Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1ca' (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/6871773-fedora-39-i386 --chroot fedora-39-i386 Version: 0.70 PID: 6032 Logging PID: 6033 Task: {'appstream': False, 'background': True, 'build_id': 6871773, 'buildroot_pkgs': [], 'chroot': 'fedora-39-i386', 'enable_net': False, 'fedora_review': False, 'git_hash': '050ca7273ec26c0203dba24ec7ab2915ed87a2cb', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:6/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.82-1', 'project_dirname': 'openblas-0.3.23:pr:6', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-i386/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/gui1ty', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/gui1ty', 'tags': [], 'task_id': '6871773-fedora-39-i386', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:6/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:6/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython'... Running: git checkout 050ca7273ec26c0203dba24ec7ab2915ed87a2cb -- cmd: ['git', 'checkout', '050ca7273ec26c0203dba24ec7ab2915ed87a2cb', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython rc: 0 stdout: stderr: Note: switching to '050ca7273ec26c0203dba24ec7ab2915ed87a2cb'. 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 050ca72 automatic import of python-biopython Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/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-1.82.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o biopython-1.82.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/psimovec/openblas-0.3.23:pr:6/python-biopython/biopython-1.82.tar.gz/md5/f0900044ae4c97008992c4a36c66f8e2/biopython-1.82.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 61.3M 0 --:--:-- --:--:-- --:--:-- 61.5M INFO: Reading stdout from command: md5sum biopython-1.82.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704719561.816847 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1704719561.816847 -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-d70a6vtc/python-biopython/python-biopython.spec) Config(fedora-39-i686) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-i686-bootstrap-1704719561.816847/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-i686-bootstrap-1704719561.816847/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/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 23 MB/s | 14 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 76 MB/s | 71 MB 00:00 local 64 MB/s | 71 MB 00:01 Last metadata expiration check: 0:00:03 ago on Mon Jan 8 13:13:09 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: python3-dnf-plugins-core noarch 4.4.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 496 k dnf-data noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549 k yum noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 155 k python3-dateutil noarch 1:2.8.2-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus x86_64 1.3.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 146 k python3-distro noarch 1.8.0-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 44 k python3-six noarch 1.16.0-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd x86_64 235-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k Transaction Summary ========================================================================================================================= Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): dbus-libs-1.14.10-1.fc40.x86_64.rpm 1.8 MB/s | 155 kB 00:00 (2/11): python3-dbus-1.3.2-4.fc39.x86_64.rpm 1.6 MB/s | 146 kB 00:00 (3/11): python3-dateutil-2.8.2-11.fc40.noarch.r 3.4 MB/s | 345 kB 00:00 (4/11): python3-distro-1.8.0-6.fc39.noarch.rpm 2.3 MB/s | 44 kB 00:00 (5/11): python3-dnf-plugins-core-4.4.4-1.fc40.n 14 MB/s | 302 kB 00:00 (6/11): python3-six-1.16.0-12.fc39.noarch.rpm 1.7 MB/s | 41 kB 00:00 (7/11): python3-systemd-235-5.fc39.x86_64.rpm 4.8 MB/s | 101 kB 00:00 (8/11): dnf-data-4.18.2-1.fc40.noarch.rpm 1.8 MB/s | 39 kB 00:00 (9/11): python3-dnf-4.18.2-1.fc40.noarch.rpm 22 MB/s | 549 kB 00:00 (10/11): dnf-4.18.2-1.fc40.noarch.rpm 13 MB/s | 496 kB 00:00 (11/11): yum-4.18.2-1.fc40.noarch.rpm 1.8 MB/s | 37 kB 00:00 -------------------------------------------------------------------------------- Total 13 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.18.2-1.fc40.noarch 1/15 Upgrading : python3-dnf-4.18.2-1.fc40.noarch 2/15 Upgrading : dnf-4.18.2-1.fc40.noarch 3/15 Running scriptlet: dnf-4.18.2-1.fc40.noarch 3/15 Installing : python3-systemd-235-5.fc39.x86_64 4/15 Installing : python3-six-1.16.0-12.fc39.noarch 5/15 Installing : python3-dateutil-1:2.8.2-11.fc40.noarch 6/15 Installing : python3-distro-1.8.0-6.fc39.noarch 7/15 Installing : dbus-libs-1:1.14.10-1.fc40.x86_64 8/15 Installing : python3-dbus-1.3.2-4.fc39.x86_64 9/15 Installing : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 10/15 Upgrading : yum-4.18.2-1.fc40.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-1.fc40.x86_64 1/15 Verifying : python3-dateutil-1:2.8.2-11.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 3/15 Verifying : python3-distro-1.8.0-6.fc39.noarch 4/15 Verifying : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 5/15 Verifying : python3-six-1.16.0-12.fc39.noarch 6/15 Verifying : python3-systemd-235-5.fc39.x86_64 7/15 Verifying : dnf-4.18.2-1.fc40.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-1.fc40.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-1.fc40.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-1.fc40.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-1.fc40.noarch dnf-data-4.18.2-1.fc40.noarch python3-dnf-4.18.2-1.fc40.noarch yum-4.18.2-1.fc40.noarch Installed: dbus-libs-1:1.14.10-1.fc40.x86_64 python3-dateutil-1:2.8.2-11.fc40.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-i686-1704719561.816847/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 47 MB/s | 14 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 40 MB/s | 60 MB 00:01 local 74 MB/s | 61 MB 00:00 Last metadata expiration check: 0:00:02 ago on Mon Jan 8 13:13:55 2024. Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash i686 5.2.21-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 i686 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 53 k coreutils i686 9.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M cpio i686 2.14-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 278 k diffutils i686 3.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 394 k fedora-release noarch 40-0.26 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.7 k findutils i686 1:4.9.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 492 k gawk i686 5.2.2-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M glibc-minimal-langpack i686 2.38.9000-30.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 89 k grep i686 3.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 294 k gzip i686 1.12-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 158 k info i686 7.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 187 k patch i686 2.7.6-22.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 138 k redhat-rpm-config noarch 275-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 74 k rpm-build i686 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k sed i686 4.8-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 300 k shadow-utils i686 2:4.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M tar i686 2:1.35-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 864 k unzip i686 6.0-62.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 180 k util-linux i686 2.39.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M which i686 2.21-40.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k xz i686 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 535 k Installing dependencies: alternatives i686 1.25-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k ansible-srpm-macros noarch 1-11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs i686 3.1.2-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125 k authselect i686 1.4.3-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 145 k authselect-libs i686 1.4.3-1.fc40 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ghc-srpm-macros-1.6.1-3.fc40.noarch.r 372 kB/s | 8.1 kB 00:00 (48/153): glibc-common-2.38.9000-30.fc40.i686.r 11 MB/s | 378 kB 00:00 (49/153): glibc-2.38.9000-30.fc40.i686.rpm 39 MB/s | 2.0 MB 00:00 (50/153): glibc-minimal-langpack-2.38.9000-30.f 3.1 MB/s | 89 kB 00:00 (51/153): gmp-6.2.1-5.fc39.i686.rpm 12 MB/s | 306 kB 00:00 (52/153): gnat-srpm-macros-6-3.fc39.noarch.rpm 380 kB/s | 8.8 kB 00:00 (53/153): glibc-gconv-extra-2.38.9000-30.fc40.i 19 MB/s | 1.7 MB 00:00 (54/153): go-srpm-macros-3.3.1-1.fc40.noarch.rp 1.2 MB/s | 28 kB 00:00 (55/153): grep-3.11-5.fc40.i686.rpm 12 MB/s | 294 kB 00:00 (56/153): info-7.1-1.fc40.i686.rpm 8.3 MB/s | 187 kB 00:00 (57/153): gzip-1.12-6.fc39.i686.rpm 6.4 MB/s | 158 kB 00:00 (58/153): jansson-2.13.1-7.fc39.i686.rpm 2.0 MB/s | 46 kB 00:00 (59/153): kernel-srpm-macros-1.0-20.fc39.noarch 489 kB/s | 10 kB 00:00 (60/153): keyutils-libs-1.6.3-1.fc40.i686.rpm 1.5 MB/s | 32 kB 00:00 (61/153): krb5-libs-1.21.2-2.fc40.i686.rpm 27 MB/s | 804 kB 00:00 (62/153): 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MB/s | 324 kB 00:00 (78/153): libmount-2.39.3-1.fc40.i686.rpm 6.4 MB/s | 162 kB 00:00 (79/153): libnghttp2-1.58.0-1.fc40.i686.rpm 3.8 MB/s | 82 kB 00:00 (80/153): libnsl2-2.0.0-6.fc39.i686.rpm 1.1 MB/s | 31 kB 00:00 (81/153): libpkgconf-1.9.5-2.fc39.i686.rpm 1.6 MB/s | 41 kB 00:00 (82/153): libpsl-0.21.2-4.fc39.i686.rpm 2.9 MB/s | 63 kB 00:00 (83/153): libpwquality-1.4.5-6.fc39.i686.rpm 4.6 MB/s | 109 kB 00:00 (84/153): libselinux-3.6-2.fc40.i686.rpm 4.3 MB/s | 93 kB 00:00 (85/153): libsemanage-3.6-1.fc40.i686.rpm 5.9 MB/s | 125 kB 00:00 (86/153): libsepol-3.6-1.fc40.i686.rpm 14 MB/s | 351 kB 00:00 (87/153): libsigsegv-2.14-5.fc39.i686.rpm 1.2 MB/s | 27 kB 00:00 (88/153): libsmartcols-2.39.3-1.fc40.i686.rpm 3.3 MB/s | 69 kB 00:00 (89/153): libssh-0.10.6-2.fc40.i686.rpm 9.4 MB/s | 227 kB 00:00 (90/153): libssh-config-0.10.6-2.fc40.noarch.rp 409 kB/s | 9.1 kB 00:00 (91/153): libtasn1-4.19.0-3.fc39.i686.rpm 3.4 MB/s | 75 kB 00:00 (92/153): libtirpc-1.3.4-1.rc1.fc40.i686.rpm 4.1 MB/s | 102 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kB 00:00 (108/153): openblas-srpm-macros-2-14.fc39.noarc 322 kB/s | 7.5 kB 00:00 (109/153): openldap-2.6.6-1.fc39.i686.rpm 11 MB/s | 273 kB 00:00 (110/153): p11-kit-0.25.3-1.fc40.i686.rpm 12 MB/s | 490 kB 00:00 (111/153): openssl-libs-3.1.4-1.fc40.i686.rpm 42 MB/s | 2.1 MB 00:00 (112/153): p11-kit-trust-0.25.3-1.fc40.i686.rpm 4.4 MB/s | 140 kB 00:00 (113/153): package-notes-srpm-macros-0.5-9.fc39 539 kB/s | 11 kB 00:00 (114/153): pam-libs-1.5.3-9.fc40.i686.rpm 2.6 MB/s | 60 kB 00:00 (115/153): pam-1.5.3-9.fc40.i686.rpm 19 MB/s | 527 kB 00:00 (116/153): patch-2.7.6-22.fc39.i686.rpm 5.3 MB/s | 138 kB 00:00 (117/153): pcre2-10.42-2.fc40.i686.rpm 9.7 MB/s | 231 kB 00:00 (118/153): pcre2-syntax-10.42-2.fc40.noarch.rpm 6.3 MB/s | 143 kB 00:00 (119/153): perl-srpm-macros-1-51.fc39.noarch.rp 385 kB/s | 8.0 kB 00:00 (120/153): pkgconf-1.9.5-2.fc39.i686.rpm 2.0 MB/s | 43 kB 00:00 (121/153): pkgconf-m4-1.9.5-2.fc39.noarch.rpm 659 kB/s | 14 kB 00:00 (122/153): pkgconf-pkg-config-1.9.5-2.fc39.i686 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sed-4.8-14.fc39.i686.rpm 12 MB/s | 300 kB 00:00 (138/153): setup-2.14.5-1.fc40.noarch.rpm 6.5 MB/s | 148 kB 00:00 (139/153): sqlite-libs-3.44.2-1.fc40.i686.rpm 21 MB/s | 733 kB 00:00 (140/153): shadow-utils-4.14.0-2.fc40.i686.rpm 29 MB/s | 1.2 MB 00:00 (141/153): systemd-libs-255.1-1.fc40.i686.rpm 14 MB/s | 744 kB 00:00 (142/153): tar-1.35-2.fc40.i686.rpm 28 MB/s | 864 kB 00:00 (143/153): unzip-6.0-62.fc39.i686.rpm 6.2 MB/s | 180 kB 00:00 (144/153): util-linux-core-2.39.3-1.fc40.i686.r 13 MB/s | 506 kB 00:00 (145/153): util-linux-2.39.3-1.fc40.i686.rpm 27 MB/s | 1.1 MB 00:00 (146/153): which-2.21-40.fc39.i686.rpm 1.1 MB/s | 42 kB 00:00 (147/153): xxhash-libs-0.8.2-1.fc39.i686.rpm 1.9 MB/s | 49 kB 00:00 (148/153): xz-5.4.5-1.fc40.i686.rpm 18 MB/s | 535 kB 00:00 (149/153): xz-libs-5.4.5-1.fc40.i686.rpm 4.2 MB/s | 118 kB 00:00 (150/153): zig-srpm-macros-1-1.fc40.noarch.rpm 382 kB/s | 8.0 kB 00:00 (151/153): zlib-ng-compat-2.1.5-1.fc40.i686.rpm 3.5 MB/s | 81 kB 00:00 (152/153): zip-3.0-39.fc40.i686.rpm 11 MB/s | 267 kB 00:00 (153/153): zstd-1.5.5-4.fc39.i686.rpm 17 MB/s | 451 kB 00:00 -------------------------------------------------------------------------------- Total 33 MB/s | 53 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.i686 1/1 Preparing : 1/1 Installing : crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 1/153 Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 1/153 Installing : fedora-release-identity-basic-40-0.26.noarch 2/153 Installing : fedora-repos-rawhide-40-0.2.noarch 3/153 Installing : fedora-gpg-keys-40-0.2.noarch 4/153 Installing : fedora-repos-40-0.2.noarch 5/153 Installing : fedora-release-common-40-0.26.noarch 6/153 Installing : fedora-release-40-0.26.noarch 7/153 Installing : setup-2.14.5-1.fc40.noarch 8/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-1.fc40.noarch 8/153 Installing : filesystem-3.18-6.fc39.i686 9/153 Installing : basesystem-11-18.fc39.noarch 10/153 Installing : rust-srpm-macros-25.2-2.fc40.noarch 11/153 Installing : qt6-srpm-macros-6.6.1-3.fc40.noarch 12/153 Installing : qt5-srpm-macros-5.15.12-1.fc40.noarch 13/153 Installing : publicsuffix-list-dafsa-20230812-1.fc40.noarch 14/153 Installing : pkgconf-m4-1.9.5-2.fc39.noarch 15/153 Installing : perl-srpm-macros-1-51.fc39.noarch 16/153 Installing : pcre2-syntax-10.42-2.fc40.noarch 17/153 Installing : package-notes-srpm-macros-0.5-9.fc39.noarch 18/153 Installing : openblas-srpm-macros-2-14.fc39.noarch 19/153 Installing : ocaml-srpm-macros-9-1.fc40.noarch 20/153 Installing : ncurses-base-6.4-8.20231001.fc40.noarch 21/153 Installing : libssh-config-0.10.6-2.fc40.noarch 22/153 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 23/153 Installing : gnat-srpm-macros-6-3.fc39.noarch 24/153 Installing : ghc-srpm-macros-1.6.1-3.fc40.noarch 25/153 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 26/153 Installing : coreutils-common-9.4-1.fc40.i686 27/153 Installing : ansible-srpm-macros-1-11.fc39.noarch 28/153 Installing : libgcc-13.2.1-6.fc40.i686 29/153 Running scriptlet: libgcc-13.2.1-6.fc40.i686 29/153 Installing : glibc-gconv-extra-2.38.9000-30.fc40.i686 30/153 Running 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Installing : libpsl-0.21.2-4.fc39.i686 85/153 Installing : zip-3.0-39.fc40.i686 86/153 Installing : zstd-1.5.5-4.fc39.i686 87/153 Installing : cyrus-sasl-lib-2.1.28-11.fc39.i686 88/153 Installing : gdbm-1:1.23-4.fc39.i686 89/153 Installing : libfdisk-2.39.3-1.fc40.i686 90/153 Installing : bzip2-1.0.8-16.fc39.i686 91/153 Installing : libxml2-2.12.3-1.fc40.i686 92/153 Installing : sqlite-libs-3.44.2-1.fc40.i686 93/153 Installing : ed-1.19-4.fc39.i686 94/153 Installing : patch-2.7.6-22.fc39.i686 95/153 Installing : cpio-2.14-5.fc40.i686 96/153 Installing : diffutils-3.10-3.fc39.i686 97/153 Installing : keyutils-libs-1.6.3-1.fc40.i686 98/153 Installing : libbrotli-1.1.0-1.fc40.i686 99/153 Installing : libffi-3.4.4-5.fc40.i686 100/153 Installing : p11-kit-0.25.3-1.fc40.i686 101/153 Installing : p11-kit-trust-0.25.3-1.fc40.i686 102/153 Running scriptlet: p11-kit-trust-0.25.3-1.fc40.i686 102/153 Installing : openssl-libs-1:3.1.4-1.fc40.i686 103/153 Installing : coreutils-9.4-1.fc40.i686 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pkgconf-pkg-config-1.9.5-2.fc39.i686 120/153 Installing : libsigsegv-2.14-5.fc39.i686 121/153 Installing : gawk-5.2.2-2.fc39.i686 122/153 Installing : libverto-0.3.2-6.fc39.i686 123/153 Installing : krb5-libs-1.21.2-2.fc40.i686 124/153 Installing : libtirpc-1.3.4-1.rc1.fc40.i686 125/153 Installing : libnsl2-2.0.0-6.fc39.i686 126/153 Installing : pam-1.5.3-9.fc40.i686 127/153 Installing : libssh-0.10.6-2.fc40.i686 128/153 Installing : libcurl-8.5.0-1.fc40.i686 129/153 Installing : elfutils-libs-0.190-4.fc40.i686 130/153 Installing : elfutils-debuginfod-client-0.190-4.fc40.i686 131/153 Installing : binutils-gold-2.41-20.fc40.i686 132/153 Running scriptlet: binutils-gold-2.41-20.fc40.i686 132/153 Installing : binutils-2.41-20.fc40.i686 133/153 Running scriptlet: binutils-2.41-20.fc40.i686 133/153 Installing : elfutils-0.190-4.fc40.i686 134/153 Installing : rpm-build-libs-4.19.1-2.fc40.i686 135/153 Installing : curl-8.5.0-1.fc40.i686 136/153 Running scriptlet: rpm-4.19.1-2.fc40.i686 137/153 Installing : rpm-4.19.1-2.fc40.i686 137/153 Installing : efi-srpm-macros-5-9.fc39.noarch 138/153 Installing : lua-srpm-macros-1-9.fc39.noarch 139/153 Installing : zig-srpm-macros-1-1.fc40.noarch 140/153 Installing : xxhash-libs-0.8.2-1.fc39.i686 141/153 Installing : gdb-minimal-14.1-1.fc40.i686 142/153 Installing : debugedit-5.0-12.fc40.i686 143/153 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 144/153 Installing : forge-srpm-macros-0.2.0-1.fc40.noarch 145/153 Installing : go-srpm-macros-3.3.1-1.fc40.noarch 146/153 Installing : python-srpm-macros-3.12-5.fc40.noarch 147/153 Installing : redhat-rpm-config-275-1.fc40.noarch 148/153 Installing : rpm-build-4.19.1-2.fc40.i686 149/153 Installing : pyproject-srpm-macros-1.11.0-1.fc40.noarch 150/153 Installing : util-linux-2.39.3-1.fc40.i686 151/153 Installing : which-2.21-40.fc39.i686 152/153 Installing : info-7.1-1.fc40.i686 153/153 Running scriptlet: filesystem-3.18-6.fc39.i686 153/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.4.3-1.fc40.i686 153/153 Running scriptlet: rpm-4.19.1-2.fc40.i686 153/153 Running scriptlet: info-7.1-1.fc40.i686 153/153 Installed: alternatives-1.25-1.fc39.i686 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.i686 authselect-1.4.3-1.fc40.i686 authselect-libs-1.4.3-1.fc40.i686 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.i686 binutils-2.41-20.fc40.i686 binutils-gold-2.41-20.fc40.i686 bzip2-1.0.8-16.fc39.i686 bzip2-libs-1.0.8-16.fc39.i686 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.i686 coreutils-common-9.4-1.fc40.i686 cpio-2.14-5.fc40.i686 cracklib-2.9.11-2.fc39.i686 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.i686 cyrus-sasl-lib-2.1.28-11.fc39.i686 debugedit-5.0-12.fc40.i686 diffutils-3.10-3.fc39.i686 dwz-0.15-3.fc39.i686 ed-1.19-4.fc39.i686 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.i686 elfutils-debuginfod-client-0.190-4.fc40.i686 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.i686 elfutils-libs-0.190-4.fc40.i686 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.26.noarch fedora-release-common-40-0.26.noarch fedora-release-identity-basic-40-0.26.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.i686 file-libs-5.45-1.fc40.i686 filesystem-3.18-6.fc39.i686 findutils-1:4.9.0-6.fc40.i686 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.i686 gdb-minimal-14.1-1.fc40.i686 gdbm-1:1.23-4.fc39.i686 gdbm-libs-1:1.23-4.fc39.i686 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-30.fc40.i686 glibc-common-2.38.9000-30.fc40.i686 glibc-gconv-extra-2.38.9000-30.fc40.i686 glibc-minimal-langpack-2.38.9000-30.fc40.i686 gmp-1:6.2.1-5.fc39.i686 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.i686 gzip-1.12-6.fc39.i686 info-7.1-1.fc40.i686 jansson-2.13.1-7.fc39.i686 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.i686 krb5-libs-1.21.2-2.fc40.i686 libacl-2.3.1-11.fc40.i686 libarchive-3.7.2-1.fc40.i686 libattr-2.5.1-9.fc40.i686 libblkid-2.39.3-1.fc40.i686 libbrotli-1.1.0-1.fc40.i686 libcap-2.69-1.fc40.i686 libcap-ng-0.8.4-2.fc40.i686 libcom_err-1.47.0-2.fc39.i686 libcurl-8.5.0-1.fc40.i686 libeconf-0.5.2-1.fc40.i686 libevent-2.1.12-9.fc39.i686 libfdisk-2.39.3-1.fc40.i686 libffi-3.4.4-5.fc40.i686 libgcc-13.2.1-6.fc40.i686 libgomp-13.2.1-6.fc40.i686 libidn2-2.3.4-3.fc39.i686 libmount-2.39.3-1.fc40.i686 libnghttp2-1.58.0-1.fc40.i686 libnsl2-2.0.0-6.fc39.i686 libpkgconf-1.9.5-2.fc39.i686 libpsl-0.21.2-4.fc39.i686 libpwquality-1.4.5-6.fc39.i686 libselinux-3.6-2.fc40.i686 libsemanage-3.6-1.fc40.i686 libsepol-3.6-1.fc40.i686 libsigsegv-2.14-5.fc39.i686 libsmartcols-2.39.3-1.fc40.i686 libssh-0.10.6-2.fc40.i686 libssh-config-0.10.6-2.fc40.noarch libstdc++-13.2.1-6.fc40.i686 libtasn1-4.19.0-3.fc39.i686 libtirpc-1.3.4-1.rc1.fc40.i686 libunistring-1.1-5.fc40.i686 libutempter-1.2.1-10.fc39.i686 libuuid-2.39.3-1.fc40.i686 libverto-0.3.2-6.fc39.i686 libxcrypt-4.4.36-3.fc40.i686 libxml2-2.12.3-1.fc40.i686 libzstd-1.5.5-4.fc39.i686 lua-libs-5.4.6-3.fc39.i686 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.i686 mpfr-4.2.1-1.fc40.i686 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.i686 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.i686 openssl-libs-1:3.1.4-1.fc40.i686 p11-kit-0.25.3-1.fc40.i686 p11-kit-trust-0.25.3-1.fc40.i686 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-9.fc40.i686 pam-libs-1.5.3-9.fc40.i686 patch-2.7.6-22.fc39.i686 pcre2-10.42-2.fc40.i686 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.i686 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.i686 popt-1.19-3.fc39.i686 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.11.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-4.fc39.i686 redhat-rpm-config-275-1.fc40.noarch rpm-4.19.1-2.fc40.i686 rpm-build-4.19.1-2.fc40.i686 rpm-build-libs-4.19.1-2.fc40.i686 rpm-libs-4.19.1-2.fc40.i686 rpm-sequoia-1.5.0-2.fc40.i686 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.i686 setup-2.14.5-1.fc40.noarch shadow-utils-2:4.14.0-2.fc40.i686 sqlite-libs-3.44.2-1.fc40.i686 systemd-libs-255.1-1.fc40.i686 tar-2:1.35-2.fc40.i686 unzip-6.0-62.fc39.i686 util-linux-2.39.3-1.fc40.i686 util-linux-core-2.39.3-1.fc40.i686 which-2.21-40.fc39.i686 xxhash-libs-0.8.2-1.fc39.i686 xz-5.4.5-1.fc40.i686 xz-libs-5.4.5-1.fc40.i686 zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.i686 zlib-ng-compat-2.1.5-1.fc40.i686 zstd-1.5.5-4.fc39.i686 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.i686 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.i686 authselect-1.4.3-1.fc40.i686 authselect-libs-1.4.3-1.fc40.i686 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.i686 binutils-2.41-20.fc40.i686 binutils-gold-2.41-20.fc40.i686 bzip2-1.0.8-16.fc39.i686 bzip2-libs-1.0.8-16.fc39.i686 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.i686 coreutils-common-9.4-1.fc40.i686 cpio-2.14-5.fc40.i686 cracklib-2.9.11-2.fc39.i686 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.i686 cyrus-sasl-lib-2.1.28-11.fc39.i686 debugedit-5.0-12.fc40.i686 diffutils-3.10-3.fc39.i686 dwz-0.15-3.fc39.i686 ed-1.19-4.fc39.i686 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.i686 elfutils-debuginfod-client-0.190-4.fc40.i686 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.i686 elfutils-libs-0.190-4.fc40.i686 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.26.noarch fedora-release-common-40-0.26.noarch fedora-release-identity-basic-40-0.26.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.i686 file-libs-5.45-1.fc40.i686 filesystem-3.18-6.fc39.i686 findutils-4.9.0-6.fc40.i686 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.i686 gdb-minimal-14.1-1.fc40.i686 gdbm-1.23-4.fc39.i686 gdbm-libs-1.23-4.fc39.i686 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-30.fc40.i686 glibc-common-2.38.9000-30.fc40.i686 glibc-gconv-extra-2.38.9000-30.fc40.i686 glibc-minimal-langpack-2.38.9000-30.fc40.i686 gmp-6.2.1-5.fc39.i686 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.i686 gzip-1.12-6.fc39.i686 info-7.1-1.fc40.i686 jansson-2.13.1-7.fc39.i686 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.i686 krb5-libs-1.21.2-2.fc40.i686 libacl-2.3.1-11.fc40.i686 libarchive-3.7.2-1.fc40.i686 libattr-2.5.1-9.fc40.i686 libblkid-2.39.3-1.fc40.i686 libbrotli-1.1.0-1.fc40.i686 libcap-2.69-1.fc40.i686 libcap-ng-0.8.4-2.fc40.i686 libcom_err-1.47.0-2.fc39.i686 libcurl-8.5.0-1.fc40.i686 libeconf-0.5.2-1.fc40.i686 libevent-2.1.12-9.fc39.i686 libfdisk-2.39.3-1.fc40.i686 libffi-3.4.4-5.fc40.i686 libgcc-13.2.1-6.fc40.i686 libgomp-13.2.1-6.fc40.i686 libidn2-2.3.4-3.fc39.i686 libmount-2.39.3-1.fc40.i686 libnghttp2-1.58.0-1.fc40.i686 libnsl2-2.0.0-6.fc39.i686 libpkgconf-1.9.5-2.fc39.i686 libpsl-0.21.2-4.fc39.i686 libpwquality-1.4.5-6.fc39.i686 libselinux-3.6-2.fc40.i686 libsemanage-3.6-1.fc40.i686 libsepol-3.6-1.fc40.i686 libsigsegv-2.14-5.fc39.i686 libsmartcols-2.39.3-1.fc40.i686 libssh-0.10.6-2.fc40.i686 libssh-config-0.10.6-2.fc40.noarch libstdc++-13.2.1-6.fc40.i686 libtasn1-4.19.0-3.fc39.i686 libtirpc-1.3.4-1.rc1.fc40.i686 libunistring-1.1-5.fc40.i686 libutempter-1.2.1-10.fc39.i686 libuuid-2.39.3-1.fc40.i686 libverto-0.3.2-6.fc39.i686 libxcrypt-4.4.36-3.fc40.i686 libxml2-2.12.3-1.fc40.i686 libzstd-1.5.5-4.fc39.i686 lua-libs-5.4.6-3.fc39.i686 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.i686 mpfr-4.2.1-1.fc40.i686 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.i686 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.i686 openssl-libs-3.1.4-1.fc40.i686 p11-kit-0.25.3-1.fc40.i686 p11-kit-trust-0.25.3-1.fc40.i686 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-9.fc40.i686 pam-libs-1.5.3-9.fc40.i686 patch-2.7.6-22.fc39.i686 pcre2-10.42-2.fc40.i686 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.i686 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.i686 popt-1.19-3.fc39.i686 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.11.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-4.fc39.i686 redhat-rpm-config-275-1.fc40.noarch rpm-4.19.1-2.fc40.i686 rpm-build-4.19.1-2.fc40.i686 rpm-build-libs-4.19.1-2.fc40.i686 rpm-libs-4.19.1-2.fc40.i686 rpm-sequoia-1.5.0-2.fc40.i686 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.i686 setup-2.14.5-1.fc40.noarch shadow-utils-4.14.0-2.fc40.i686 sqlite-libs-3.44.2-1.fc40.i686 systemd-libs-255.1-1.fc40.i686 tar-1.35-2.fc40.i686 unzip-6.0-62.fc39.i686 util-linux-2.39.3-1.fc40.i686 util-linux-core-2.39.3-1.fc40.i686 which-2.21-40.fc39.i686 xxhash-libs-0.8.2-1.fc39.i686 xz-5.4.5-1.fc40.i686 xz-libs-5.4.5-1.fc40.i686 zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.i686 zlib-ng-compat-2.1.5-1.fc40.i686 zstd-1.5.5-4.fc39.i686 Start: buildsrpm Start: rpmbuild -bs Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1704672000 Wrote: /builddir/build/SRPMS/python-biopython-1.82-1.fc40.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-d70a6vtc/python-biopython/python-biopython.spec) Config(child) 1 minutes 43 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.82-1.fc40.src.rpm) Config(fedora-39-i686) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-i686-bootstrap-1704719561.816847/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-i686-bootstrap-1704719561.816847/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-i686-1704719561.816847/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Finish: chroot init Start: build phase for python-biopython-1.82-1.fc40.src.rpm Start: build setup for python-biopython-1.82-1.fc40.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1704672000 Wrote: /builddir/build/SRPMS/python-biopython-1.82-1.fc40.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 43 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 65 kB/s | 3.8 kB 00:00 local 91 kB/s | 3.8 kB 00:00 Dependencies resolved. ============================================================================================================================== Package Arch Version Repository Size ============================================================================================================================== Installing: gcc i686 13.2.1-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 34 M mysql-connector-python3 noarch 8.0.21-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 538 k python3-devel i686 3.12.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274 k python3-mysqlclient i686 2.1.1-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 97 k python3-numpy i686 1:1.26.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.8 M python3-psycopg2 i686 2.9.9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 203 k python3-rdflib noarch 6.2.0-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 882 k python3-reportlab noarch 4.0.8-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.2 M python3-setuptools noarch 68.2.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M Installing dependencies: abattis-cantarell-vf-fonts noarch 0.301-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k annobin-docs noarch 12.35-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 91 k annobin-plugin-gcc i686 12.35-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 959 k cairo i686 1.18.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 755 k cpp i686 13.2.1-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 M default-fonts-core-sans noarch 4.0-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k dejavu-sans-fonts noarch 2.37-21.fc40 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k Transaction Summary ============================================================================================================================== Install 88 Packages Total download size: 105 M Installed size: 380 M Downloading Packages: (1/88): flexiblas-3.3.1-5.fc39.i686.rpm 870 kB/s | 33 kB 00:00 (2/88): flexiblas-openblas-openmp-3.3.1-5.fc39. 407 kB/s | 18 kB 00:00 (3/88): graphite2-1.3.14-13.fc40.i686.rpm 4.0 MB/s | 97 kB 00:00 (4/88): python3-pillow-10.2.0-1.fc40.i686.rpm 16 MB/s | 899 kB 00:00 (5/88): flexiblas-netlib-3.3.1-5.fc39.i686.rpm 26 MB/s | 3.1 MB 00:00 (6/88): abattis-cantarell-vf-fonts-0.301-10.fc3 1.5 MB/s | 121 kB 00:00 (7/88): annobin-docs-12.35-1.fc40.noarch.rpm 1.4 MB/s | 91 kB 00:00 (8/88): cairo-1.18.0-1.fc40.i686.rpm 17 MB/s | 755 kB 00:00 (9/88): default-fonts-core-sans-4.0-9.fc40.noar 1.2 MB/s | 25 kB 00:00 (10/88): annobin-plugin-gcc-12.35-1.fc40.i686.r 9.6 MB/s | 959 kB 00:00 (11/88): expat-2.5.0-3.fc39.i686.rpm 2.3 MB/s | 114 kB 00:00 (12/88): dejavu-sans-fonts-2.37-21.fc40.noarch. 21 MB/s | 1.3 MB 00:00 (13/88): fontconfig-2.15.0-1.fc40.i686.rpm 11 MB/s | 265 kB 00:00 (14/88): fonts-filesystem-2.0.5-12.fc39.noarch. 305 kB/s | 8.2 kB 00:00 (15/88): freetype-2.13.1-2.fc39.i686.rpm 17 MB/s | 419 kB 00:00 (16/88): fribidi-1.0.13-2.fc39.i686.rpm 3.2 MB/s | 92 kB 00:00 (17/88): gc-8.2.2-4.fc39.i686.rpm 4.8 MB/s | 113 kB 00:00 (18/88): cpp-13.2.1-6.fc40.i686.rpm 58 MB/s | 11 MB 00:00 (19/88): gcc-plugin-annobin-13.2.1-6.fc40.i686. 2.3 MB/s | 50 kB 00:00 (20/88): glibc-devel-2.38.9000-30.fc40.i686.rpm 4.5 MB/s | 100 kB 00:00 (21/88): glib2-2.78.3-1.fc40.i686.rpm 54 MB/s | 2.9 MB 00:00 (22/88): glibc-headers-x86-2.38.9000-30.fc40.no 21 MB/s | 514 kB 00:00 (23/88): google-noto-fonts-common-20230801-4.fc 979 kB/s | 17 kB 00:00 (24/88): gnutls-3.8.2-2.fc40.i686.rpm 34 MB/s | 1.1 MB 00:00 (25/88): google-noto-sans-vf-fonts-20230801-4.f 21 MB/s | 583 kB 00:00 (26/88): 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463 kB/s | 8.6 kB 00:00 (57/88): mpdecimal-2.5.1-7.fc39.i686.rpm 4.7 MB/s | 91 kB 00:00 (58/88): mysql-connector-python3-8.0.21-10.fc39 17 MB/s | 538 kB 00:00 (59/88): nettle-3.9.1-2.fc39.i686.rpm 16 MB/s | 439 kB 00:00 (60/88): openblas-0.3.25-1.fc40.i686.rpm 2.0 MB/s | 38 kB 00:00 (61/88): openjpeg2-2.5.0-5.fc40.i686.rpm 8.5 MB/s | 188 kB 00:00 (62/88): pixman-0.42.2-2.fc39.i686.rpm 12 MB/s | 298 kB 00:00 (63/88): openblas-openmp-0.3.25-1.fc40.i686.rpm 39 MB/s | 3.9 MB 00:00 (64/88): protobuf-3.19.6-6.fc39.i686.rpm 26 MB/s | 1.1 MB 00:00 (65/88): pyproject-rpm-macros-1.11.0-1.fc40.noa 1.9 MB/s | 42 kB 00:00 (66/88): python-rpm-macros-3.12-5.fc40.noarch.r 954 kB/s | 19 kB 00:00 (67/88): python-pip-wheel-23.3.1-2.fc40.noarch. 32 MB/s | 1.5 MB 00:00 (68/88): python3-3.12.1-2.fc40.i686.rpm 1.4 MB/s | 27 kB 00:00 (69/88): python3-chardet-5.2.0-2.fc40.noarch.rp 13 MB/s | 273 kB 00:00 (70/88): python3-devel-3.12.1-2.fc40.i686.rpm 13 MB/s | 274 kB 00:00 (71/88): python3-isodate-0.6.1-9.fc39.noarch.rp 3.6 MB/s | 67 kB 00:00 (72/88): python3-mysqlclient-2.1.1-5.fc39.i686. 4.2 MB/s | 97 kB 00:00 (73/88): python3-libs-3.12.1-2.fc40.i686.rpm 44 MB/s | 9.0 MB 00:00 (74/88): python3-numpy-1.26.2-1.fc40.i686.rpm 34 MB/s | 6.8 MB 00:00 (75/88): python3-olefile-0.47-1.fc40.noarch.rpm 2.6 MB/s | 73 kB 00:00 (76/88): python3-packaging-23.2-2.fc40.noarch.r 4.1 MB/s | 115 kB 00:00 (77/88): python3-psycopg2-2.9.9-1.fc40.i686.rpm 6.9 MB/s | 203 kB 00:00 (78/88): python3-protobuf-3.19.6-6.fc39.i686.rp 6.3 MB/s | 397 kB 00:00 (79/88): python3-pyparsing-3.1.1-1.fc40.noarch. 12 MB/s | 261 kB 00:00 (80/88): python3-rdflib-6.2.0-4.fc39.noarch.rpm 12 MB/s | 882 kB 00:00 (81/88): python3-rpm-generators-14-8.fc40.noarc 1.2 MB/s | 30 kB 00:00 (82/88): python3-rpm-macros-3.12-5.fc40.noarch. 581 kB/s | 14 kB 00:00 (83/88): python3-reportlab-4.0.8-2.fc40.noarch. 18 MB/s | 3.2 MB 00:00 (84/88): python3-setuptools-68.2.2-1.fc40.noarc 13 MB/s | 1.4 MB 00:00 (85/88): python3-six-1.16.0-12.fc39.noarch.rpm 1.2 MB/s | 41 kB 00:00 (86/88): xml-common-0.6.3-62.fc40.noarch.rpm 1.7 MB/s | 31 kB 00:00 (87/88): tzdata-2023d-1.fc40.noarch.rpm 12 MB/s | 433 kB 00:00 (88/88): gcc-13.2.1-6.fc40.i686.rpm 17 MB/s | 34 MB 00:01 -------------------------------------------------------------------------------- Total 46 MB/s | 105 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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default-fonts-core-sans-4.0-9.fc40.noarch 16/88 Installing : glibc-headers-x86-2.38.9000-30.fc40.noarch 17/88 Installing : libxcrypt-devel-4.4.36-3.fc40.i686 18/88 Installing : glibc-devel-2.38.9000-30.fc40.i686 19/88 Installing : annobin-docs-12.35-1.fc40.noarch 20/88 Installing : libwebp-1.3.2-2.fc40.i686 21/88 Installing : libpng-2:1.6.40-1.fc40.i686 22/88 Installing : libmpc-1.3.1-3.fc39.i686 23/88 Installing : libjpeg-turbo-2.1.4-3.fc39.i686 24/88 Installing : libgfortran-13.2.1-6.fc40.i686 25/88 Installing : openblas-openmp-0.3.25-1.fc40.i686 26/88 Installing : cpp-13.2.1-6.fc40.i686 27/88 Installing : mariadb-connector-c-3.3.8-1.fc40.i686 28/88 Installing : protobuf-3.19.6-6.fc39.i686 29/88 Installing : pixman-0.42.2-2.fc39.i686 30/88 Installing : openjpeg2-2.5.0-5.fc40.i686 31/88 Installing : nettle-3.9.1-2.fc39.i686 32/88 Installing : gnutls-3.8.2-2.fc40.i686 33/88 Installing : glib2-2.78.3-1.fc40.i686 34/88 Installing : mpdecimal-2.5.1-7.fc39.i686 35/88 Installing : libubsan-13.2.1-6.fc40.i686 36/88 Installing : libtool-ltdl-2.4.7-8.fc40.i686 37/88 Installing : libquadmath-13.2.1-6.fc40.i686 38/88 Installing : flexiblas-netlib-3.3.1-5.fc39.i686 39/88 Installing : flexiblas-openblas-openmp-3.3.1-5.fc39.i686 40/88 Installing : flexiblas-3.3.1-5.fc39.i686 41/88 Installing : libpq-16.1-1.fc40.i686 42/88 Installing : liblerc-4.0.0-4.fc39.i686 43/88 Installing : libimagequant-4.0.3-2.fc40.i686 44/88 Installing : libb2-0.98.1-9.fc39.i686 45/88 Installing : libatomic-13.2.1-6.fc40.i686 46/88 Installing : libasan-13.2.1-6.fc40.i686 47/88 Installing : libXau-1.0.11-4.fc40.i686 48/88 Installing : libxcb-1.16-2.fc40.i686 49/88 Installing : libX11-1.8.7-1.fc40.i686 50/88 Installing : libXext-1.3.5-4.fc40.i686 51/88 Installing : libXrender-0.9.11-4.fc40.i686 52/88 Installing : lcms2-2.15-2.fc39.i686 53/88 Installing : jbigkit-libs-2.1-27.fc40.i686 54/88 Installing : libtiff-4.5.0-3.fc40.i686 55/88 Installing : gc-8.2.2-4.fc39.i686 56/88 Installing : guile22-2.2.7-9.fc39.i686 57/88 Installing : make-1:4.4.1-2.fc39.i686 58/88 Installing : gcc-13.2.1-6.fc40.i686 59/88 Running scriptlet: gcc-13.2.1-6.fc40.i686 59/88 Installing : fribidi-1.0.13-2.fc39.i686 60/88 Installing : expat-2.5.0-3.fc39.i686 61/88 Installing : python3-3.12.1-2.fc40.i686 62/88 Installing : python3-libs-3.12.1-2.fc40.i686 63/88 Installing : python3-chardet-5.2.0-2.fc40.noarch 64/88 Installing : python3-olefile-0.47-1.fc40.noarch 65/88 Installing : python3-packaging-23.2-2.fc40.noarch 66/88 Installing : python3-rpm-generators-14-8.fc40.noarch 67/88 Installing : python3-pyparsing-3.1.1-1.fc40.noarch 68/88 Installing : python3-setuptools-68.2.2-1.fc40.noarch 69/88 Installing : python3-six-1.16.0-12.fc39.noarch 70/88 Installing : python3-isodate-0.6.1-9.fc39.noarch 71/88 Installing : python3-protobuf-3.19.6-6.fc39.i686 72/88 Installing : graphite2-1.3.14-13.fc40.i686 73/88 Installing : mysql-connector-python3-8.0.21-10.fc39.noarch 74/88 Installing : python3-rdflib-6.2.0-4.fc39.noarch 75/88 Installing : python3-devel-3.12.1-2.fc40.i686 76/88 Installing : cairo-1.18.0-1.fc40.i686 77/88 Installing : harfbuzz-8.3.0-2.fc40.i686 78/88 Installing : freetype-2.13.1-2.fc39.i686 79/88 Installing : fontconfig-2.15.0-1.fc40.i686 80/88 Running scriptlet: fontconfig-2.15.0-1.fc40.i686 80/88 Installing : libraqm-0.8.0-5.fc39.i686 81/88 Installing : python3-pillow-10.2.0-1.fc40.i686 82/88 Installing : python3-reportlab-4.0.8-2.fc40.noarch 83/88 Installing : python3-mysqlclient-2.1.1-5.fc39.i686 84/88 Installing : python3-numpy-1:1.26.2-1.fc40.i686 85/88 Installing : python3-psycopg2-2.9.9-1.fc40.i686 86/88 Installing : annobin-plugin-gcc-12.35-1.fc40.i686 87/88 Running scriptlet: annobin-plugin-gcc-12.35-1.fc40.i686 87/88 Installing : gcc-plugin-annobin-13.2.1-6.fc40.i686 88/88 Running scriptlet: gcc-plugin-annobin-13.2.1-6.fc40.i686 88/88 Running scriptlet: fontconfig-2.15.0-1.fc40.i686 88/88 Running scriptlet: gcc-plugin-annobin-13.2.1-6.fc40.i686 88/88 Installed: abattis-cantarell-vf-fonts-0.301-10.fc39.noarch annobin-docs-12.35-1.fc40.noarch annobin-plugin-gcc-12.35-1.fc40.i686 cairo-1.18.0-1.fc40.i686 cpp-13.2.1-6.fc40.i686 default-fonts-core-sans-4.0-9.fc40.noarch dejavu-sans-fonts-2.37-21.fc40.noarch expat-2.5.0-3.fc39.i686 flexiblas-3.3.1-5.fc39.i686 flexiblas-netlib-3.3.1-5.fc39.i686 flexiblas-openblas-openmp-3.3.1-5.fc39.i686 fontconfig-2.15.0-1.fc40.i686 fonts-filesystem-1:2.0.5-12.fc39.noarch freetype-2.13.1-2.fc39.i686 fribidi-1.0.13-2.fc39.i686 gc-8.2.2-4.fc39.i686 gcc-13.2.1-6.fc40.i686 gcc-plugin-annobin-13.2.1-6.fc40.i686 glib2-2.78.3-1.fc40.i686 glibc-devel-2.38.9000-30.fc40.i686 glibc-headers-x86-2.38.9000-30.fc40.noarch gnutls-3.8.2-2.fc40.i686 google-noto-fonts-common-20230801-4.fc40.noarch google-noto-sans-vf-fonts-20230801-4.fc40.noarch graphite2-1.3.14-13.fc40.i686 guile22-2.2.7-9.fc39.i686 harfbuzz-8.3.0-2.fc40.i686 jbigkit-libs-2.1-27.fc40.i686 kernel-headers-6.7.0-0.rc8.61.fc40.i686 lcms2-2.15-2.fc39.i686 libX11-1.8.7-1.fc40.i686 libX11-common-1.8.7-1.fc40.noarch libXau-1.0.11-4.fc40.i686 libXext-1.3.5-4.fc40.i686 libXrender-0.9.11-4.fc40.i686 libasan-13.2.1-6.fc40.i686 libatomic-13.2.1-6.fc40.i686 libb2-0.98.1-9.fc39.i686 libgfortran-13.2.1-6.fc40.i686 libimagequant-4.0.3-2.fc40.i686 libjpeg-turbo-2.1.4-3.fc39.i686 liblerc-4.0.0-4.fc39.i686 libmpc-1.3.1-3.fc39.i686 libpng-2:1.6.40-1.fc40.i686 libpq-16.1-1.fc40.i686 libquadmath-13.2.1-6.fc40.i686 libraqm-0.8.0-5.fc39.i686 libtiff-4.5.0-3.fc40.i686 libtool-ltdl-2.4.7-8.fc40.i686 libubsan-13.2.1-6.fc40.i686 libwebp-1.3.2-2.fc40.i686 libxcb-1.16-2.fc40.i686 libxcrypt-devel-4.4.36-3.fc40.i686 make-1:4.4.1-2.fc39.i686 mariadb-connector-c-3.3.8-1.fc40.i686 mariadb-connector-c-config-3.3.8-1.fc40.noarch mpdecimal-2.5.1-7.fc39.i686 mysql-connector-python3-8.0.21-10.fc39.noarch nettle-3.9.1-2.fc39.i686 openblas-0.3.25-1.fc40.i686 openblas-openmp-0.3.25-1.fc40.i686 openjpeg2-2.5.0-5.fc40.i686 pixman-0.42.2-2.fc39.i686 protobuf-3.19.6-6.fc39.i686 pyproject-rpm-macros-1.11.0-1.fc40.noarch python-pip-wheel-23.3.1-2.fc40.noarch python-rpm-macros-3.12-5.fc40.noarch python3-3.12.1-2.fc40.i686 python3-chardet-5.2.0-2.fc40.noarch python3-devel-3.12.1-2.fc40.i686 python3-isodate-0.6.1-9.fc39.noarch python3-libs-3.12.1-2.fc40.i686 python3-mysqlclient-2.1.1-5.fc39.i686 python3-numpy-1:1.26.2-1.fc40.i686 python3-olefile-0.47-1.fc40.noarch python3-packaging-23.2-2.fc40.noarch python3-pillow-10.2.0-1.fc40.i686 python3-protobuf-3.19.6-6.fc39.i686 python3-psycopg2-2.9.9-1.fc40.i686 python3-pyparsing-3.1.1-1.fc40.noarch python3-rdflib-6.2.0-4.fc39.noarch python3-reportlab-4.0.8-2.fc40.noarch python3-rpm-generators-14-8.fc40.noarch python3-rpm-macros-3.12-5.fc40.noarch python3-setuptools-68.2.2-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch tzdata-2023d-1.fc40.noarch xml-common-0.6.3-62.fc40.noarch Complete! Finish: build setup for python-biopython-1.82-1.fc40.src.rpm Start: rpmbuild python-biopython-1.82-1.fc40.src.rpm Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1704672000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.cZwJQi + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf python-biopython-1.82 + /usr/bin/mkdir -p python-biopython-1.82 + cd python-biopython-1.82 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.82.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/python-biopython-1.82-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.82-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd biopython-1.82 ~/build/BUILD/python-biopython-1.82/biopython-1.82 ~/build/BUILD/python-biopython-1.82 + find Scripts -type f -exec chmod -x '{}' ';' + find Doc -type f -exec chmod -x '{}' ';' + find Doc -type f -exec sed -i 's/\r//' '{}' ';' + find Bio -type f -exec chmod -x '{}' ';' + find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';' + popd + cp -a biopython-1.82 python3 ~/build/BUILD/python-biopython-1.82 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.dBVbeA + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.82 + pushd python3 ~/build/BUILD/python-biopython-1.82/python3 ~/build/BUILD/python-biopython-1.82 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' running build running build_py creating build creating build/lib.linux-i686-cpython-312 creating build/lib.linux-i686-cpython-312/Bio copying Bio/File.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/LogisticRegression.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/MarkovModel.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/MaxEntropy.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/NaiveBayes.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/Seq.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/SeqFeature.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/SeqRecord.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/__init__.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/_utils.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/bgzf.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/kNN.py -> build/lib.linux-i686-cpython-312/Bio copying Bio/pairwise2.py -> build/lib.linux-i686-cpython-312/Bio creating build/lib.linux-i686-cpython-312/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-i686-cpython-312/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Affy creating build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-i686-cpython-312/Bio/Align creating build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Align/Applications creating build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices creating build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/AlignIO creating build/lib.linux-i686-cpython-312/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Alphabet creating build/lib.linux-i686-cpython-312/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Application creating build/lib.linux-i686-cpython-312/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-i686-cpython-312/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-cpython-312/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-i686-cpython-312/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-i686-cpython-312/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Blast creating build/lib.linux-i686-cpython-312/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-i686-cpython-312/Bio/CAPS creating build/lib.linux-i686-cpython-312/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Cluster creating build/lib.linux-i686-cpython-312/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-i686-cpython-312/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-i686-cpython-312/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-i686-cpython-312/Bio/codonalign creating build/lib.linux-i686-cpython-312/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Compass creating build/lib.linux-i686-cpython-312/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-i686-cpython-312/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-i686-cpython-312/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-i686-cpython-312/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Data creating build/lib.linux-i686-cpython-312/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-i686-cpython-312/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-i686-cpython-312/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-i686-cpython-312/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Emboss creating build/lib.linux-i686-cpython-312/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-i686-cpython-312/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Entrez creating build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-i686-cpython-312/Bio/ExPASy creating build/lib.linux-i686-cpython-312/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-i686-cpython-312/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-i686-cpython-312/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-i686-cpython-312/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-i686-cpython-312/Bio/GenBank creating build/lib.linux-i686-cpython-312/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-i686-cpython-312/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Geo creating build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-i686-cpython-312/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Graphics creating build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram creating build/lib.linux-i686-cpython-312/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-cpython-312/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-cpython-312/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-i686-cpython-312/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-i686-cpython-312/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-i686-cpython-312/Bio/HMM creating build/lib.linux-i686-cpython-312/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-i686-cpython-312/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG creating build/lib.linux-i686-cpython-312/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/Compound creating build/lib.linux-i686-cpython-312/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/Enzyme creating build/lib.linux-i686-cpython-312/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/Gene creating build/lib.linux-i686-cpython-312/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/Map creating build/lib.linux-i686-cpython-312/Bio/PDB creating build/lib.linux-i686-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-i686-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-i686-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-i686-cpython-312/Bio/PDB/mmtf creating build/lib.linux-i686-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-i686-cpython-312/Bio/KEGG/KGML creating build/lib.linux-i686-cpython-312/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Medline creating build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-i686-cpython-312/Bio/motifs creating build/lib.linux-i686-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-i686-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-i686-cpython-312/Bio/motifs/applications creating build/lib.linux-i686-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-i686-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-i686-cpython-312/Bio/motifs/jaspar creating build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Nexus creating build/lib.linux-i686-cpython-312/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-i686-cpython-312/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-i686-cpython-312/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-i686-cpython-312/Bio/NMR creating build/lib.linux-i686-cpython-312/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Pathway creating build/lib.linux-i686-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-i686-cpython-312/Bio/PDB creating build/lib.linux-i686-cpython-312/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-i686-cpython-312/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-i686-cpython-312/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-i686-cpython-312/Bio/phenotype creating build/lib.linux-i686-cpython-312/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-i686-cpython-312/Bio/PopGen creating build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop creating build/lib.linux-i686-cpython-312/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-i686-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-i686-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-i686-cpython-312/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Restriction creating build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-i686-cpython-312/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SCOP creating build/lib.linux-i686-cpython-312/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO creating build/lib.linux-i686-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/_model creating build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO creating build/lib.linux-i686-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HHsuiteIO creating build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO creating build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO creating build/lib.linux-i686-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-i686-cpython-312/Bio/SearchIO/InterproscanIO creating build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-i686-cpython-312/Bio/SeqIO creating build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-i686-cpython-312/Bio/SeqUtils creating build/lib.linux-i686-cpython-312/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing creating build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications creating build/lib.linux-i686-cpython-312/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SVDSuperimposer creating build/lib.linux-i686-cpython-312/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-cpython-312/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-i686-cpython-312/Bio/SwissProt creating build/lib.linux-i686-cpython-312/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-i686-cpython-312/Bio/TogoWS creating build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-i686-cpython-312/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-i686-cpython-312/Bio/Phylo creating build/lib.linux-i686-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/Applications creating build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-i686-cpython-312/Bio/Phylo/PAML creating build/lib.linux-i686-cpython-312/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-i686-cpython-312/Bio/UniGene creating build/lib.linux-i686-cpython-312/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-i686-cpython-312/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-i686-cpython-312/Bio/UniProt creating build/lib.linux-i686-cpython-312/BioSQL copying BioSQL/__init__.py -> build/lib.linux-i686-cpython-312/BioSQL copying BioSQL/Loader.py -> build/lib.linux-i686-cpython-312/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-i686-cpython-312/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-i686-cpython-312/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-i686-cpython-312/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:204: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:204: _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-i686-cpython-312/Bio copying Bio/py.typed -> build/lib.linux-i686-cpython-312/Bio copying Bio/Align/_codonaligner.c -> build/lib.linux-i686-cpython-312/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-i686-cpython-312/Bio/Align creating build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-i686-cpython-312/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-i686-cpython-312/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-i686-cpython-312/Bio/Cluster creating build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs creating build/lib.linux-i686-cpython-312/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-i686-cpython-312/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-i686-cpython-312/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-i686-cpython-312/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-i686-cpython-312/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-i686-cpython-312/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-i686-cpython-312/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-i686-cpython-312 creating build/temp.linux-i686-cpython-312/Bio creating build/temp.linux-i686-cpython-312/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/Align/_codonaligner.c -o build/temp.linux-i686-cpython-312/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/Align/_codonaligner.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/Align/_codonaligner.cpython-312-i386-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-i686-cpython-312/Bio/Align/_pairwisealigner.o Bio/Align/_pairwisealigner.c: In function ‘Aligner_watermansmithbeyer_global_align_compare’: Bio/Align/_pairwisealigner.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_pairwisealigner.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_pairwisealigner.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_pairwisealigner.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_pairwisealigner.c: In function ‘Aligner_watermansmithbeyer_local_align_compare’: Bio/Align/_pairwisealigner.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_pairwisealigner.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_pairwisealigner.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_pairwisealigner.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_pairwisealigner.c:6874:34: Bio/Align/_pairwisealigner.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_pairwisealigner.c: In function ‘Aligner_align’: Bio/Align/_pairwisealigner.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_pairwisealigner.c:6874:34: Bio/Align/_pairwisealigner.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_pairwisealigner.c: In function ‘Aligner_align’: Bio/Align/_pairwisealigner.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_pairwisealigner.c:6880:34: Bio/Align/_pairwisealigner.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_pairwisealigner.c: In function ‘Aligner_align’: Bio/Align/_pairwisealigner.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_pairwisealigner.c:6880:34: Bio/Align/_pairwisealigner.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_pairwisealigner.c: In function ‘Aligner_align’: Bio/Align/_pairwisealigner.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/Align/_pairwisealigner.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/Align/_pairwisealigner.cpython-312-i386-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-i686-cpython-312/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/python3.12/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.12/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,pack-relative-relocs -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/cpairwise2module.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/cpairwise2.cpython-312-i386-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-i686-cpython-312/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-i686-cpython-312/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/Nexus/cnexus.cpython-312-i386-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-i686-cpython-312/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-i686-cpython-312/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/motifs/_pwm.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/motifs/_pwm.cpython-312-i386-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-i686-cpython-312/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-i686-cpython-312/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-cpython-312/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/Cluster/cluster.o build/temp.linux-i686-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/Cluster/_cluster.cpython-312-i386-linux-gnu.so building 'Bio.PDB.kdtrees' extension creating build/temp.linux-i686-cpython-312/Bio/PDB gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-i686-cpython-312/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/PDB/kdtrees.cpython-312-i386-linux-gnu.so building 'Bio.PDB.ccealign' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-i686-cpython-312/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/PDB/ccealign.cpython-312-i386-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-i686-cpython-312/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-i686-cpython-312/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib -o build/lib.linux-i686-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-i386-linux-gnu.so ~/build/BUILD/python-biopython-1.82 + popd + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.dG5r90 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.82 + pushd python3 ~/build/BUILD/python-biopython-1.82/python3 ~/build/BUILD/python-biopython-1.82 + /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 --install-data=/usr/share/python-biopython running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12 creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/py.typed -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL copying build/lib.linux-i686-cpython-312/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/cpairwise2.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/py.typed -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniProt copying build/lib.linux-i686-cpython-312/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniProt copying build/lib.linux-i686-cpython-312/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniProt creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniGene copying build/lib.linux-i686-cpython-312/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniGene creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-i686-cpython-312/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-i686-cpython-312/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-i686-cpython-312/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-i686-cpython-312/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-i686-cpython-312/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-i686-cpython-312/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo copying build/lib.linux-i686-cpython-312/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/TogoWS copying build/lib.linux-i686-cpython-312/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/TogoWS creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SwissProt copying build/lib.linux-i686-cpython-312/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SwissProt copying build/lib.linux-i686-cpython-312/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SwissProt creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SVDSuperimposer copying build/lib.linux-i686-cpython-312/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SVDSuperimposer creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-i686-cpython-312/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing copying build/lib.linux-i686-cpython-312/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-i686-cpython-312/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-i686-cpython-312/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/InterproscanIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HHsuiteIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-i686-cpython-312/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP copying build/lib.linux-i686-cpython-312/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction copying build/lib.linux-i686-cpython-312/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction copying build/lib.linux-i686-cpython-312/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction copying build/lib.linux-i686-cpython-312/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction copying build/lib.linux-i686-cpython-312/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-i686-cpython-312/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype copying build/lib.linux-i686-cpython-312/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype copying build/lib.linux-i686-cpython-312/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype copying build/lib.linux-i686-cpython-312/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-i686-cpython-312/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-i686-cpython-312/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-i686-cpython-312/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-i686-cpython-312/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR copying build/lib.linux-i686-cpython-312/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR copying build/lib.linux-i686-cpython-312/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR copying build/lib.linux-i686-cpython-312/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/cnexus.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus copying build/lib.linux-i686-cpython-312/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/_pwm.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/jaspar copying build/lib.linux-i686-cpython-312/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/jaspar copying build/lib.linux-i686-cpython-312/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/jaspar creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-i686-cpython-312/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-i686-cpython-312/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-i686-cpython-312/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs copying build/lib.linux-i686-cpython-312/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Medline copying build/lib.linux-i686-cpython-312/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Medline creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/ccealign.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/kdtrees.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB copying build/lib.linux-i686-cpython-312/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-i686-cpython-312/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-i686-cpython-312/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-i686-cpython-312/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-i686-cpython-312/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-i686-cpython-312/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-i686-cpython-312/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Map copying build/lib.linux-i686-cpython-312/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Map creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Gene copying build/lib.linux-i686-cpython-312/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Gene creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-i686-cpython-312/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Enzyme creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Compound copying build/lib.linux-i686-cpython-312/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Compound copying build/lib.linux-i686-cpython-312/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG copying build/lib.linux-i686-cpython-312/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM copying build/lib.linux-i686-cpython-312/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM copying build/lib.linux-i686-cpython-312/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM copying build/lib.linux-i686-cpython-312/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM copying build/lib.linux-i686-cpython-312/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM copying build/lib.linux-i686-cpython-312/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-i686-cpython-312/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics copying build/lib.linux-i686-cpython-312/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Geo copying build/lib.linux-i686-cpython-312/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Geo copying build/lib.linux-i686-cpython-312/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Geo creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank copying build/lib.linux-i686-cpython-312/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank copying build/lib.linux-i686-cpython-312/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank copying build/lib.linux-i686-cpython-312/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank copying build/lib.linux-i686-cpython-312/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-i686-cpython-312/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/XSDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/XSDs creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/esummary_gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/epost.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/elink.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-i686-cpython-312/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez copying build/lib.linux-i686-cpython-312/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss copying build/lib.linux-i686-cpython-312/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss copying build/lib.linux-i686-cpython-312/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss copying build/lib.linux-i686-cpython-312/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss copying build/lib.linux-i686-cpython-312/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data copying build/lib.linux-i686-cpython-312/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data copying build/lib.linux-i686-cpython-312/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data copying build/lib.linux-i686-cpython-312/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data copying build/lib.linux-i686-cpython-312/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Compass copying build/lib.linux-i686-cpython-312/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Compass creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign copying build/lib.linux-i686-cpython-312/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign copying build/lib.linux-i686-cpython-312/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign copying build/lib.linux-i686-cpython-312/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster copying build/lib.linux-i686-cpython-312/Bio/Cluster/_cluster.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster copying build/lib.linux-i686-cpython-312/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster copying build/lib.linux-i686-cpython-312/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster copying build/lib.linux-i686-cpython-312/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster copying build/lib.linux-i686-cpython-312/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/CAPS copying build/lib.linux-i686-cpython-312/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/CAPS creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast copying build/lib.linux-i686-cpython-312/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast copying build/lib.linux-i686-cpython-312/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast copying build/lib.linux-i686-cpython-312/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast copying build/lib.linux-i686-cpython-312/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast copying build/lib.linux-i686-cpython-312/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Application copying build/lib.linux-i686-cpython-312/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Application creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Alphabet copying build/lib.linux-i686-cpython-312/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Alphabet creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-i686-cpython-312/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/_pairwisealigner.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/_codonaligner.cpython-312-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/_pairwisealigner.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/_codonaligner.c -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-i686-cpython-312/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-i686-cpython-312/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/chain.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/analysis.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align copying build/lib.linux-i686-cpython-312/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Affy copying build/lib.linux-i686-cpython-312/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Affy copying build/lib.linux-i686-cpython-312/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Affy copying build/lib.linux-i686-cpython-312/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio copying build/lib.linux-i686-cpython-312/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL/Loader.py to Loader.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/BioSQL/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniProt/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniProt/GOA.py to GOA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/UniGene/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/_io.py to _io.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Newick.py to Newick.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/_index.py to _index.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model/query.py to query.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/_index.py to _index.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Residues.py to Residues.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Raf.py to Raf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Hie.py to Hie.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Dom.py to Dom.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Des.py to Des.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SCOP/Cla.py to Cla.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction/Restriction.py to Restriction.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PopGen/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/phenotype/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Pathway/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR/xpktools.py to xpktools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus/Trees.py to Trees.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus/StandardData.py to StandardData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus/Nodes.py to Nodes.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Nexus/Nexus.py to Nexus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/jaspar/db.py to db.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/xms.py to xms.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/transfac.py to transfac.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/thresholds.py to thresholds.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/pfm.py to pfm.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/minimal.py to minimal.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/meme.py to meme.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/matrix.py to matrix.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/mast.py to mast.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/alignace.py to alignace.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/motifs/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Medline/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/vectors.py to vectors.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/qcprot.py to qcprot.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/ic_data.py to ic_data.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/cealign.py to cealign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Structure.py to Structure.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Selection.py to Selection.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/SASA.py to SASA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Residue.py to Residue.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PSEA.py to PSEA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PICIO.py to PICIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PDBList.py to PDBList.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Model.py to Model.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Entity.py to Entity.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Dice.py to Dice.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/DSSP.py to DSSP.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Chain.py to Chain.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/Atom.py to Atom.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/KEGG/REST.py to REST.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM/Utilities.py to Utilities.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM/Trainer.py to Trainer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Geo/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Geo/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank/utils.py to utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/GenBank/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Entrez/Parser.py to Parser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Emboss/Applications.py to Applications.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data/PDBData.py to PDBData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Compass/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/codonalign/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Cluster/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/CAPS/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Blast/Applications.py to Applications.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Application/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/tabular.py to tabular.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/stockholm.py to stockholm.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/sam.py to sam.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/psl.py to psl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/phylip.py to phylip.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/nexus.py to nexus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/msf.py to msf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/mauve.py to mauve.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/maf.py to maf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/interfaces.py to interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/hhr.py to hhr.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/fasta.py to fasta.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/exonerate.py to exonerate.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/emboss.py to emboss.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/clustal.py to clustal.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/chain.py to chain.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/bigbed.py to bigbed.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/bed.py to bed.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/analysis.py to analysis.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/a2m.py to a2m.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Affy/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/pairwise2.py to pairwise2.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/kNN.py to kNN.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/bgzf.py to bgzf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/Seq.py to Seq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/File.py to File.cpython-312.pyc writing byte-compilation script '/tmp/tmp7yh5btid.py' /usr/bin/python3 /tmp/tmp7yh5btid.py removing /tmp/tmp7yh5btid.py running install_egg_info 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' Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/biopython-1.82-py3.12.egg-info running install_scripts + xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 + find Scripts -name '*.py' Scripts/xbbtools/xbbtools.py: updating Scripts/xbbtools/xbb_widget.py: updating Scripts/xbbtools/xbb_utils.py: updating Scripts/xbbtools/xbb_translations.py: updating Scripts/xbbtools/xbb_search.py: updating Scripts/xbbtools/xbb_help.py: updating Scripts/xbbtools/xbb_blastbg.py: updating Scripts/xbbtools/xbb_blast.py: updating Scripts/xbbtools/nextorf.py: updating Scripts/update_ncbi_codon_table.py: no change Scripts/scop_pdb.py: updating Scripts/query_pubmed.py: updating Scripts/SeqGui/SeqGui.py: no change Scripts/Restriction/rebase_update.py: updating Scripts/Restriction/ranacompiler.py: updating Scripts/Performance/biosql_performance_read.py: updating Scripts/Performance/biosql_performance_load.py: updating Scripts/PDB/hsexpo.py: updating Scripts/PDB/generate_three_to_one_dict.py: no change Scripts/GenBank/check_output_simple.py: updating Scripts/GenBank/check_output.py: updating + popd ~/build/BUILD/python-biopython-1.82 + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.82-1.fc40 --unique-debug-suffix -1.82-1.fc40.i386 --unique-debug-src-base python-biopython-1.82-1.fc40.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.82 find-debuginfo: starting Extracting debug info from 9 files DWARF-compressing 9 files sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-biopython-1.82-1.fc40.i386 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-1.82-1.fc40.i386/usr/lib/debug/usr/lib/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.C1ysaM + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.82 + pushd python3/Tests ~/build/BUILD/python-biopython-1.82/python3/Tests ~/build/BUILD/python-biopython-1.82 + xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 + find . -name run_tests.py ./run_tests.py: updating + find ../ -name __init__.py + xargs rm -f ++ 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 Tutorial ++ grep -v bgzf ++ grep -v SearchIO_blast ++ grep -v Phylo ++ grep -v pairwise_aligner ++ grep -v Nexus ++ grep -v Align_bigbed ++ grep -v SubsMat + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.017 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 4.400 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.060 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.061 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.072 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.061 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.211 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.091 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.430 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.103 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.192 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.684 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.663 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.217 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.102 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 3.603 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages C.UTF-8 + /usr/bin/python3 run_tests.py --offline -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 0.106 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.168 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages C.UTF-8 + /usr/bin/python3 run_tests.py --offline -v test_Align_fasta.py test_Align_fasta ... ok 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 0.098 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_hhr.py test_Align_hhr ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_7rbx_A_hhsearch_trunc.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_allx.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.377 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.572 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.108 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.071 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.122 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.151 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.575 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_sam.py C.UTF-8 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 0.465 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 2.602 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.503 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.019 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.148 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py test_BioSQL_psycopg2_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 5.124 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py test_Blast_Record ... ok test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.193 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.105 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.084 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Cluster.py test_Cluster ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] 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 0.044 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py test_CodonTable ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding) Check a few ambiguous codons for correct coding. ... ok test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons) Check if stop codons are properly extended. ... ok test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons) Test various ambiguous codons as start codon. ... ok test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons) Test various ambiguous codons as stop codon. ... ok test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables) Check if all IDs and all names are present in ambiguous tables. ... ok test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables) Check if all unambiguous codon tables have all entries. ... ok test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables) Check if we have the same number of tables for each type. ... ok test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table) Raise errors in AmbiguousForwardTable. ... ok test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins) Raise errors in list_possible proteins. ... ok test_print_table (test_CodonTable.PrintTable.test_print_table) Test output of __str__ function. ... ok test_table01 (test_CodonTable.SingleTableTests.test_table01) Check table 1: Standard. ... ok test_table02 (test_CodonTable.SingleTableTests.test_table02) Check table 2: Vertebrate Mitochondrial. ... ok test_table03 (test_CodonTable.SingleTableTests.test_table03) Check table 3: Yeast Mitochondrial. ... ok test_table04 (test_CodonTable.SingleTableTests.test_table04) Check table 4: Mold Mitochondrial and others. ... ok test_table05 (test_CodonTable.SingleTableTests.test_table05) Check table 5: Invertebrate Mitochondrial. ... ok test_table06 (test_CodonTable.SingleTableTests.test_table06) Check table 6: Ciliate and Other Nuclear. ... ok test_table09 (test_CodonTable.SingleTableTests.test_table09) Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok test_table10 (test_CodonTable.SingleTableTests.test_table10) Check table 10: Euplotid Nuclear. ... ok test_table11 (test_CodonTable.SingleTableTests.test_table11) Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok test_table12 (test_CodonTable.SingleTableTests.test_table12) Check table 12: Alternative Yeast Nuclear. ... ok test_table13 (test_CodonTable.SingleTableTests.test_table13) Check table 13: Ascidian Mitochondrial. ... ok test_table14 (test_CodonTable.SingleTableTests.test_table14) Check table 14: Alternative Flatworm Mitochondrial. ... ok test_table16 (test_CodonTable.SingleTableTests.test_table16) Check table 16: Chlorophycean Mitochondrial. ... ok test_table21 (test_CodonTable.SingleTableTests.test_table21) Check table 21: Trematode Mitochondrial. ... ok test_table22 (test_CodonTable.SingleTableTests.test_table22) Check table 22: Scenedesmus obliquus Mitochondrial. ... ok test_table23 (test_CodonTable.SingleTableTests.test_table23) Check table 9: Thraustochytrium Mitochondrial. ... ok test_table24 (test_CodonTable.SingleTableTests.test_table24) Check table 24: Pterobranchia Mitochondrial. ... ok test_table25 (test_CodonTable.SingleTableTests.test_table25) Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok test_table26 (test_CodonTable.SingleTableTests.test_table26) Check table 26: Pachysolen tannophilus Nuclear. ... ok test_table27 (test_CodonTable.SingleTableTests.test_table27) Check table 27: Karyorelict Nuclear. ... ok test_table28 (test_CodonTable.SingleTableTests.test_table28) Check table 28: Condylostoma Nuclear. ... ok test_table29 (test_CodonTable.SingleTableTests.test_table29) Check table 29: Mesodinium Nuclear. ... ok test_table30 (test_CodonTable.SingleTableTests.test_table30) Check table 30: Peritrich Nuclear. ... ok test_table31 (test_CodonTable.SingleTableTests.test_table31) Check table 31: Blastocrithidia Nuclear. ... ok test_table32 (test_CodonTable.SingleTableTests.test_table32) Check table 32: Balanophoraceae Plastid. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.058 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.071 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Compass.py test_Compass ... ok testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 2.032 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Emboss.py test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss. ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.013 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez.py test_Entrez ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux 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 4.151 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py test_Entrez_parser ... ok test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas) Test parsing XML using Schemas. ... ok test_fasta (test_Entrez_parser.EFetchTest.test_fasta) Test error handling when presented with Fasta non-XML data. ... ok test_genbank (test_Entrez_parser.EFetchTest.test_genbank) Test error handling when presented with GenBank non-XML data. ... ok test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ... ok test_pmc (test_Entrez_parser.EFetchTest.test_pmc) Test parsing XML returned by EFetch from PubMed Central. ... ok test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ... ok test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ... ok test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ... ok test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html) Test error handling when presented with HTML (so XML-like) data. ... ok test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping) Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags) Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ... ok test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ... ok test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration) Test error handling for a missing XML declaration. ... ok test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition) Test error handling for a missing DTD or XML Schema. ... ok test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ... ok test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ... ok test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ... ok test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ... ok test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ... ok test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ... ok test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ... ok test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ... ok test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ... ok test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ... ok test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ... ok test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ... ok test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ... ok test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ... ok test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ... ok test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ... ok test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ... ok test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ... ok test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ... ok test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ... ok test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ... ok test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ... ok test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ... ok test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ... ok test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ... ok test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ... ok test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ... ok test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none) Test parsing ESummary XML where an Integer is not defined. ... ok test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ... ok test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ... ok test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ... ok test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ... ok test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ... ok test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ... ok test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ... ok test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ... ok test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO stream (bytes not string). ... ok test_closed_file (test_Entrez_parser.GeneralTests.test_closed_file) Test parsing closed file fails gracefully. ... ok test_parse_bytes_stream (test_Entrez_parser.GeneralTests.test_parse_bytes_stream) Test parsing a file opened in binary mode. ... ok test_parse_text_file (test_Entrez_parser.GeneralTests.test_parse_text_file) Test parsing a file opened in text mode. ... ok test_pickle (test_Entrez_parser.GeneralTests.test_pickle) Test if records created by the parser can be pickled. ... ok test_read_bytes_stream (test_Entrez_parser.GeneralTests.test_read_bytes_stream) Test reading a file opened in binary mode. ... ok test_read_text_file (test_Entrez_parser.GeneralTests.test_read_text_file) Test reading a file opened in text mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.626 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.008 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py test_ExPASy ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.007 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.120 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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_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 0.356 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 3.792 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.151 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 1.569 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.225 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 1.214 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.481 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.056 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.109 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 8.211 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py test_KGML_graphics_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.042 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.849 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.051 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.059 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 1.253 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.056 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.254 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.010 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.085 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 1.203 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.010 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.013 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.008 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.185 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.950 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 2.595 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.211 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.090 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages C.UTF-8 + /usr/bin/python3 run_tests.py --offline -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 0.099 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.442 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.135 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 2.315 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` C.UTF-8 + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py test_PDB_MMCIF2Dict ... ok 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 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py test_PDB_MMCIFIO ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel) Write a multi-model, multi-chain mmCIF file. ... ok test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select) Write a selection of the structure using a Select subclass. ... ok test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict) Write an mmCIF dictionary out, read it in and compare them. ... ok test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue) Write a single residue using MMCIFIO. ... ok test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain) Write a single residue (chain id == X) using MMCIFIO. ... ok test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain) Write a single orphan residue using MMCIFIO. ... ok test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure) Write a full structure using MMCIFIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.303 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 1.518 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.067 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.277 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.064 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.102 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages C.UTF-8 + /usr/bin/python3 run_tests.py --offline -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 0.100 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.077 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 4.484 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.447 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.086 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.306 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.099 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.095 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.074 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.115 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.020 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.084 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.083 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py test_ProtParam ... ok test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity) Calculate protein aromaticity. ... ok test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH) Test charge_at_pH function. ... ok test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids) Calculate amino acid counts. ... ok test_flexibility (test_ProtParam.ProtParamTest.test_flexibility) Calculate protein flexibility. ... ok test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent) Calculate amino acid percentages. ... ok test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight) Calculate protein molecular weight. ... ok test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight) Calculate monoisotopic molecular weight. ... ok test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_gravy (test_ProtParam.ProtParamTest.test_gravy) Calculate gravy. Tests all pre-defined scales. ... ok test_instability_index (test_ProtParam.ProtParamTest.test_instability_index) Calculate protein instability index. ... ok test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point) Calculate the isoelectric point. ... ok test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient) Molar extinction coefficient. ... ok test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale) Calculate the Kite Doolittle scale. ... ok test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction) Calculate secondary structure fractions. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py test_RCSBFormats ... ok 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 0.598 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Restriction.py test_Restriction ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers) Test to be sure isochizomer and neoschizomers are as expected. ... ok test_comparisons (test_Restriction.EnzymeComparison.test_comparisons) Test comparison operators between different enzymes. ... ok test_change (test_Restriction.RestrictionBatchPrintTest.test_change) Test that change() changes something. ... ok test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3) Test that print_as('map'); print_that() correctly wraps round. ... ok test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions) Test Fancier restriction analysis. ... ok test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis) Sequence analysis with a restriction batch. ... ok test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch) Creating and modifying a restriction batch. ... ok test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches) Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches) Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq) Test several methods of FormattedSeq. ... ok test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters) Test if non-IUPAC letters raise a TypeError. ... ok test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object) Test if sequence must be a Seq or MutableSeq object. ... ok test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences) Deal with cutting circular sequences. ... ok test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions) Check if cutting after first and penultimate position works. ... ok test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting) Test basic cutting with EarI (ambiguous overhang). ... ok test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting) Test basic cutting with EcoRI (5'overhang). ... ok test_init (test_Restriction.SimpleEnzyme.test_init) Check for error during __init__. ... ok test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting) Test basic cutting with KpnI (3'overhang). ... ok test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites) Check if overlapping recognition sites are properly handled. ... ok test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands) Check if recognition sites on both strands are properly handled. ... ok test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts) Check if '/' and '//' work as '.search' and '.catalyse'. ... ok test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting) Test basic cutting with SmaI (blunt cutter). ... ok test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting) Test basic cutting with SnaI (unknown). ... ok test_print_that (test_Restriction.TestPrintOutputs.test_print_that) Test print_that function. ... ok test_str_method (test_Restriction.TestPrintOutputs.test_str_method) Test __str__ and __repr__ outputs. ... ok test_supplier (test_Restriction.TestPrintOutputs.test_supplier) Test output of supplier list for different enzyme types. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.221 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py test_SCOP_Cla ... ok 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 0.074 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.074 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.078 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.081 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.076 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.073 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.105 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001) Test blat-psl indexing, multiple queries. ... ok test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002) Test blat-psl indexing, single query, no hits. ... ok test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003) Test blat-psl indexing, single query, single hit. ... ok test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004) Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005) Test blat-psl indexing, multiple queries, no header. ... ok test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006) Test blat-pslx indexing, multiple queries. ... ok test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007) Test blat-pslx indexing, single query, no hits. ... ok test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008) Test blat-pslx indexing, single query, single hit. ... ok test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009) Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010) Test blat-pslx indexing, multiple queries, no header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.141 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py test_SearchIO_exonerate ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar) Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c) Compares vulgar-text coordinate parsing for the coding2coding model. ... ok test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g) Compares vulgar-text coordinate parsing for the genome2genome model. ... ok test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d) Compares vulgar-text coordinate parsing for the protein2dna model. ... ok test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local) Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome) Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding) Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts) Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome) Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein) Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome) Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome) Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner) Test parsing exonerate output (exn_22_m_ner.exn). ... ok test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts) Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome) Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped) Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans) Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple) Test parsing exonerate output (exn_22_q_multiple.exn). ... ok test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts) Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron) Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar) Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts) Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.152 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.070 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.113 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.129 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.139 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.180 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.137 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.069 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.065 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.069 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.196 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.058 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py test_SearchIO_model ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] 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 0.110 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py test_SearchIO_write ... ok test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields) Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl) Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx) Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl) Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query) Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx) Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query) Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab) Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.312 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py test_SeqFeature ... /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqFeature.py:953: 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_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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py test_SeqIO ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux 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 20.383 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.303 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.087 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.122 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 2.723 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.534 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.098 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.089 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py test_SeqIO_TwoBitIO ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.124 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( ok 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 0.648 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 21.055 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py test_SeqIO_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.073 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py test_SeqIO_write ... ok test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.109 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.151 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py test_Seq_objs ... ok test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok test_le (test_Seq_objs.ComparisonTests.test_le) ... ok test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq) Test if feature extraction works properly for unknown sequences. ... ok test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend) Check extending a MutableSeq object. ... ok test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error) Check MutableSeq __init__ raises the appropriate exceptions. ... ok test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem) Check setting sequence contents of a MutableSeq object. ... ok test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error) Check Seq __init__ raises the appropriate exceptions. ... ok test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap) Check count_overlap exception matches python string count method. ... ok test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG) Check our count_overlap method using GG with variable ends and starts. ... ok test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN) Check our count_overlap method using NN with variable ends and starts. ... ok test_equality (test_Seq_objs.StringMethodTests.test_equality) Test equality when mixing types. ... ok test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq) Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed) Check MutableSeq objects can be joined. ... ok test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file) Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq) Checks if Seq join correctly concatenates sequence with the spacer. ... ok test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file) Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok test_search (test_Seq_objs.StringMethodTests.test_search) Check the search method of Seq objects. ... ok test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok test_str_count (test_Seq_objs.StringMethodTests.test_str_count) Check matches the python string count method. ... ok test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG) Check our count_overlap method using GG. ... ok test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN) Check our count_overlap method using NN. ... ok test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode) Check matches the python string encode method. ... ok test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith) Check matches the python string endswith method. ... ok test_str_find (test_Seq_objs.StringMethodTests.test_str_find) Check matches the python string find method. ... ok test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem) Check slicing and indexing works like a string. ... ok test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok test_str_index (test_Seq_objs.StringMethodTests.test_str_index) Check matches the python string index method. ... ok test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower) Check matches the python string islower method. ... ok test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper) Check matches the python string isupper method. ... ok test_str_length (test_Seq_objs.StringMethodTests.test_str_length) Check matches the python string __len__ method. ... ok test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower) Check matches the python string lower method. ... ok test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip) Check matches the python string lstrip method. ... ok test_str_removeprefix (test_Seq_objs.StringMethodTests.test_str_removeprefix) Check matches the python string removeprefix method. ... ok test_str_removesuffix (test_Seq_objs.StringMethodTests.test_str_removesuffix) Check matches the python string removesuffix method. ... ok test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace) Check matches the python string replace method. ... ok test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind) Check matches the python string rfind method. ... ok test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex) Check matches the python string rindex method. ... ok test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit) Check matches the python string rsplit method. ... ok test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip) Check matches the python string rstrip method. ... ok test_str_split (test_Seq_objs.StringMethodTests.test_str_split) Check matches the python string split method. ... ok test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith) Check matches the python string startswith method. ... ok test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip) Check matches the python string strip method. ... ok test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper) Check matches the python string upper method. ... ok test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription) Check obj.back_transcribe() method. ... ok test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement) Check obj.complement() method. ... ok test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement) Check obj.reverse_complement() method. ... ok test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription) Check obj.transcribe() method. ... ok test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate) Check obj.translate() method. ... ok test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons) Check obj.translate() method with ambiguous codons. ... ok test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons) Check obj.translate() method with invalid codons. ... ok test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops) Check obj.translate() method with stop codons. ... ok test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable) Check creating a MutableSeq object. ... ok test_toseq (test_Seq_objs.StringMethodTests.test_toseq) Check creating a Seq object. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.066 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.101 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.228 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.083 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py test_TogoWS ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.730 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py test_UniProt_GOA ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator) Test GOA GAF file iterator. ... ok test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator) Test GOA GPA file iterator. ... ok test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator) Test GOA GPI file iterator, gpi-version: 1.1. ... ok test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two) Test GOA GPI file iterator, gpi-version: 1.2. ... ok test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing) Test record_has, and writerec. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.020 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py test_Uniprot ... ok test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6) Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8) Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok test_P60904 (test_Uniprot.TestUniprot.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P84001 (test_Uniprot.TestUniprot.test_P84001) Parse mass spec structured comment with unknown loc. ... ok test_Q13639 (test_Uniprot.TestUniprot.test_Q13639) Compare SwissProt text and uniprot XML versions of Q13639. ... ok test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex) Compare SwissProt text and uniprot XML versions of several examples. ... ok test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index) Index SwissProt text and uniprot XML versions of several examples. ... ok test_sp016 (test_Uniprot.TestUniprot.test_sp016) Parsing SwissProt file sp016. ... ok test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed) Checks if parser supports new XML Element (submittedName). ... ok test_uni001 (test_Uniprot.TestUniprot.test_uni001) Parsing Uniprot file uni001. ... ok test_uni003 (test_Uniprot.TestUniprot.test_uni003) Parsing Uniprot file uni003. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.227 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align.py test_align ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] 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 0.175 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py test_align_substitution_matrices ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix) Test basic matrix operations. ... ok test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector) Test basic vector operations. ... ok test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq) Test nucleotide frequency calculations. ... ok test_pickling (test_align_substitution_matrices.TestBasics.test_pickling) Test pickling a substitution matrix. ... ok test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq) Test amino acid frequency calculations. ... ok test_read_write (test_align_substitution_matrices.TestBasics.test_read_write) Test reading and writing substitution matrices. ... ok test_loading (test_align_substitution_matrices.TestLoading.test_loading) Confirm that all provided substitution matrices can be loaded. ... ok test_reading (test_align_substitution_matrices.TestLoading.test_reading) Confirm matrix reading works with filename or handle. ... ok test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies) Test calculating substitution frequencies. ... ok test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities) Test calculating substitution probabilities. ... ok test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities) Test symmetrizing substitution probabilities. ... ok test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities) Test calculating expected amino acid probabilities. ... ok test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities) Test calculating expected amino acid substitution probabilities. ... ok test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores) Test calculating amino acid substitution log-ratios. ... ok test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident) Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.456 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py test_cellosaurus ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test__str__ (test_cellosaurus.TestCellosaurus.test__str__) Test string function. ... ok test_parse (test_cellosaurus.TestCellosaurus.test_parse) Test parsing function. ... ok test_read (test_cellosaurus.TestCellosaurus.test_read) Test read function. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 5.978 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.060 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.065 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.066 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.398 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py test_motifs_online ... skipping. internet not available Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.115 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok 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 0.105 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.239 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 9.264 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. ---------------------------------------------------------------------- Ran 1 test in 0.006 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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. Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.109 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prodoc.py test_prodoc ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc) Parsing an excerpt of prosite.doc. ... ok test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100) Reading Prodoc record PDOC00100. ... ok test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113) Reading Prodoc record PDOC00113. ... ok test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144) Reading Prodoc record PDOC00144. ... ok test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149) Reading Prodoc record PDOC00149. ... ok test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340) Reading Prodoc record PDOC00340. ... ok test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424) Reading Prodoc record PDOC00424. ... ok test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472) Reading Prodoc record PDOC00472. ... ok test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640) Reading Prodoc record PDOC00640. ... ok test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787) Reading Prodoc record PDOC00787. ... ok test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933) Reading Prodoc record PDOC00933. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_seq.py test_seq ... ok Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values) Test that other tests do not introduce characters to our values. ... ok test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok test_seq (test_seq.TestAttributes.test_seq) ... ok test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok test_immutable (test_seq.TestComplement.test_immutable) ... ok test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements) Test double reverse complement preserves the sequence. ... ok test_add_method (test_seq.TestMutableSeq.test_add_method) Test adding wrong type to MutableSeq. ... ok test_appending (test_seq.TestMutableSeq.test_appending) ... ok test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok test_complement (test_seq.TestMutableSeq.test_complement) ... ok test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok test_count (test_seq.TestMutableSeq.test_count) ... ok test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison) Test __eq__ comparison method. ... ok test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok test_index (test_seq.TestMutableSeq.test_index) ... ok test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok test_length (test_seq.TestMutableSeq.test_length) ... ok test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction) Test MutableSeq object initialization. ... ok test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison) Test __ne__ comparison method. ... ok test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok test_repr (test_seq.TestMutableSeq.test_repr) ... ok test_reverse (test_seq.TestMutableSeq.test_reverse) Test using reverse method. ... ok test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride) Test reverse using -1 stride. ... ok test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n) Test setting wobble codon to N (set slice with stride 3). ... ok test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok test_as_string (test_seq.TestSeq.test_as_string) Test converting Seq to string. ... ok test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide) Test getting first nucleotide of Seq. ... ok test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide) Test getting last nucleotide of Seq. ... ok test_length (test_seq.TestSeq.test_length) Test len method on Seq object. ... ok test_replace (test_seq.TestSeq.test_replace) ... ok test_repr (test_seq.TestSeq.test_repr) Test representation of Seq object. ... ok test_reverse (test_seq.TestSeq.test_reverse) Test reverse using -1 stride. ... ok test_seq_construction (test_seq.TestSeq.test_seq_construction) Test Seq object initialization. ... ok test_slicing (test_seq.TestSeq.test_slicing) Test slicing of Seq. ... ok test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok test_defined (test_seq.TestSeqDefined.test_defined) ... ok test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok test_imul_method (test_seq.TestSeqMultiplication.test_imul_method) Test imul method; relies on addition and mull methods. ... ok test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions) Test imul method exceptions. ... ok test_mul_method (test_seq.TestSeqMultiplication.test_mul_method) Test mul method; relies on addition method. ... ok test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions) Test mul method exceptions. ... ok test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method) Test rmul method; relies on addition method. ... ok test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions) Test rmul method exceptions. ... ok test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types) Test incompatible types __gt__ comparison method. ... ok test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types) Test incompatible types __ge__ comparison method. ... ok test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types) Test incompatible types __lt__ comparison method. ... ok test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types) Test incompatible types __le__ comparison method. ... ok test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion) Test __ne__ comparison method. ... ok test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok test_stops (test_seq.TestStopCodons.test_stops) ... ok test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok test_translation (test_seq.TestTranslating.test_translation) ... ok test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins) Check translation fails on a protein. ... ok test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons) Check for error and warning messages. ... ok test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type) Test translation table cannot be CodonTable. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds C.UTF-8 + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat | grep -v Align_bigbed` + echo C.UTF-8 + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/lib/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -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 0.053 seconds Skipping any tests requiring internet access Python version: 3.12.1 (main, Dec 18 2023, 00:00:00) [GCC 13.2.1 20231205 (Red Hat 13.2.1-6)] Operating system: posix linux ~/build/BUILD/python-biopython-1.82 + popd + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-biopython-1.82-1.fc40.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2wvwiW + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.82 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.DOZbmm + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.82 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python3-biopython + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.82/python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.82-1.fc40 python3-biopython = 1.82-1.fc40 python3-biopython(x86-32) = 1.82-1.fc40 python3.12-biopython = 1.82-1.fc40 python3.12dist(biopython) = 1.82 python3dist(biopython) = 1.82 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 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_ABI_DT_RELR) python(abi) = 3.12 python3.12dist(numpy) rtld(GNU_HASH) Processing files: python-biopython-doc-1.82-1.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.VhOxXP + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.82 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python-biopython-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python-biopython-doc + cp -pr /builddir/build/BUILD/python-biopython-1.82/biopython-1.82/Doc /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/doc/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.kGEdJj + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.82 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python-biopython-doc + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python-biopython-doc + cp -pr /builddir/build/BUILD/python-biopython-1.82/biopython-1.82/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386/usr/share/licenses/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython-doc = 1.82-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-biopython-debugsource-1.82-1.fc40.i686 Provides: python-biopython-debugsource = 1.82-1.fc40 python-biopython-debugsource(x86-32) = 1.82-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.82-1.fc40.i686 Provides: debuginfo(build-id) = 1064dc69c8caf3ee26ccd2a44499dda96c2282a6 debuginfo(build-id) = 1d0e81fbd48a4d4e9f4ab25085a167b4ce4d17bd debuginfo(build-id) = 50bbdf40bbfb5c9f0c23e3e99a95edb5367a903b debuginfo(build-id) = 5178d9c472ef06370744a3f9a00f6ec8774d96f4 debuginfo(build-id) = 668ba90df547d70958fff63df2e179057aa1a195 debuginfo(build-id) = a4e63dee7580bc572b0e49fc7a8024230b2341a0 debuginfo(build-id) = e0f5ec52067eb71fae8a70c3e24608612817c8f1 debuginfo(build-id) = e4639be4ad3a7f3cddd0a165b0ccb9cede9d68d5 debuginfo(build-id) = fc272dd256f40e725bad7a850f712c3c008de737 python-biopython-debuginfo = 1.82-1.fc40 python3-biopython-debuginfo = 1.82-1.fc40 python3-biopython-debuginfo(x86-32) = 1.82-1.fc40 python3.12-biopython-debuginfo = 1.82-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(x86-32) = 1.82-1.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 Wrote: /builddir/build/RPMS/python-biopython-doc-1.82-1.fc40.noarch.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.82-1.fc40.i686.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.82-1.fc40.i686.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.82-1.fc40.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.3D64nJ + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.82 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.82-1.fc40.i386 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.iS2plK + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/python-biopython-1.82-SPECPARTS + rm -rf python-biopython-1.82 python-biopython-1.82.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-biopython-1.82-1.fc40.src.rpm Finish: build phase for python-biopython-1.82-1.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-i686-1704719561.816847/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.82-1.fc40.src.rpm) Config(child) 4 minutes 1 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": "python3-biopython", "epoch": null, "version": "1.82", "release": "1.fc40", "arch": "i686" }, { "name": "python-biopython-debugsource", "epoch": null, "version": "1.82", "release": "1.fc40", "arch": "i686" }, { "name": "python3-biopython-debuginfo", "epoch": null, "version": "1.82", "release": "1.fc40", "arch": "i686" }, { "name": "python-biopython-doc", "epoch": null, "version": "1.82", "release": "1.fc40", "arch": "noarch" }, { "name": "python-biopython", "epoch": null, "version": "1.82", "release": "1.fc40", "arch": "src" } ] } RPMResults finished