72/154 Verifying : pkgconf-m4-1.8.0-6.fc38.noarch 73/154 Verifying : pkgconf-pkg-config-1.8.0-6.fc38.x86_64 74/154 Verifying : popt-1.19-2.fc38.x86_64 75/154 Verifying : python-srpm-macros-3.11-10.fc38.noarch 76/154 Verifying : sed-4.8-12.fc38.x86_64 77/154 Verifying : setup-2.14.3-2.fc38.noarch 78/154 Verifying : shadow-utils-2:4.13-6.fc38.x86_64 79/154 Verifying : sqlite-libs-3.40.1-2.fc38.x86_64 80/154 Verifying : tar-2:1.34-8.fc38.x86_64 81/154 Verifying : unzip-6.0-60.fc38.x86_64 82/154 Verifying : which-2.21-39.fc38.x86_64 83/154 Verifying : xz-5.4.1-1.fc38.x86_64 84/154 Verifying : xz-libs-5.4.1-1.fc38.x86_64 85/154 Verifying : zlib-1.2.13-3.fc38.x86_64 86/154 Verifying : alternatives-1.26-1.fc38.x86_64 87/154 Verifying : ansible-srpm-macros-1-12.fc38.noarch 88/154 Verifying : audit-libs-3.1.2-8.fc38.x86_64 89/154 Verifying : authselect-1.4.3-1.fc38.x86_64 90/154 Verifying : authselect-libs-1.4.3-1.fc38.x86_64 91/154 Verifying : bash-5.2.26-1.fc38.x86_64 92/154 Verifying : binutils-2.39-16.fc38.x86_64 93/154 Verifying : binutils-gold-2.39-16.fc38.x86_64 94/154 Verifying : ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noar 95/154 Verifying : coreutils-9.1-12.fc38.x86_64 96/154 Verifying : coreutils-common-9.1-12.fc38.x86_64 97/154 Verifying : cracklib-2.9.11-1.fc38.x86_64 98/154 Verifying : curl-8.0.1-7.fc38.x86_64 99/154 Verifying : debugedit-5.0-9.fc38.x86_64 100/154 Verifying : diffutils-3.10-1.fc38.x86_64 101/154 Verifying : elfutils-0.191-1.fc38.x86_64 102/154 Verifying : elfutils-debuginfod-client-0.191-1.fc38.x86_64 103/154 Verifying : elfutils-default-yama-scope-0.191-1.fc38.noarch 104/154 Verifying : elfutils-libelf-0.191-1.fc38.x86_64 105/154 Verifying : elfutils-libs-0.191-1.fc38.x86_64 106/154 Verifying : fedora-release-38-36.noarch 107/154 Verifying : fedora-release-common-38-36.noarch 108/154 Verifying : fedora-release-identity-basic-38-36.noarch 109/154 Verifying : forge-srpm-macros-0.2.0-3.fc38.noarch 110/154 Verifying : gdb-minimal-14.1-3.fc38.x86_64 111/154 Verifying : glibc-2.37-18.fc38.x86_64 112/154 Verifying : glibc-common-2.37-18.fc38.x86_64 113/154 Verifying : glibc-gconv-extra-2.37-18.fc38.x86_64 114/154 Verifying : glibc-minimal-langpack-2.37-18.fc38.x86_64 115/154 Verifying : go-srpm-macros-3.5.0-1.fc38.noarch 116/154 Verifying : kernel-srpm-macros-1.0-19.fc38.noarch 117/154 Verifying : keyutils-libs-1.6.3-1.fc38.x86_64 118/154 Verifying : krb5-libs-1.21-3.fc38.x86_64 119/154 Verifying : libacl-2.3.1-7.fc38.x86_64 120/154 Verifying : libcap-2.48-8.fc38.x86_64 121/154 Verifying : libcurl-8.0.1-7.fc38.x86_64 122/154 Verifying : libeconf-0.5.2-1.fc38.x86_64 123/154 Verifying : libgcc-13.2.1-7.fc38.x86_64 124/154 Verifying : libgomp-13.2.1-7.fc38.x86_64 125/154 Verifying : libidn2-2.3.7-1.fc38.x86_64 126/154 Verifying : libnghttp2-1.52.0-2.fc38.x86_64 127/154 Verifying : libssh-0.10.6-2.fc38.x86_64 128/154 Verifying : libssh-config-0.10.6-2.fc38.noarch 129/154 Verifying : libstdc++-13.2.1-7.fc38.x86_64 130/154 Verifying : libtirpc-1.3.4-1.rc3.fc38.x86_64 131/154 Verifying : libxcrypt-4.4.36-1.fc38.x86_64 132/154 Verifying : libzstd-1.5.5-1.fc38.x86_64 133/154 Verifying : lua-srpm-macros-1-13.fc38.noarch 134/154 Verifying : ncurses-base-6.4-7.20230520.fc38.1.noarch 135/154 Verifying : ncurses-libs-6.4-7.20230520.fc38.1.x86_64 136/154 Verifying : openldap-2.6.6-1.fc38.x86_64 137/154 Verifying : openssl-libs-1:3.0.9-2.fc38.x86_64 138/154 Verifying : p11-kit-0.25.3-1.fc38.x86_64 139/154 Verifying : p11-kit-trust-0.25.3-1.fc38.x86_64 140/154 Verifying : package-notes-srpm-macros-0.5-8.fc38.noarch 141/154 Verifying : publicsuffix-list-dafsa-20240107-1.fc38.noarch 142/154 Verifying : pyproject-srpm-macros-1.12.0-1.fc38.noarch 143/154 Verifying : qt5-srpm-macros-5.15.12-1.fc38.noarch 144/154 Verifying : qt6-srpm-macros-6.6.0-1.fc38.noarch 145/154 Verifying : readline-8.2-4.fc38.x86_64 146/154 Verifying : redhat-rpm-config-257-1.fc38.noarch 147/154 Verifying : rpm-sequoia-1.6.0-1.fc38.x86_64 148/154 Verifying : rpmautospec-rpm-macros-0.6.3-1.fc38.noarch 149/154 Verifying : systemd-libs-253.17-1.fc38.x86_64 150/154 Verifying : tzdata-2024a-1.fc38.noarch 151/154 Verifying : xxhash-libs-0.8.2-1.fc38.x86_64 152/154 Verifying : zip-3.0-37.fc38.x86_64 153/154 Verifying : zstd-1.5.5-1.fc38.x86_64 154/154 Installed: alternatives-1.26-1.fc38.x86_64 ansible-srpm-macros-1-12.fc38.noarch audit-libs-3.1.2-8.fc38.x86_64 authselect-1.4.3-1.fc38.x86_64 authselect-libs-1.4.3-1.fc38.x86_64 basesystem-11-15.fc38.noarch bash-5.2.26-1.fc38.x86_64 binutils-2.39-16.fc38.x86_64 binutils-gold-2.39-16.fc38.x86_64 bzip2-1.0.8-13.fc38.x86_64 bzip2-libs-1.0.8-13.fc38.x86_64 ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noarch coreutils-9.1-12.fc38.x86_64 coreutils-common-9.1-12.fc38.x86_64 cpio-2.13-14.fc38.x86_64 cracklib-2.9.11-1.fc38.x86_64 crypto-policies-20230301-1.gita12f7b2.fc38.noarch curl-8.0.1-7.fc38.x86_64 cyrus-sasl-lib-2.1.28-9.fc38.x86_64 debugedit-5.0-9.fc38.x86_64 diffutils-3.10-1.fc38.x86_64 dwz-0.15-2.fc38.x86_64 ed-1.19-2.fc38.x86_64 efi-srpm-macros-5-7.fc38.noarch elfutils-0.191-1.fc38.x86_64 elfutils-debuginfod-client-0.191-1.fc38.x86_64 elfutils-default-yama-scope-0.191-1.fc38.noarch elfutils-libelf-0.191-1.fc38.x86_64 elfutils-libs-0.191-1.fc38.x86_64 fedora-gpg-keys-38-1.noarch fedora-release-38-36.noarch fedora-release-common-38-36.noarch fedora-release-identity-basic-38-36.noarch fedora-repos-38-1.noarch file-5.45-5.fc38.x86_64 file-libs-5.45-5.fc38.x86_64 filesystem-3.18-3.fc38.x86_64 findutils-1:4.9.0-3.fc38.x86_64 fonts-srpm-macros-1:2.0.5-11.fc38.noarch forge-srpm-macros-0.2.0-3.fc38.noarch fpc-srpm-macros-1.3-7.fc38.noarch gawk-5.1.1-5.fc38.x86_64 gdb-minimal-14.1-3.fc38.x86_64 gdbm-libs-1:1.23-3.fc38.x86_64 ghc-srpm-macros-1.6.1-1.fc38.noarch glibc-2.37-18.fc38.x86_64 glibc-common-2.37-18.fc38.x86_64 glibc-gconv-extra-2.37-18.fc38.x86_64 glibc-minimal-langpack-2.37-18.fc38.x86_64 gmp-1:6.2.1-4.fc38.x86_64 gnat-srpm-macros-6-2.fc38.noarch go-srpm-macros-3.5.0-1.fc38.noarch grep-3.8-3.fc38.x86_64 gzip-1.12-3.fc38.x86_64 info-7.0.2-2.fc38.x86_64 jansson-2.13.1-6.fc38.x86_64 kernel-srpm-macros-1.0-19.fc38.noarch keyutils-libs-1.6.3-1.fc38.x86_64 krb5-libs-1.21-3.fc38.x86_64 libacl-2.3.1-7.fc38.x86_64 libarchive-3.6.1-4.fc38.x86_64 libattr-2.5.1-6.fc38.x86_64 libblkid-2.39.1-2.fc38.x86_64 libbrotli-1.1.0-3.fc38.x86_64 libcap-2.48-8.fc38.x86_64 libcap-ng-0.8.5-1.fc38.x86_64 libcom_err-1.46.5-4.fc38.x86_64 libcurl-8.0.1-7.fc38.x86_64 libdb-5.3.28-55.fc38.x86_64 libeconf-0.5.2-1.fc38.x86_64 libevent-2.1.12-8.fc38.x86_64 libfdisk-2.39.1-2.fc38.x86_64 libffi-3.4.4-2.fc38.x86_64 libgcc-13.2.1-7.fc38.x86_64 libgomp-13.2.1-7.fc38.x86_64 libidn2-2.3.7-1.fc38.x86_64 libmount-2.39.1-2.fc38.x86_64 libnghttp2-1.52.0-2.fc38.x86_64 libnsl2-2.0.0-5.fc38.x86_64 libpkgconf-1.8.0-6.fc38.x86_64 libpsl-0.21.2-2.fc38.x86_64 libpwquality-1.4.5-9.fc38.x86_64 libselinux-3.5-4.fc38.x86_64 libsemanage-3.5-4.fc38.x86_64 libsepol-3.5-1.fc38.x86_64 libsigsegv-2.14-4.fc38.x86_64 libsmartcols-2.39.1-2.fc38.x86_64 libssh-0.10.6-2.fc38.x86_64 libssh-config-0.10.6-2.fc38.noarch libstdc++-13.2.1-7.fc38.x86_64 libtasn1-4.19.0-2.fc38.x86_64 libtirpc-1.3.4-1.rc3.fc38.x86_64 libunistring-1.1-3.fc38.x86_64 libunistring1.0-1.0-1.fc38.x86_64 libutempter-1.2.1-8.fc38.x86_64 libuuid-2.39.1-2.fc38.x86_64 libverto-0.3.2-5.fc38.x86_64 libxcrypt-4.4.36-1.fc38.x86_64 libxml2-2.12.6-1.fc38.x86_64 libzstd-1.5.5-1.fc38.x86_64 lua-libs-5.4.4-9.fc38.x86_64 lua-srpm-macros-1-13.fc38.noarch lz4-libs-1.9.4-2.fc38.x86_64 mpfr-4.1.1-3.fc38.x86_64 ncurses-base-6.4-7.20230520.fc38.1.noarch ncurses-libs-6.4-7.20230520.fc38.1.x86_64 ocaml-srpm-macros-7-3.fc38.noarch openblas-srpm-macros-2-13.fc38.noarch openldap-2.6.6-1.fc38.x86_64 openssl-libs-1:3.0.9-2.fc38.x86_64 p11-kit-0.25.3-1.fc38.x86_64 p11-kit-trust-0.25.3-1.fc38.x86_64 package-notes-srpm-macros-0.5-8.fc38.noarch pam-1.5.2-16.fc38.x86_64 pam-libs-1.5.2-16.fc38.x86_64 patch-2.7.6-19.fc38.x86_64 pcre2-10.42-1.fc38.1.x86_64 pcre2-syntax-10.42-1.fc38.1.noarch perl-srpm-macros-1-48.fc38.noarch pkgconf-1.8.0-6.fc38.x86_64 pkgconf-m4-1.8.0-6.fc38.noarch pkgconf-pkg-config-1.8.0-6.fc38.x86_64 popt-1.19-2.fc38.x86_64 publicsuffix-list-dafsa-20240107-1.fc38.noarch pyproject-srpm-macros-1.12.0-1.fc38.noarch python-srpm-macros-3.11-10.fc38.noarch qt5-srpm-macros-5.15.12-1.fc38.noarch qt6-srpm-macros-6.6.0-1.fc38.noarch readline-8.2-4.fc38.x86_64 redhat-rpm-config-257-1.fc38.noarch rpm-4.18.91-3.fc38.x86_64 rpm-build-4.18.91-3.fc38.x86_64 rpm-build-libs-4.18.91-3.fc38.x86_64 rpm-libs-4.18.91-3.fc38.x86_64 rpm-sequoia-1.6.0-1.fc38.x86_64 rpmautospec-rpm-macros-0.6.3-1.fc38.noarch rust-srpm-macros-26.2-1.fc38.noarch sed-4.8-12.fc38.x86_64 setup-2.14.3-2.fc38.noarch shadow-utils-2:4.13-6.fc38.x86_64 sqlite-libs-3.40.1-2.fc38.x86_64 systemd-libs-253.17-1.fc38.x86_64 tar-2:1.34-8.fc38.x86_64 tzdata-2024a-1.fc38.noarch unzip-6.0-60.fc38.x86_64 util-linux-2.39.1-2.fc38.x86_64 util-linux-core-2.39.1-2.fc38.x86_64 which-2.21-39.fc38.x86_64 xxhash-libs-0.8.2-1.fc38.x86_64 xz-5.4.1-1.fc38.x86_64 xz-libs-5.4.1-1.fc38.x86_64 zip-3.0-37.fc38.x86_64 zlib-1.2.13-3.fc38.x86_64 zstd-1.5.5-1.fc38.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-1.26-1.fc38.x86_64 ansible-srpm-macros-1-12.fc38.noarch audit-libs-3.1.2-8.fc38.x86_64 authselect-1.4.3-1.fc38.x86_64 authselect-libs-1.4.3-1.fc38.x86_64 basesystem-11-15.fc38.noarch bash-5.2.26-1.fc38.x86_64 binutils-2.39-16.fc38.x86_64 binutils-gold-2.39-16.fc38.x86_64 bzip2-1.0.8-13.fc38.x86_64 bzip2-libs-1.0.8-13.fc38.x86_64 ca-certificates-2023.2.60_v7.0.306-1.0.fc38.noarch coreutils-9.1-12.fc38.x86_64 coreutils-common-9.1-12.fc38.x86_64 cpio-2.13-14.fc38.x86_64 cracklib-2.9.11-1.fc38.x86_64 crypto-policies-20230301-1.gita12f7b2.fc38.noarch curl-8.0.1-7.fc38.x86_64 cyrus-sasl-lib-2.1.28-9.fc38.x86_64 debugedit-5.0-9.fc38.x86_64 diffutils-3.10-1.fc38.x86_64 dwz-0.15-2.fc38.x86_64 ed-1.19-2.fc38.x86_64 efi-srpm-macros-5-7.fc38.noarch elfutils-0.191-1.fc38.x86_64 elfutils-debuginfod-client-0.191-1.fc38.x86_64 elfutils-default-yama-scope-0.191-1.fc38.noarch elfutils-libelf-0.191-1.fc38.x86_64 elfutils-libs-0.191-1.fc38.x86_64 fedora-gpg-keys-38-1.noarch fedora-release-38-36.noarch fedora-release-common-38-36.noarch fedora-release-identity-basic-38-36.noarch fedora-repos-38-1.noarch file-5.45-5.fc38.x86_64 file-libs-5.45-5.fc38.x86_64 filesystem-3.18-3.fc38.x86_64 findutils-4.9.0-3.fc38.x86_64 fonts-srpm-macros-2.0.5-11.fc38.noarch forge-srpm-macros-0.2.0-3.fc38.noarch fpc-srpm-macros-1.3-7.fc38.noarch gawk-5.1.1-5.fc38.x86_64 gdb-minimal-14.1-3.fc38.x86_64 gdbm-libs-1.23-3.fc38.x86_64 ghc-srpm-macros-1.6.1-1.fc38.noarch glibc-2.37-18.fc38.x86_64 glibc-common-2.37-18.fc38.x86_64 glibc-gconv-extra-2.37-18.fc38.x86_64 glibc-minimal-langpack-2.37-18.fc38.x86_64 gmp-6.2.1-4.fc38.x86_64 gnat-srpm-macros-6-2.fc38.noarch go-srpm-macros-3.5.0-1.fc38.noarch gpg-pubkey-eb10b464-6202d9c6 grep-3.8-3.fc38.x86_64 gzip-1.12-3.fc38.x86_64 info-7.0.2-2.fc38.x86_64 jansson-2.13.1-6.fc38.x86_64 kernel-srpm-macros-1.0-19.fc38.noarch keyutils-libs-1.6.3-1.fc38.x86_64 krb5-libs-1.21-3.fc38.x86_64 libacl-2.3.1-7.fc38.x86_64 libarchive-3.6.1-4.fc38.x86_64 libattr-2.5.1-6.fc38.x86_64 libblkid-2.39.1-2.fc38.x86_64 libbrotli-1.1.0-3.fc38.x86_64 libcap-2.48-8.fc38.x86_64 libcap-ng-0.8.5-1.fc38.x86_64 libcom_err-1.46.5-4.fc38.x86_64 libcurl-8.0.1-7.fc38.x86_64 libdb-5.3.28-55.fc38.x86_64 libeconf-0.5.2-1.fc38.x86_64 libevent-2.1.12-8.fc38.x86_64 libfdisk-2.39.1-2.fc38.x86_64 libffi-3.4.4-2.fc38.x86_64 libgcc-13.2.1-7.fc38.x86_64 libgomp-13.2.1-7.fc38.x86_64 libidn2-2.3.7-1.fc38.x86_64 libmount-2.39.1-2.fc38.x86_64 libnghttp2-1.52.0-2.fc38.x86_64 libnsl2-2.0.0-5.fc38.x86_64 libpkgconf-1.8.0-6.fc38.x86_64 libpsl-0.21.2-2.fc38.x86_64 libpwquality-1.4.5-9.fc38.x86_64 libselinux-3.5-4.fc38.x86_64 libsemanage-3.5-4.fc38.x86_64 libsepol-3.5-1.fc38.x86_64 libsigsegv-2.14-4.fc38.x86_64 libsmartcols-2.39.1-2.fc38.x86_64 libssh-0.10.6-2.fc38.x86_64 libssh-config-0.10.6-2.fc38.noarch libstdc++-13.2.1-7.fc38.x86_64 libtasn1-4.19.0-2.fc38.x86_64 libtirpc-1.3.4-1.rc3.fc38.x86_64 libunistring-1.1-3.fc38.x86_64 libunistring1.0-1.0-1.fc38.x86_64 libutempter-1.2.1-8.fc38.x86_64 libuuid-2.39.1-2.fc38.x86_64 libverto-0.3.2-5.fc38.x86_64 libxcrypt-4.4.36-1.fc38.x86_64 libxml2-2.12.6-1.fc38.x86_64 libzstd-1.5.5-1.fc38.x86_64 lua-libs-5.4.4-9.fc38.x86_64 lua-srpm-macros-1-13.fc38.noarch lz4-libs-1.9.4-2.fc38.x86_64 mpfr-4.1.1-3.fc38.x86_64 ncurses-base-6.4-7.20230520.fc38.1.noarch ncurses-libs-6.4-7.20230520.fc38.1.x86_64 ocaml-srpm-macros-7-3.fc38.noarch openblas-srpm-macros-2-13.fc38.noarch openldap-2.6.6-1.fc38.x86_64 openssl-libs-3.0.9-2.fc38.x86_64 p11-kit-0.25.3-1.fc38.x86_64 p11-kit-trust-0.25.3-1.fc38.x86_64 package-notes-srpm-macros-0.5-8.fc38.noarch pam-1.5.2-16.fc38.x86_64 pam-libs-1.5.2-16.fc38.x86_64 patch-2.7.6-19.fc38.x86_64 pcre2-10.42-1.fc38.1.x86_64 pcre2-syntax-10.42-1.fc38.1.noarch perl-srpm-macros-1-48.fc38.noarch pkgconf-1.8.0-6.fc38.x86_64 pkgconf-m4-1.8.0-6.fc38.noarch pkgconf-pkg-config-1.8.0-6.fc38.x86_64 popt-1.19-2.fc38.x86_64 publicsuffix-list-dafsa-20240107-1.fc38.noarch pyproject-srpm-macros-1.12.0-1.fc38.noarch python-srpm-macros-3.11-10.fc38.noarch qt5-srpm-macros-5.15.12-1.fc38.noarch qt6-srpm-macros-6.6.0-1.fc38.noarch readline-8.2-4.fc38.x86_64 redhat-rpm-config-257-1.fc38.noarch rpm-4.18.91-3.fc38.x86_64 rpm-build-4.18.91-3.fc38.x86_64 rpm-build-libs-4.18.91-3.fc38.x86_64 rpm-libs-4.18.91-3.fc38.x86_64 rpm-sequoia-1.6.0-1.fc38.x86_64 rpmautospec-rpm-macros-0.6.3-1.fc38.noarch rust-srpm-macros-26.2-1.fc38.noarch sed-4.8-12.fc38.x86_64 setup-2.14.3-2.fc38.noarch shadow-utils-4.13-6.fc38.x86_64 sqlite-libs-3.40.1-2.fc38.x86_64 systemd-libs-253.17-1.fc38.x86_64 tar-1.34-8.fc38.x86_64 tzdata-2024a-1.fc38.noarch unzip-6.0-60.fc38.x86_64 util-linux-2.39.1-2.fc38.x86_64 util-linux-core-2.39.1-2.fc38.x86_64 which-2.21-39.fc38.x86_64 xxhash-libs-0.8.2-1.fc38.x86_64 xz-5.4.1-1.fc38.x86_64 xz-libs-5.4.1-1.fc38.x86_64 zip-3.0-37.fc38.x86_64 zlib-1.2.13-3.fc38.x86_64 zstd-1.5.5-1.fc38.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-38-x86_64-1713011165.797942/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-38-x86_64-1713011165.797942/root/var/log/dnf.log /var/lib/mock/fedora-38-x86_64-1713011165.797942/root/var/log/dnf.librepo.log /var/lib/mock/fedora-38-x86_64-1713011165.797942/root/var/log/dnf.rpm.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-y9fh2ob9/python-biopython/python-biopython.spec) Config(child) 1 minutes 40 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-1.83-5.fc38.src.rpm) Config(fedora-38-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-38-x86_64-bootstrap-1713011165.797942/root. INFO: reusing tmpfs at /var/lib/mock/fedora-38-x86_64-bootstrap-1713011165.797942/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-38-x86_64-1713011165.797942/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-4.18.91-3.fc38.x86_64 rpm-sequoia-1.5.0-2.fc38.x86_64 python3-dnf-4.19.2-1.fc38.noarch python3-dnf-plugins-core-4.6.0-1.fc38.noarch yum-4.19.2-1.fc38.noarch Finish: chroot init Start: build phase for python-biopython-1.83-5.fc38.src.rpm Start: build setup for python-biopython-1.83-5.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 30 kB/s | 1.5 kB 00:00 fedora 73 kB/s | 24 kB 00:00 updates 223 kB/s | 22 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc x86_64 13.2.1-7.fc38 updates 34 M pyproject-rpm-macros noarch 1.12.0-1.fc38 updates 41 k python3-devel x86_64 3.11.8-2.fc38 updates 270 k python3-reportlab noarch 4.0.4-2.fc38 updates 3.4 M Installing dependencies: annobin-docs noarch 12.40-1.fc38 updates 87 k annobin-plugin-gcc x86_64 12.40-1.fc38 updates 955 k cairo x86_64 1.17.8-4.fc38 updates 704 k cpp x86_64 13.2.1-7.fc38 updates 11 M dejavu-sans-fonts noarch 2.37-20.fc38 fedora 1.3 M expat x86_64 2.6.0-1.fc38 updates 112 k fontconfig x86_64 2.14.2-2.fc38 updates 295 k fonts-filesystem noarch 1:2.0.5-11.fc38 fedora 8.1 k freetype x86_64 2.13.0-2.fc38 fedora 414 k fribidi x86_64 1.0.12-3.fc38 fedora 89 k gc x86_64 8.2.2-3.fc38 fedora 110 k gcc-plugin-annobin x86_64 13.2.1-7.fc38 updates 52 k glib2 x86_64 2.76.6-1.fc38 updates 2.8 M glibc-devel x86_64 2.37-18.fc38 updates 54 k glibc-headers-x86 noarch 2.37-18.fc38 updates 536 k gnutls x86_64 3.8.4-1.fc38 updates 1.1 M google-noto-fonts-common noarch 20230201-2.fc38 updates 16 k google-noto-sans-vf-fonts noarch 20230201-2.fc38 updates 579 k graphite2 x86_64 1.3.14-11.fc38 fedora 95 k guile22 x86_64 2.2.7-7.fc38 fedora 6.5 M harfbuzz x86_64 7.1.0-1.fc38 fedora 889 k jbigkit-libs x86_64 2.1-25.fc38 fedora 53 k kernel-headers x86_64 6.8.3-100.fc38 updates 1.6 M langpacks-core-font-en noarch 3.0-32.fc38 updates 9.6 k lcms2 x86_64 2.15-1.fc38 fedora 178 k libX11 x86_64 1.8.7-1.fc38 updates 650 k libX11-common noarch 1.8.7-1.fc38 updates 176 k libXau x86_64 1.0.11-2.fc38 fedora 32 k libXext x86_64 1.3.5-2.fc38 fedora 39 k libXrender x86_64 0.9.11-2.fc38 fedora 27 k libb2 x86_64 0.98.1-8.fc38 fedora 25 k libimagequant x86_64 2.17.0-4.fc38 fedora 63 k libjpeg-turbo x86_64 2.1.4-2.fc38 fedora 183 k liblerc x86_64 4.0.0-3.fc38 fedora 202 k libmpc x86_64 1.3.1-2.fc38 fedora 70 k libpng x86_64 2:1.6.37-14.fc38 fedora 120 k libraqm x86_64 0.8.0-4.fc38 fedora 20 k libtiff x86_64 4.4.0-8.fc38 updates 201 k libtool-ltdl x86_64 2.4.7-6.fc38 fedora 37 k libwebp x86_64 1.3.2-2.fc38 updates 284 k libxcb x86_64 1.13.1-11.fc38 fedora 231 k libxcrypt-devel x86_64 4.4.36-1.fc38 updates 30 k make x86_64 1:4.4.1-1.fc38 updates 588 k mpdecimal x86_64 2.5.1-6.fc38 fedora 89 k nettle x86_64 3.8-3.fc38 fedora 412 k openjpeg2 x86_64 2.5.2-1.fc38 updates 178 k pixman x86_64 0.42.2-1.fc38 fedora 285 k python-pip-wheel noarch 23.1.2-6.fc38 copr_base 1.4 M python-rpm-macros noarch 3.11-10.fc38 fedora 20 k python-setuptools-wheel noarch 69.0.3-3.fc38 copr_base 680 k python3 x86_64 3.11.8-2.fc38 updates 28 k python3-libs x86_64 3.11.8-2.fc38 updates 9.6 M python3-olefile noarch 0.46-19.fc38 copr_base 68 k python3-packaging noarch 23.2-1.fc38 copr_base 119 k python3-pillow x86_64 10.3.0-1.fc38 copr_base 923 k python3-rpm-generators noarch 14-4.fc38 updates 30 k python3-rpm-macros noarch 3.11-10.fc38 fedora 15 k xml-common noarch 0.6.3-60.fc38 fedora 31 k Transaction Summary ================================================================================ Install 62 Packages Total download size: 84 M Installed size: 284 M Downloading Packages: (1/62): python3-olefile-0.46-19.fc38.noarch.rpm 888 kB/s | 68 kB 00:00 (2/62): python-setuptools-wheel-69.0.3-3.fc38.n 7.1 MB/s | 680 kB 00:00 (3/62): python3-packaging-23.2-1.fc38.noarch.rp 3.2 MB/s | 119 kB 00:00 (4/62): python-pip-wheel-23.1.2-6.fc38.noarch.r 12 MB/s | 1.4 MB 00:00 (5/62): python3-pillow-10.3.0-1.fc38.x86_64.rpm 28 MB/s | 923 kB 00:00 (6/62): fonts-filesystem-2.0.5-11.fc38.noarch.r 54 kB/s | 8.1 kB 00:00 (7/62): fribidi-1.0.12-3.fc38.x86_64.rpm 413 kB/s | 89 kB 00:00 (8/62): gc-8.2.2-3.fc38.x86_64.rpm 768 kB/s | 110 kB 00:00 (9/62): freetype-2.13.0-2.fc38.x86_64.rpm 816 kB/s | 414 kB 00:00 (10/62): dejavu-sans-fonts-2.37-20.fc38.noarch. 2.3 MB/s | 1.3 MB 00:00 (11/62): graphite2-1.3.14-11.fc38.x86_64.rpm 1.2 MB/s | 95 kB 00:00 (12/62): harfbuzz-7.1.0-1.fc38.x86_64.rpm 11 MB/s | 889 kB 00:00 (13/62): jbigkit-libs-2.1-25.fc38.x86_64.rpm 673 kB/s | 53 kB 00:00 (14/62): lcms2-2.15-1.fc38.x86_64.rpm 2.4 MB/s | 178 kB 00:00 (15/62): libXau-1.0.11-2.fc38.x86_64.rpm 432 kB/s | 32 kB 00:00 (16/62): libXext-1.3.5-2.fc38.x86_64.rpm 532 kB/s | 39 kB 00:00 (17/62): libXrender-0.9.11-2.fc38.x86_64.rpm 368 kB/s | 27 kB 00:00 (18/62): libb2-0.98.1-8.fc38.x86_64.rpm 356 kB/s | 25 kB 00:00 (19/62): libimagequant-2.17.0-4.fc38.x86_64.rpm 866 kB/s | 63 kB 00:00 (20/62): guile22-2.2.7-7.fc38.x86_64.rpm 17 MB/s | 6.5 MB 00:00 (21/62): libjpeg-turbo-2.1.4-2.fc38.x86_64.rpm 2.4 MB/s | 183 kB 00:00 (22/62): liblerc-4.0.0-3.fc38.x86_64.rpm 2.7 MB/s | 202 kB 00:00 (23/62): libmpc-1.3.1-2.fc38.x86_64.rpm 975 kB/s | 70 kB 00:00 (24/62): libpng-1.6.37-14.fc38.x86_64.rpm 1.6 MB/s | 120 kB 00:00 (25/62): libraqm-0.8.0-4.fc38.x86_64.rpm 279 kB/s | 20 kB 00:00 (26/62): libtool-ltdl-2.4.7-6.fc38.x86_64.rpm 507 kB/s | 37 kB 00:00 (27/62): libxcb-1.13.1-11.fc38.x86_64.rpm 3.1 MB/s | 231 kB 00:00 (28/62): mpdecimal-2.5.1-6.fc38.x86_64.rpm 1.2 MB/s | 89 kB 00:00 (29/62): nettle-3.8-3.fc38.x86_64.rpm 5.3 MB/s | 412 kB 00:00 (30/62): pixman-0.42.2-1.fc38.x86_64.rpm 3.7 MB/s | 285 kB 00:00 (31/62): python-rpm-macros-3.11-10.fc38.noarch. 268 kB/s | 20 kB 00:00 (32/62): python3-rpm-macros-3.11-10.fc38.noarch 209 kB/s | 15 kB 00:00 (33/62): xml-common-0.6.3-60.fc38.noarch.rpm 428 kB/s | 31 kB 00:00 (34/62): annobin-docs-12.40-1.fc38.noarch.rpm 535 kB/s | 87 kB 00:00 (35/62): annobin-plugin-gcc-12.40-1.fc38.x86_64 3.9 MB/s | 955 kB 00:00 (36/62): cairo-1.17.8-4.fc38.x86_64.rpm 3.0 MB/s | 704 kB 00:00 (37/62): expat-2.6.0-1.fc38.x86_64.rpm 2.3 MB/s | 112 kB 00:00 (38/62): fontconfig-2.14.2-2.fc38.x86_64.rpm 4.5 MB/s | 295 kB 00:00 (39/62): gcc-plugin-annobin-13.2.1-7.fc38.x86_6 1.3 MB/s | 52 kB 00:00 (40/62): glib2-2.76.6-1.fc38.x86_64.rpm 19 MB/s | 2.8 MB 00:00 (41/62): cpp-13.2.1-7.fc38.x86_64.rpm 27 MB/s | 11 MB 00:00 (42/62): glibc-devel-2.37-18.fc38.x86_64.rpm 1.2 MB/s | 54 kB 00:00 (43/62): glibc-headers-x86-2.37-18.fc38.noarch. 12 MB/s | 536 kB 00:00 (44/62): google-noto-fonts-common-20230201-2.fc 477 kB/s | 16 kB 00:00 (45/62): gnutls-3.8.4-1.fc38.x86_64.rpm 16 MB/s | 1.1 MB 00:00 (46/62): google-noto-sans-vf-fonts-20230201-2.f 11 MB/s | 579 kB 00:00 (47/62): kernel-headers-6.8.3-100.fc38.x86_64.r 19 MB/s | 1.6 MB 00:00 (48/62): langpacks-core-font-en-3.0-32.fc38.noa 180 kB/s | 9.6 kB 00:00 (49/62): libX11-common-1.8.7-1.fc38.noarch.rpm 4.3 MB/s | 176 kB 00:00 (50/62): libX11-1.8.7-1.fc38.x86_64.rpm 12 MB/s | 650 kB 00:00 (51/62): libtiff-4.4.0-8.fc38.x86_64.rpm 4.5 MB/s | 201 kB 00:00 (52/62): libwebp-1.3.2-2.fc38.x86_64.rpm 5.0 MB/s | 284 kB 00:00 (53/62): libxcrypt-devel-4.4.36-1.fc38.x86_64.r 703 kB/s | 30 kB 00:00 (54/62): make-4.4.1-1.fc38.x86_64.rpm 11 MB/s | 588 kB 00:00 (55/62): openjpeg2-2.5.2-1.fc38.x86_64.rpm 3.2 MB/s | 178 kB 00:00 (56/62): python3-3.11.8-2.fc38.x86_64.rpm 421 kB/s | 28 kB 00:00 (57/62): pyproject-rpm-macros-1.12.0-1.fc38.noa 295 kB/s | 41 kB 00:00 (58/62): python3-devel-3.11.8-2.fc38.x86_64.rpm 4.7 MB/s | 270 kB 00:00 (59/62): gcc-13.2.1-7.fc38.x86_64.rpm 40 MB/s | 34 MB 00:00 (60/62): python3-reportlab-4.0.4-2.fc38.noarch. 28 MB/s | 3.4 MB 00:00 (61/62): python3-rpm-generators-14-4.fc38.noarc 573 kB/s | 30 kB 00:00 (62/62): python3-libs-3.11.8-2.fc38.x86_64.rpm 46 MB/s | 9.6 MB 00:00 -------------------------------------------------------------------------------- Total 26 MB/s | 84 MB 00:03 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.11-10.fc38.noarch 1/62 Installing : fonts-filesystem-1:2.0.5-11.fc38.noarch 2/62 Installing : python3-rpm-macros-3.11-10.fc38.noarch 3/62 Installing : libwebp-1.3.2-2.fc38.x86_64 4/62 Installing : libpng-2:1.6.37-14.fc38.x86_64 5/62 Installing : libmpc-1.3.1-2.fc38.x86_64 6/62 Installing : libjpeg-turbo-2.1.4-2.fc38.x86_64 7/62 Installing : cpp-13.2.1-7.fc38.x86_64 8/62 Installing : pyproject-rpm-macros-1.12.0-1.fc38.noarch 9/62 Installing : dejavu-sans-fonts-2.37-20.fc38.noarch 10/62 Installing : openjpeg2-2.5.2-1.fc38.x86_64 11/62 Installing : libX11-common-1.8.7-1.fc38.noarch 12/62 Installing : kernel-headers-6.8.3-100.fc38.x86_64 13/62 Installing : google-noto-fonts-common-20230201-2.fc38.noarch 14/62 Installing : google-noto-sans-vf-fonts-20230201-2.fc38.noarch 15/62 Installing : langpacks-core-font-en-3.0-32.fc38.noarch 16/62 Installing : glibc-headers-x86-2.37-18.fc38.noarch 17/62 Installing : libxcrypt-devel-4.4.36-1.fc38.x86_64 18/62 Installing : glibc-devel-2.37-18.fc38.x86_64 19/62 Installing : expat-2.6.0-1.fc38.x86_64 20/62 Installing : annobin-docs-12.40-1.fc38.noarch 21/62 Running scriptlet: xml-common-0.6.3-60.fc38.noarch 22/62 Installing : xml-common-0.6.3-60.fc38.noarch 22/62 Installing : pixman-0.42.2-1.fc38.x86_64 23/62 Installing : nettle-3.8-3.fc38.x86_64 24/62 Installing : gnutls-3.8.4-1.fc38.x86_64 25/62 Installing : glib2-2.76.6-1.fc38.x86_64 26/62 Installing : mpdecimal-2.5.1-6.fc38.x86_64 27/62 Installing : libtool-ltdl-2.4.7-6.fc38.x86_64 28/62 Installing : liblerc-4.0.0-3.fc38.x86_64 29/62 Installing : libimagequant-2.17.0-4.fc38.x86_64 30/62 Installing : libb2-0.98.1-8.fc38.x86_64 31/62 Installing : libXau-1.0.11-2.fc38.x86_64 32/62 Installing : libxcb-1.13.1-11.fc38.x86_64 33/62 Installing : libX11-1.8.7-1.fc38.x86_64 34/62 Installing : libXext-1.3.5-2.fc38.x86_64 35/62 Installing : libXrender-0.9.11-2.fc38.x86_64 36/62 Installing : lcms2-2.15-1.fc38.x86_64 37/62 Installing : jbigkit-libs-2.1-25.fc38.x86_64 38/62 Installing : libtiff-4.4.0-8.fc38.x86_64 39/62 Installing : graphite2-1.3.14-11.fc38.x86_64 40/62 Installing : cairo-1.17.8-4.fc38.x86_64 41/62 Installing : harfbuzz-7.1.0-1.fc38.x86_64 42/62 Installing : freetype-2.13.0-2.fc38.x86_64 43/62 Installing : fontconfig-2.14.2-2.fc38.x86_64 44/62 Running scriptlet: fontconfig-2.14.2-2.fc38.x86_64 44/62 Installing : gc-8.2.2-3.fc38.x86_64 45/62 Installing : guile22-2.2.7-7.fc38.x86_64 46/62 Installing : make-1:4.4.1-1.fc38.x86_64 47/62 Installing : gcc-13.2.1-7.fc38.x86_64 48/62 Running scriptlet: gcc-13.2.1-7.fc38.x86_64 48/62 Installing : fribidi-1.0.12-3.fc38.x86_64 49/62 Installing : libraqm-0.8.0-4.fc38.x86_64 50/62 Installing : python-setuptools-wheel-69.0.3-3.fc38.noarch 51/62 Installing : python-pip-wheel-23.1.2-6.fc38.noarch 52/62 Installing : python3-3.11.8-2.fc38.x86_64 53/62 Installing : python3-libs-3.11.8-2.fc38.x86_64 54/62 Installing : python3-olefile-0.46-19.fc38.noarch 55/62 Installing : python3-pillow-10.3.0-1.fc38.x86_64 56/62 Installing : python3-packaging-23.2-1.fc38.noarch 57/62 Installing : python3-rpm-generators-14-4.fc38.noarch 58/62 Installing : python3-devel-3.11.8-2.fc38.x86_64 59/62 Installing : python3-reportlab-4.0.4-2.fc38.noarch 60/62 Installing : annobin-plugin-gcc-12.40-1.fc38.x86_64 61/62 Running scriptlet: annobin-plugin-gcc-12.40-1.fc38.x86_64 61/62 Installing : gcc-plugin-annobin-13.2.1-7.fc38.x86_64 62/62 Running scriptlet: gcc-plugin-annobin-13.2.1-7.fc38.x86_64 62/62 Running scriptlet: fontconfig-2.14.2-2.fc38.x86_64 62/62 Running scriptlet: gcc-plugin-annobin-13.2.1-7.fc38.x86_64 62/62 Verifying : python-pip-wheel-23.1.2-6.fc38.noarch 1/62 Verifying : python-setuptools-wheel-69.0.3-3.fc38.noarch 2/62 Verifying : python3-olefile-0.46-19.fc38.noarch 3/62 Verifying : python3-packaging-23.2-1.fc38.noarch 4/62 Verifying : python3-pillow-10.3.0-1.fc38.x86_64 5/62 Verifying : dejavu-sans-fonts-2.37-20.fc38.noarch 6/62 Verifying : fonts-filesystem-1:2.0.5-11.fc38.noarch 7/62 Verifying : freetype-2.13.0-2.fc38.x86_64 8/62 Verifying : fribidi-1.0.12-3.fc38.x86_64 9/62 Verifying : gc-8.2.2-3.fc38.x86_64 10/62 Verifying : graphite2-1.3.14-11.fc38.x86_64 11/62 Verifying : guile22-2.2.7-7.fc38.x86_64 12/62 Verifying : harfbuzz-7.1.0-1.fc38.x86_64 13/62 Verifying : jbigkit-libs-2.1-25.fc38.x86_64 14/62 Verifying : lcms2-2.15-1.fc38.x86_64 15/62 Verifying : libXau-1.0.11-2.fc38.x86_64 16/62 Verifying : libXext-1.3.5-2.fc38.x86_64 17/62 Verifying : libXrender-0.9.11-2.fc38.x86_64 18/62 Verifying : libb2-0.98.1-8.fc38.x86_64 19/62 Verifying : libimagequant-2.17.0-4.fc38.x86_64 20/62 Verifying : libjpeg-turbo-2.1.4-2.fc38.x86_64 21/62 Verifying : liblerc-4.0.0-3.fc38.x86_64 22/62 Verifying : libmpc-1.3.1-2.fc38.x86_64 23/62 Verifying : libpng-2:1.6.37-14.fc38.x86_64 24/62 Verifying : libraqm-0.8.0-4.fc38.x86_64 25/62 Verifying : libtool-ltdl-2.4.7-6.fc38.x86_64 26/62 Verifying : libxcb-1.13.1-11.fc38.x86_64 27/62 Verifying : mpdecimal-2.5.1-6.fc38.x86_64 28/62 Verifying : nettle-3.8-3.fc38.x86_64 29/62 Verifying : pixman-0.42.2-1.fc38.x86_64 30/62 Verifying : python-rpm-macros-3.11-10.fc38.noarch 31/62 Verifying : python3-rpm-macros-3.11-10.fc38.noarch 32/62 Verifying : xml-common-0.6.3-60.fc38.noarch 33/62 Verifying : annobin-docs-12.40-1.fc38.noarch 34/62 Verifying : annobin-plugin-gcc-12.40-1.fc38.x86_64 35/62 Verifying : cairo-1.17.8-4.fc38.x86_64 36/62 Verifying : cpp-13.2.1-7.fc38.x86_64 37/62 Verifying : expat-2.6.0-1.fc38.x86_64 38/62 Verifying : fontconfig-2.14.2-2.fc38.x86_64 39/62 Verifying : gcc-13.2.1-7.fc38.x86_64 40/62 Verifying : gcc-plugin-annobin-13.2.1-7.fc38.x86_64 41/62 Verifying : glib2-2.76.6-1.fc38.x86_64 42/62 Verifying : glibc-devel-2.37-18.fc38.x86_64 43/62 Verifying : glibc-headers-x86-2.37-18.fc38.noarch 44/62 Verifying : gnutls-3.8.4-1.fc38.x86_64 45/62 Verifying : google-noto-fonts-common-20230201-2.fc38.noarch 46/62 Verifying : google-noto-sans-vf-fonts-20230201-2.fc38.noarch 47/62 Verifying : kernel-headers-6.8.3-100.fc38.x86_64 48/62 Verifying : langpacks-core-font-en-3.0-32.fc38.noarch 49/62 Verifying : libX11-1.8.7-1.fc38.x86_64 50/62 Verifying : libX11-common-1.8.7-1.fc38.noarch 51/62 Verifying : libtiff-4.4.0-8.fc38.x86_64 52/62 Verifying : libwebp-1.3.2-2.fc38.x86_64 53/62 Verifying : libxcrypt-devel-4.4.36-1.fc38.x86_64 54/62 Verifying : make-1:4.4.1-1.fc38.x86_64 55/62 Verifying : openjpeg2-2.5.2-1.fc38.x86_64 56/62 Verifying : pyproject-rpm-macros-1.12.0-1.fc38.noarch 57/62 Verifying : python3-3.11.8-2.fc38.x86_64 58/62 Verifying : python3-devel-3.11.8-2.fc38.x86_64 59/62 Verifying : python3-libs-3.11.8-2.fc38.x86_64 60/62 Verifying : python3-reportlab-4.0.4-2.fc38.noarch 61/62 Verifying : python3-rpm-generators-14-4.fc38.noarch 62/62 Installed: annobin-docs-12.40-1.fc38.noarch annobin-plugin-gcc-12.40-1.fc38.x86_64 cairo-1.17.8-4.fc38.x86_64 cpp-13.2.1-7.fc38.x86_64 dejavu-sans-fonts-2.37-20.fc38.noarch expat-2.6.0-1.fc38.x86_64 fontconfig-2.14.2-2.fc38.x86_64 fonts-filesystem-1:2.0.5-11.fc38.noarch freetype-2.13.0-2.fc38.x86_64 fribidi-1.0.12-3.fc38.x86_64 gc-8.2.2-3.fc38.x86_64 gcc-13.2.1-7.fc38.x86_64 gcc-plugin-annobin-13.2.1-7.fc38.x86_64 glib2-2.76.6-1.fc38.x86_64 glibc-devel-2.37-18.fc38.x86_64 glibc-headers-x86-2.37-18.fc38.noarch gnutls-3.8.4-1.fc38.x86_64 google-noto-fonts-common-20230201-2.fc38.noarch google-noto-sans-vf-fonts-20230201-2.fc38.noarch graphite2-1.3.14-11.fc38.x86_64 guile22-2.2.7-7.fc38.x86_64 harfbuzz-7.1.0-1.fc38.x86_64 jbigkit-libs-2.1-25.fc38.x86_64 kernel-headers-6.8.3-100.fc38.x86_64 langpacks-core-font-en-3.0-32.fc38.noarch lcms2-2.15-1.fc38.x86_64 libX11-1.8.7-1.fc38.x86_64 libX11-common-1.8.7-1.fc38.noarch libXau-1.0.11-2.fc38.x86_64 libXext-1.3.5-2.fc38.x86_64 libXrender-0.9.11-2.fc38.x86_64 libb2-0.98.1-8.fc38.x86_64 libimagequant-2.17.0-4.fc38.x86_64 libjpeg-turbo-2.1.4-2.fc38.x86_64 liblerc-4.0.0-3.fc38.x86_64 libmpc-1.3.1-2.fc38.x86_64 libpng-2:1.6.37-14.fc38.x86_64 libraqm-0.8.0-4.fc38.x86_64 libtiff-4.4.0-8.fc38.x86_64 libtool-ltdl-2.4.7-6.fc38.x86_64 libwebp-1.3.2-2.fc38.x86_64 libxcb-1.13.1-11.fc38.x86_64 libxcrypt-devel-4.4.36-1.fc38.x86_64 make-1:4.4.1-1.fc38.x86_64 mpdecimal-2.5.1-6.fc38.x86_64 nettle-3.8-3.fc38.x86_64 openjpeg2-2.5.2-1.fc38.x86_64 pixman-0.42.2-1.fc38.x86_64 pyproject-rpm-macros-1.12.0-1.fc38.noarch python-pip-wheel-23.1.2-6.fc38.noarch python-rpm-macros-3.11-10.fc38.noarch python-setuptools-wheel-69.0.3-3.fc38.noarch python3-3.11.8-2.fc38.x86_64 python3-devel-3.11.8-2.fc38.x86_64 python3-libs-3.11.8-2.fc38.x86_64 python3-olefile-0.46-19.fc38.noarch python3-packaging-23.2-1.fc38.noarch python3-pillow-10.3.0-1.fc38.x86_64 python3-reportlab-4.0.4-2.fc38.noarch python3-rpm-generators-14-4.fc38.noarch python3-rpm-macros-3.11-10.fc38.noarch xml-common-0.6.3-60.fc38.noarch Complete! Finish: build setup for python-biopython-1.83-5.fc38.src.rpm Start: rpmbuild python-biopython-1.83-5.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.gXJnYi + 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 + /usr/bin/mkdir -p 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 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.cEZ2eH + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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=py311 + 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-1.83-5.fc38.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-1.83-5.fc38.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 26 kB/s | 1.5 kB 00:00 fedora 62 kB/s | 24 kB 00:00 updates 107 kB/s | 22 kB 00:00 Package gcc-13.2.1-7.fc38.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-packaging-23.2-1.fc38.noarch is already installed. Package python3-reportlab-4.0.4-2.fc38.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-pip noarch 23.1.2-6.fc38 copr_base 2.9 M python3-setuptools noarch 69.0.3-3.fc38 copr_base 1.4 M python3-wheel noarch 1:0.43.0-1.fc38 copr_base 153 k Transaction Summary ================================================================================ Install 3 Packages Total download size: 4.5 M Installed size: 23 M Downloading Packages: (1/3): python3-wheel-0.43.0-1.fc38.noarch.rpm 1.7 MB/s | 153 kB 00:00 (2/3): python3-setuptools-69.0.3-3.fc38.noarch. 11 MB/s | 1.4 MB 00:00 (3/3): python3-pip-23.1.2-6.fc38.noarch.rpm 21 MB/s | 2.9 MB 00:00 -------------------------------------------------------------------------------- Total 31 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-setuptools-69.0.3-3.fc38.noarch 1/3 Installing : python3-pip-23.1.2-6.fc38.noarch 2/3 Installing : python3-wheel-1:0.43.0-1.fc38.noarch 3/3 Running scriptlet: python3-wheel-1:0.43.0-1.fc38.noarch 3/3 Verifying : python3-pip-23.1.2-6.fc38.noarch 1/3 Verifying : python3-setuptools-69.0.3-3.fc38.noarch 2/3 Verifying : python3-wheel-1:0.43.0-1.fc38.noarch 3/3 Installed: python3-pip-23.1.2-6.fc38.noarch python3-setuptools-69.0.3-3.fc38.noarch python3-wheel-1:0.43.0-1.fc38.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.DvHet3 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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=py311 + 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-1.83-5.fc38.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.0.3) 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-1.83-5.fc38.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/top_level.txt' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/LICENSE.rst' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 28 kB/s | 1.5 kB 00:00 fedora 182 kB/s | 24 kB 00:00 updates 94 kB/s | 22 kB 00:00 Package gcc-13.2.1-7.fc38.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-packaging-23.2-1.fc38.noarch is already installed. Package python3-pip-23.1.2-6.fc38.noarch is already installed. Package python3-reportlab-4.0.4-2.fc38.noarch is already installed. Package python3-setuptools-69.0.3-3.fc38.noarch is already installed. Package python3-wheel-1:0.43.0-1.fc38.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-numpy x86_64 1:1.24.4-2.fc38 copr_base 7.7 M Installing dependencies: flexiblas x86_64 3.4.2-1.fc38 updates 25 k flexiblas-netlib x86_64 3.4.2-1.fc38 updates 3.1 M flexiblas-openblas-openmp x86_64 3.4.2-1.fc38 updates 17 k libgfortran x86_64 13.2.1-7.fc38 updates 910 k libquadmath x86_64 13.2.1-7.fc38 updates 200 k openblas x86_64 0.3.21-4.fc38 fedora 35 k openblas-openmp x86_64 0.3.21-4.fc38 fedora 5.1 M Transaction Summary ================================================================================ Install 8 Packages Total download size: 17 M Installed size: 99 M Downloading Packages: (1/8): python3-numpy-1.24.4-2.fc38.x86_64.rpm 43 MB/s | 7.7 MB 00:00 (2/8): openblas-0.3.21-4.fc38.x86_64.rpm 196 kB/s | 35 kB 00:00 (3/8): flexiblas-3.4.2-1.fc38.x86_64.rpm 134 kB/s | 25 kB 00:00 (4/8): openblas-openmp-0.3.21-4.fc38.x86_64.rpm 13 MB/s | 5.1 MB 00:00 (5/8): flexiblas-openblas-openmp-3.4.2-1.fc38.x 433 kB/s | 17 kB 00:00 (6/8): libquadmath-13.2.1-7.fc38.x86_64.rpm 667 kB/s | 200 kB 00:00 (7/8): libgfortran-13.2.1-7.fc38.x86_64.rpm 2.2 MB/s | 910 kB 00:00 (8/8): flexiblas-netlib-3.4.2-1.fc38.x86_64.rpm 3.7 MB/s | 3.1 MB 00:00 -------------------------------------------------------------------------------- Total 11 MB/s | 17 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libgfortran-13.2.1-7.fc38.x86_64 1/8 Installing : libquadmath-13.2.1-7.fc38.x86_64 2/8 Installing : openblas-0.3.21-4.fc38.x86_64 3/8 Installing : openblas-openmp-0.3.21-4.fc38.x86_64 4/8 Installing : flexiblas-netlib-3.4.2-1.fc38.x86_64 5/8 Installing : flexiblas-3.4.2-1.fc38.x86_64 6/8 Installing : flexiblas-openblas-openmp-3.4.2-1.fc38.x86_64 7/8 Installing : python3-numpy-1:1.24.4-2.fc38.x86_64 8/8 Running scriptlet: python3-numpy-1:1.24.4-2.fc38.x86_64 8/8 Verifying : python3-numpy-1:1.24.4-2.fc38.x86_64 1/8 Verifying : openblas-0.3.21-4.fc38.x86_64 2/8 Verifying : openblas-openmp-0.3.21-4.fc38.x86_64 3/8 Verifying : flexiblas-3.4.2-1.fc38.x86_64 4/8 Verifying : flexiblas-netlib-3.4.2-1.fc38.x86_64 5/8 Verifying : flexiblas-openblas-openmp-3.4.2-1.fc38.x86_64 6/8 Verifying : libgfortran-13.2.1-7.fc38.x86_64 7/8 Verifying : libquadmath-13.2.1-7.fc38.x86_64 8/8 Installed: flexiblas-3.4.2-1.fc38.x86_64 flexiblas-netlib-3.4.2-1.fc38.x86_64 flexiblas-openblas-openmp-3.4.2-1.fc38.x86_64 libgfortran-13.2.1-7.fc38.x86_64 libquadmath-13.2.1-7.fc38.x86_64 openblas-0.3.21-4.fc38.x86_64 openblas-openmp-0.3.21-4.fc38.x86_64 python3-numpy-1:1.24.4-2.fc38.x86_64 Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.5aGpeV + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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=py311 + 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-1.83-5.fc38.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.0.3) 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 1.24.4) + cat /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/top_level.txt' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/LICENSE.rst' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 33 kB/s | 1.5 kB 00:00 fedora 101 kB/s | 24 kB 00:00 updates 96 kB/s | 22 kB 00:00 Package gcc-13.2.1-7.fc38.x86_64 is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package pyproject-rpm-macros-1.12.0-1.fc38.noarch is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-devel-3.11.8-2.fc38.x86_64 is already installed. Package python3-numpy-1:1.24.4-2.fc38.x86_64 is already installed. Package python3-packaging-23.2-1.fc38.noarch is already installed. Package python3-pip-23.1.2-6.fc38.noarch is already installed. Package python3-reportlab-4.0.4-2.fc38.noarch is already installed. Package python3-setuptools-69.0.3-3.fc38.noarch is already installed. Package python3-wheel-1:0.43.0-1.fc38.noarch is already installed. Dependencies resolved. Nothing to do. Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1712966400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.x0pOOI + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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=py311 + 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-1.83-5.fc38.x86_64-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 69.0.3) 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 1.24.4) + cat /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-buildrequires + rm -rfv biopython-1.83.dist-info/ removed 'biopython-1.83.dist-info/top_level.txt' removed 'biopython-1.83.dist-info/METADATA' removed 'biopython-1.83.dist-info/LICENSE' removed 'biopython-1.83.dist-info/LICENSE.rst' removed directory 'biopython-1.83.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ANIYG9 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-st_gd8q_/biopython.egg-info writing /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/biopython.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/biopython.egg-info/dependency_links.txt writing requirements to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/biopython.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/biopython.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/biopython.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/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-st_gd8q_/biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-st_gd8q_/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-311 creating build/lib.linux-x86_64-cpython-311/Bio copying Bio/File.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-311/Bio creating build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy creating build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices creating build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO creating build/lib.linux-x86_64-cpython-311/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Alphabet creating build/lib.linux-x86_64-cpython-311/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Application creating build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast creating build/lib.linux-x86_64-cpython-311/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/CAPS creating build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign creating build/lib.linux-x86_64-cpython-311/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Compass creating build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Data creating build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss creating build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez creating build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy creating build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank creating build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo creating build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics creating build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram creating build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM creating build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map creating build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML creating build/lib.linux-x86_64-cpython-311/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Medline creating build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs creating build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications creating build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar creating build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus creating build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR creating build/lib.linux-x86_64-cpython-311/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway creating build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype creating build/lib.linux-x86_64-cpython-311/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen creating build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop creating build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction creating build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications creating build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer creating build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt creating build/lib.linux-x86_64-cpython-311/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/TogoWS creating build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML creating build/lib.linux-x86_64-cpython-311/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniGene creating build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt creating build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-311/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/python3.11/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/python3.11/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/python3.11/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-311/Bio copying Bio/py.typed -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Align/_codonaligner.c -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-x86_64-cpython-311/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/Bio creating build/temp.linux-x86_64-cpython-311/Bio/Align gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/Align/_codonaligner.c -o build/temp.linux-x86_64-cpython-311/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Align/_codonaligner.cpython-311-x86_64-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-x86_64-cpython-311/Bio/Align/_pairwisealigner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Align/_pairwisealigner.cpython-311-x86_64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.11/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-x86_64-cpython-311/Bio/Nexus gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-x86_64-cpython-311/Bio/motifs gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-x86_64-cpython-311/Bio/Cluster gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.kdtrees' extension creating build/temp.linux-x86_64-cpython-311/Bio/PDB gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.ccealign' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealign.cpython-311-x86_64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-x86_64-cpython-311/Bio/SeqIO gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-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/Bio copying build/lib.linux-x86_64-cpython-311/Bio/File.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/LogisticRegression.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MarkovModel.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MaxEntropy.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/NaiveBayes.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/Seq.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqFeature.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqRecord.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/__init__.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/_utils.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/bgzf.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/kNN.py -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/pairwise2.py -> build/bdist.linux-x86_64/wheel/Bio creating build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/CelFile.py -> build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Affy creating build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/AlignInfo.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/a2m.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/analysis.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bed.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigbed.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigmaf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigpsl.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/chain.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/clustal.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/emboss.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/exonerate.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/fasta.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/hhr.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/maf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/mauve.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/msf.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/nexus.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/phylip.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/psl.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/sam.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/stockholm.py -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/tabular.py -> build/bdist.linux-x86_64/wheel/Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Prank.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Align/Applications creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices copying build/lib.linux-x86_64-cpython-311/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/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/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-311/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/_codonaligner.c -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_pairwisealigner.c -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_codonaligner.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_pairwisealigner.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MafIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MauveIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MsfIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/NexusIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/AlignIO creating build/bdist.linux-x86_64/wheel/Bio/Alphabet copying build/lib.linux-x86_64-cpython-311/Bio/Alphabet/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Alphabet creating build/bdist.linux-x86_64/wheel/Bio/Application copying build/lib.linux-x86_64-cpython-311/Bio/Application/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Application creating build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Applications.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIWWW.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIXML.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Record.py -> build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Blast creating build/bdist.linux-x86_64/wheel/Bio/CAPS copying build/lib.linux-x86_64-cpython-311/Bio/CAPS/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/CAPS creating build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.c -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.h -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.c -> build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Cluster creating build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonalignment.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonseq.py -> build/bdist.linux-x86_64/wheel/Bio/codonalign creating build/bdist.linux-x86_64/wheel/Bio/Compass copying build/lib.linux-x86_64-cpython-311/Bio/Compass/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Compass creating build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/CodonTable.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/IUPACData.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/PDBData.py -> build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Data creating build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Applications.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Primer3.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Emboss creating build/bdist.linux-x86_64/wheel/Bio/Entrez copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/Parser.py -> build/bdist.linux-x86_64/wheel/Bio/Entrez copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Entrez creating build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-common1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-display1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-format1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-link1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/chars.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/common.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/display.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/elink.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/epost.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esummary_gene.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/format.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isobox.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs creating build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs creating build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Enzyme.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prodoc.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prosite.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-x86_64/wheel/Bio/ExPASy creating build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Record.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Scanner.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/utils.py -> build/bdist.linux-x86_64/wheel/Bio/GenBank creating build/bdist.linux-x86_64/wheel/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/Record.py -> build/bdist.linux-x86_64/wheel/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Geo creating build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Comparative.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Distribution.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/KGML_vis.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/__init__.py -> 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-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram creating build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/MarkovModel.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Trainer.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Utilities.py -> build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/HMM creating build/bdist.linux-x86_64/wheel/Bio/KEGG copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/REST.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Map copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/Map creating build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML creating 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-311/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Atom.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Chain.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/DSSP.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Dice.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Entity.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/FragmentMapper.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/HSExposure.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIFParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Model.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NACCESS.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBExceptions.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBList.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBParser.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PICIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PSEA.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Polypeptide.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Residue.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ResidueDepth.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SASA.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SCADIO.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Selection.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Structure.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureAlignment.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureBuilder.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Superimposer.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/cealign.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_data.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_rebuild.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/internal_coords.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmcifio.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/qcprot.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/vectors.py -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.c -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.c -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealign.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/PDB creating build/bdist.linux-x86_64/wheel/Bio/Medline copying build/lib.linux-x86_64-cpython-311/Bio/Medline/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Medline creating build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/alignace.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/clusterbuster.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/mast.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/matrix.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/meme.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/minimal.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/pfm.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/thresholds.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/transfac.py -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/xms.py -> build/bdist.linux-x86_64/wheel/Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/applications creating build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/db.py -> build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.c -> build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nexus.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nodes.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/StandardData.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Trees.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.c -> build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/Nexus creating build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/NOEtools.py -> build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/xpktools.py -> build/bdist.linux-x86_64/wheel/Bio/NMR creating build/bdist.linux-x86_64/wheel/Bio/Pathway copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/__init__.py -> 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-311/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep creating build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/phen_micro.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/pm_fitting.py -> build/bdist.linux-x86_64/wheel/Bio/phenotype creating build/bdist.linux-x86_64/wheel/Bio/PopGen copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/__init__.py -> 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-311/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop creating build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/PrintFormat.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Restriction creating build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Cla.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Des.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Dom.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Hie.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Raf.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Residues.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SCOP creating build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlatIO.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_index.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_utils.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hit.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/query.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO creating build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AbiIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AceIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/GckIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/IgIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/NibIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PdbIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PhdIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PirIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/QualityIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SffIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SwissIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TabIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_index.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio/SeqIO creating build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/lcc.py -> build/bdist.linux-x86_64/wheel/Bio/SeqUtils creating build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Ace.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Phd.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/__init__.py -> 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-311/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications creating build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer creating build/bdist.linux-x86_64/wheel/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/KeyWList.py -> build/bdist.linux-x86_64/wheel/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/SwissProt creating build/bdist.linux-x86_64/wheel/Bio/TogoWS copying build/lib.linux-x86_64-cpython-311/Bio/TogoWS/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/TogoWS creating build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/BaseTree.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAOIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Consensus.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXML.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Newick.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NewickIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NexusIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXML.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_io.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_utils.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo creating build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications creating build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML creating build/bdist.linux-x86_64/wheel/Bio/UniGene copying build/lib.linux-x86_64-cpython-311/Bio/UniGene/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/UniGene creating build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/GOA.py -> build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/__init__.py -> build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2module.c -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/py.typed -> build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/Bio creating build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeq.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeqDatabase.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/DBUtils.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/Loader.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/__init__.py -> build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/py.typed -> build/bdist.linux-x86_64/wheel/BioSQL running install_egg_info Copying biopython.egg-info to build/bdist.linux-x86_64/wheel/biopython-1.83-py3.11.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-bp9t4ugm/.tmp-jskkiz8o/biopython-1.83-cp311-cp311-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-311-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-311-x86_64-linux-gnu.so' adding 'Bio/Align/_pairwisealigner.c' adding 'Bio/Align/_pairwisealigner.cpython-311-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-311-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-311-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-311-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-311-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-311-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-311-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-cp311-cp311-linux_x86_64.whl size=3052325 sha256=3fb688bf8087cff117a5dbbe26ef51a1d7d1176443a0cacd4445cfe88c3c5d15 Stored in directory: /builddir/.cache/pip/wheels/b6/d0/aa/4e82fcee7fe4a7821e086018cc9474e6a6dcbe406043b23424 Successfully built biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.5cyHgu + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-cp311-cp311-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-1.83-5.fc38.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 23.1.2 from /usr/lib/python3.11/site-packages/pip (python 3.11) Looking in links: /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir Processing ./pyproject-wheeldir/biopython-1.83-cp311-cp311-linux_x86_64.whl Installing collected packages: biopython Successfully installed biopython-1.83 + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/bin ']' + rm -f /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages ']' + '[' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages '!=' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages ']' + '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages ']' + site_dirs+=("/usr/lib64/python3.11/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.11/site-packages/biopython-1.83.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/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-1.83-5.fc38.x86_64 --record /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.83.dist-info/RECORD --output /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-record + rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.83.dist-info/RECORD removed '/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.83.dist-info/RECORD' + rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.83.dist-info/REQUESTED removed '/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.83.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_PERCENTAGES_COUNT=8 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-modules --buildroot /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 --sitelib /usr/lib/python3.11/site-packages --sitearch /usr/lib64/python3.11/site-packages --python-version 3.11 --pyproject-record /builddir/build/BUILD/python-biopython-1.83-5.fc38.x86_64-pyproject-record --prefix /usr Bio BioSQL + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.83-5.fc38 --unique-debug-suffix -1.83-5.fc38.x86_64 --unique-debug-src-base python-biopython-1.83-5.fc38.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 /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal /usr/bin/gdb.minimal 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-1.83-5.fc38.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 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/debug/usr/lib64/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.l9p54O + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 ' ~/build/BUILD/biopython-1.83/Tests ~/build/BUILD/biopython-1.83 + 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 + pushd Tests ++ 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 ++ grep -v test_Align_bigbed.py ++ grep -v test_Tutorial.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.046 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO.py test_AlignIO ... ok 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 2.869 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_ClustalIO.py test_AlignIO_ClustalIO ... ok 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 0.046 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok 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 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok 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 0.053 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok 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 0.078 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_convert.py test_AlignIO_convert ... ok 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 0.194 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_Alignment.py test_Align_Alignment ... ok 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 0.415 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_a2m.py test_Align_a2m ... ok 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 0.092 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bed.py test_Align_bed ... ok 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 0.183 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.631 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigpsl.py test_Align_bigpsl ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.594 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_chain.py test_Align_chain ... ok 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 0.229 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_clustal.py test_Align_clustal ... ok 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 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_codonalign.py test_Align_codonalign ... ok 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 3.164 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_emboss.py test_Align_emboss ... ok 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 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.149 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.070 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_hhr.py test_Align_hhr ... ok 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 0.306 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.430 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_msf.py test_Align_msf ... ok 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 0.051 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.108 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_psl.py test_Align_psl ... ok 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 0.417 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_sam.py test_Align_sam ... ok 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 0.316 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_stockholm.py test_Align_stockholm ... ok 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 1.663 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.500 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.024 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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) ---------------------------------------------------------------------- Ran 1 test in 0.110 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.120 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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) ---------------------------------------------------------------------- Ran 1 test in 0.135 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.135 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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) ---------------------------------------------------------------------- Ran 1 test in 0.154 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_psycopg2_online.py test_BioSQL_psycopg2_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.156 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 4.940 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.110 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Blast_Record.py test_Blast_Record ... ok test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.039 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_CAPS.py test_CAPS ... ok 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 0.137 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.061 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Cluster.py test_Cluster ... ok Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.040 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_CodonTable.py test_CodonTable ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_ColorSpiral.py test_ColorSpiral ... ok 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 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.023 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Consensus.py test_Consensus ... ok 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 1.409 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_EMBL_unittest.py test_EMBL_unittest ... ok 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 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.123 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_EmbossPrimer.py test_EmbossPrimer ... ok 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 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 4.157 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.516 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.010 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_File.py test_File ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GenBank.py test_GenBank ... ok 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 0.285 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 2.930 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.113 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.700 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.172 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsGeneral.py test_GraphicsGeneral ... ok 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 0.869 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.338 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_HMMGeneral.py test_HMMGeneral ... ok 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 0.040 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG.py test_KEGG ... ok 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 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_graphics.py test_KGML_graphics ... ok 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 5.677 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_nographics.py test_KGML_nographics ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 1.016 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_KeyWList.py test_KeyWList ... ok 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 0.040 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_LogisticRegression.py test_LogisticRegression ... ok 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 0.048 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.067 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_MafIO_index.py test_MafIO_index ... ok 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 0.755 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.047 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_MarkovModel.py test_MarkovModel ... ok 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 0.175 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Medline.py test_Medline ... ok 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 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBIXML.py test_NCBIXML ... ok 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 0.510 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.012 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBI_qblast.py test_NCBI_qblast ... ok 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 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.012 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_NaiveBayes.py test_NaiveBayes ... ok 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 0.010 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.371 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_baseml.py test_PAML_baseml ... ok 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 0.117 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_codeml.py test_PAML_codeml ... ok 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 0.741 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.061 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_yn00.py test_PAML_yn00 ... ok 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 0.069 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDBList.py test_PDBList ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_CEAligner.py test_PDB_CEAligner ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 2.072 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.160 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Dice.py test_PDB_Dice ... ok test_dice (test_PDB_Dice.DiceTests.test_dice) Self test for PDB.Dice module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.069 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Disordered.py test_PDB_Disordered ... ok 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 0.076 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Exposure.py test_PDB_Exposure ... ok 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 0.312 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_FragmentMapper.py test_PDB_FragmentMapper ... ok test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper) Self test for FragmentMapper module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_KDTree.py test_PDB_KDTree ... ok 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 1.580 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.077 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIFIO.py test_PDB_MMCIFIO ... ok 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 0.200 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 1.144 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_NACCESS.py test_PDB_NACCESS ... ok 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 0.053 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.215 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PDBParser.py test_PDB_PDBParser ... ok 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 0.125 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Polypeptide.py test_PDB_Polypeptide ... ok 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 0.099 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_ResidueDepth.py test_PDB_ResidueDepth ... ok 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 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SASA.py test_PDB_SASA ... ok 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 ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux Ran 1 test in 3.161 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SMCRA.py test_PDB_SMCRA ... ok 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 0.321 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_StructureAlignment.py test_PDB_StructureAlignment ... ok 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 0.224 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Superimposer.py test_PDB_Superimposer ... ok test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer) Test on module that superimpose two protein structures. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.070 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_parse_pdb_header.py test_PDB_parse_pdb_header ... ok 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 0.084 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_vectors.py test_PDB_vectors ... ok 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 0.053 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PQR.py test_PQR ... ok 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 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Pathway.py test_Pathway ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.067 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.444 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PhyloXML.py test_PhyloXML ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.343 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_NeXML.py test_Phylo_NeXML ... ok 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 0.135 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.054 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop_nodepend.py test_PopGen_GenePop_nodepend ... ok 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 0.018 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_RCSBFormats.py test_RCSBFormats ... ok Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.424 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Restriction.py test_Restriction ... ok 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 0.152 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Astral.py test_SCOP_Astral ... ok 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 ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.060 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Des.py test_SCOP_Des ... ok 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 0.057 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Dom.py test_SCOP_Dom ... ok 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 0.057 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.057 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Raf.py test_SCOP_Raf ... ok 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 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Residues.py test_SCOP_Residues ... ok 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 0.058 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SVDSuperimposer.py test_SVDSuperimposer ... ok test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab.py test_SearchIO_blast_tab ... ok 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 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab_index.py test_SearchIO_blast_tab_index ... ok 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 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml.py test_SearchIO_blast_xml ... ok 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 0.182 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml_index.py test_SearchIO_blast_xml_index ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 1.035 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl.py test_SearchIO_blat_psl ... ok 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 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux 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 0.098 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate.py test_SearchIO_exonerate ... ok 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 0.106 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_text_index ... ok 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 0.061 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_vulgar_index.py test_SearchIO_exonerate_vulgar_index ... ok 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 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_fasta_m10_index.py test_SearchIO_fasta_m10_index ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hhsuite2_text.py test_SearchIO_hhsuite2_text ... ok 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 0.088 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text ... ok 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 0.124 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer2_text_index ... ok 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 0.096 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.050 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_domtab_index ... ok 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 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab ... ok 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 0.047 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_tab_index ... ok 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 0.054 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.129 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_text_index.py test_SearchIO_hmmer3_text_index ... ok 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 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.079 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux Ran 1 test in 0.213 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqFeature.py test_SeqFeature ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/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 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 16.180 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.276 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_FastaIO.py test_SeqIO_FastaIO ... ok 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 0.064 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Gck.py test_SeqIO_Gck ... ok 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 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Insdc.py test_SeqIO_Insdc ... ok 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 0.115 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 2.224 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_QualityIO.py test_SeqIO_QualityIO ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.440 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_SeqXML.py test_SeqIO_SeqXML ... ok 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 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_TwoBitIO.py test_SeqIO_TwoBitIO ... ok 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 0.835 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Xdna.py test_SeqIO_Xdna ... ok 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 0.069 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/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 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 0.491 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 13.072 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_online.py test_SeqIO_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.145 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqRecord.py test_SeqRecord ... ok 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 0.147 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqUtils.py test_SeqUtils ... ok 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 0.077 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 1.163 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SffIO.py test_SffIO ... ok 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 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_SwissProt.py test_SwissProt ... ok 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 0.168 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.070 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_TogoWS.py test_TogoWS ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_TreeConstruction.py test_TreeConstruction ... ok 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 0.419 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_UniGene.py test_UniGene ... ok 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 0.026 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_UniProt_GOA.py test_UniProt_GOA ... ok 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 0.019 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.262 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.064 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_align.py test_align ... ok Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 0.128 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_align_substitution_matrices.py test_align_substitution_matrices ... ok 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 0.377 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 2.206 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_cellosaurus.py test_cellosaurus ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 3.931 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_geo.py test_geo ... ok 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 0.058 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_kNN.py test_kNN ... ok 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 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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) ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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) ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs.py test_motifs ... ok 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 0.409 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs_online.py test_motifs_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2.py test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/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 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 0.104 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2_no_C.py test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/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 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 0.081 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise_aligner.py test_pairwise_aligner ... ok 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 0.256 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.222 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 6.578 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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. ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_prodoc.py test_prodoc ... ok 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 0.016 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_prosite.py test_prosite ... ok 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 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /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: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_seq.py test_seq ... ok 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 Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.068 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-1.83-5.fc38.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib64/python3.11/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/lib/python3.11/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_translate.py test_translate ... ok 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 0.042 seconds Skipping any tests requiring internet access Python version: 3.11.8 (main, Feb 28 2024, 00:00:00) [GCC 13.2.1 20231011 (Red Hat 13.2.1-4)] Operating system: posix linux + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-biopython-1.83-5.fc38.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.UfmzIK + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/share/doc/python3-biopython + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/biopython-1.83/Doc /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/biopython-1.83/Scripts /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.83-5.fc38 python3-biopython = 1.83-5.fc38 python3-biopython(x86-64) = 1.83-5.fc38 python3.11-biopython = 1.83-5.fc38 python3.11dist(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) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH) Processing files: python-biopython-debugsource-1.83-5.fc38.x86_64 Provides: python-biopython-debugsource = 1.83-5.fc38 python-biopython-debugsource(x86-64) = 1.83-5.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.83-5.fc38.x86_64 Provides: debuginfo(build-id) = 2ca4ce051d1df1fcec77e94d0b6c62f012abc25f debuginfo(build-id) = 4ae6e45f18e530c42876416fefcd03e683c96eaa debuginfo(build-id) = 6565c5ef600971c70ba95bfd9804d4a7447f162d debuginfo(build-id) = 65aa41a8270afce4aa490eb6d1e71338d2631931 debuginfo(build-id) = 7b4c0c3a66ab76b414c071014bcb1fcaf0c2a773 debuginfo(build-id) = 95605579726db89800b3e7085d3abaac06efc4f7 debuginfo(build-id) = a39bba16db424cd91c17cb17aa64768ef5f19b32 debuginfo(build-id) = ae1015cf29efc4e17726ed1c74cb00a7e9f8452b debuginfo(build-id) = cb89ef50a82f305197dd883fc7380c90ec179c36 python-biopython-debuginfo = 1.83-5.fc38 python3-biopython-debuginfo = 1.83-5.fc38 python3-biopython-debuginfo(x86-64) = 1.83-5.fc38 python3.11-biopython-debuginfo = 1.83-5.fc38 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) = 1.83-5.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc38.src.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.83-5.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.83-5.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.83-5.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.NZIRfN + umask 022 + cd /builddir/build/BUILD + cd biopython-1.83 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-5.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.kP6QFP + umask 022 + cd /builddir/build/BUILD + rm -rf biopython-1.83 biopython-1.83.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-biopython-1.83-5.fc38.src.rpm Finish: build phase for python-biopython-1.83-5.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-38-x86_64-1713011165.797942/root/var/log/dnf.log /var/lib/mock/fedora-38-x86_64-1713011165.797942/root/var/log/dnf.librepo.log /var/lib/mock/fedora-38-x86_64-1713011165.797942/root/var/log/dnf.rpm.log INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.83-5.fc38.src.rpm) Config(child) 3 minutes 48 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-debugsource", "epoch": null, "version": "1.83", "release": "5.fc38", "arch": "x86_64" }, { "name": "python3-biopython", "epoch": null, "version": "1.83", "release": "5.fc38", "arch": "x86_64" }, { "name": "python3-biopython-debuginfo", "epoch": null, "version": "1.83", "release": "5.fc38", "arch": "x86_64" }, { "name": "python-biopython", "epoch": null, "version": "1.83", "release": "5.fc38", "arch": "src" } ] } RPMResults finished