Warning: Permanently added '54.197.205.66' (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/7305665-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64


Version: 0.72
PID: 14112
Logging PID: 14113
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 7305665,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '83a6c30d088ef0e48b74aa864929b2f828283303',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:8/python-biopython',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'python-biopython',
 'package_version': '1.83-5',
 'project_dirname': 'openblas-0.3.23:pr:8',
 '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-rawhide-aarch64/',
            '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/music',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'https://src.fedoraproject.org/user/music',
 'tags': [],
 'task_id': '7305665-fedora-rawhide-aarch64',
 '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:8/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:8/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython'...

Running: git checkout 83a6c30d088ef0e48b74aa864929b2f828283303 --

cmd: ['git', 'checkout', '83a6c30d088ef0e48b74aa864929b2f828283303', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython
rc: 0
stdout: 
stderr: Note: switching to '83a6c30d088ef0e48b74aa864929b2f828283303'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 83a6c30 automatic import of python-biopython

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading biopython-1.83.tar.gz
INFO: Reading stdout from command: curl --help all
/usr/bin/tail: INFO: Calling: curl -H Pragma: -o biopython-1.83.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23:pr:8/python-biopython/biopython-1.83.tar.gz/md5/fa95c92de7cfbb153b070e3da5aaf14a/biopython-1.83.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
/var/lib/copr-rpmbuild/main.log: file truncated
                                 Dload  Upload   Total   Spent    Left  Speed
100 18.5M  100 18.5M    0     0  27.3M      0 --:--:-- --:--:-- --:--:-- 27.3M
INFO: Reading stdout from command: md5sum biopython-1.83.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713009811.077841 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.5 starting (python version = 3.12.1, NVR = mock-5.5-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1713009811.077841 -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-giklwl1_/python-biopython/python-biopython.spec)  Config(fedora-rawhide-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.5
INFO: Mock Version: 5.5
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1713009811.077841/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:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1713009811.077841/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/d2f50f4eeba0ad8567f8772d4983837ea1a7326aa22c277d1dce642e410f76d1/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/d2f50f4eeba0ad8567f8772d4983837ea1a7326aa22c277d1dce642e410f76d1/merged) with podman image umount
INFO: Using 'dnf' instead of 'dnf5' for bootstrap chroot
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf5 tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  42 MB/s | 3.2 MB     00:00    
Additional repo http_kojipkgs_fedoraproject_org  64 MB/s |  17 MB     00:00    
fedora                                           27 MB/s |  19 MB     00:00    
Dependencies resolved.
===========================================================================================================
 Package        Arch     Version       Repository                                                      Size
===========================================================================================================
Installing:
 dnf5           aarch64  5.1.17-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  642 k
 dnf5-plugins   aarch64  5.1.17-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  329 k
Installing dependencies:
 fmt            aarch64  10.2.1-4.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  121 k
 libdnf5        aarch64  5.1.17-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  912 k
 libdnf5-cli    aarch64  5.1.17-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  219 k
 sdbus-cpp      aarch64  1.5.0-2.fc41  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  103 k
 systemd-libs   aarch64  255.4-1.fc41  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  694 k

Transaction Summary
===========================================================================================================
Install  7 Packages

Total download size: 2.9 M
Installed size: 9.9 M
Downloading Packages:
(1/7): dnf5-5.1.17-1.fc41.aarch64.rpm           6.6 MB/s | 642 kB     00:00    
(2/7): dnf5-plugins-5.1.17-1.fc41.aarch64.rpm   2.8 MB/s | 329 kB     00:00    
(3/7): fmt-10.2.1-4.fc41.aarch64.rpm            1.0 MB/s | 121 kB     00:00    
(4/7): libdnf5-5.1.17-1.fc41.aarch64.rpm         32 MB/s | 912 kB     00:00    
(5/7): sdbus-cpp-1.5.0-2.fc41.aarch64.rpm       4.1 MB/s | 103 kB     00:00    
(6/7): systemd-libs-255.4-1.fc41.aarch64.rpm     23 MB/s | 694 kB     00:00    
(7/7): libdnf5-cli-5.1.17-1.fc41.aarch64.rpm    4.7 MB/s | 219 kB     00:00    
--------------------------------------------------------------------------------
Total                                            18 MB/s | 2.9 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : fmt-10.2.1-4.fc41.aarch64                              1/7 
  Installing       : libdnf5-5.1.17-1.fc41.aarch64                          2/7 
  Installing       : libdnf5-cli-5.1.17-1.fc41.aarch64                      3/7 
  Installing       : systemd-libs-255.4-1.fc41.aarch64                      4/7 
  Installing       : sdbus-cpp-1.5.0-2.fc41.aarch64                         5/7 
  Installing       : dnf5-5.1.17-1.fc41.aarch64                             6/7 
  Installing       : dnf5-plugins-5.1.17-1.fc41.aarch64                     7/7 
  Running scriptlet: dnf5-plugins-5.1.17-1.fc41.aarch64                     7/7 

Installed:
  dnf5-5.1.17-1.fc41.aarch64             dnf5-plugins-5.1.17-1.fc41.aarch64     
  fmt-10.2.1-4.fc41.aarch64              libdnf5-5.1.17-1.fc41.aarch64          
  libdnf5-cli-5.1.17-1.fc41.aarch64      sdbus-cpp-1.5.0-2.fc41.aarch64         
  systemd-libs-255.4-1.fc41.aarch64     

Complete!
INFO: Switching package manager from dnf to the dnf5 (direct choice)
Finish(bootstrap): installing dnf5 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-rawhide-aarch64-1713009811.077841/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 dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-1.fc40.aarch64
  rpm-sequoia-1.6.0-2.fc40.aarch64
  python3-dnf-4.19.2-1.fc41.noarch
  yum-4.19.2-1.fc41.noarch
  dnf5-5.1.17-1.fc41.aarch64
  dnf5-plugins-5.1.17-1.fc41.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  50.4 KiB/s |   9.6 KiB |  00m00s
 Copr repository                        100% | 109.8 KiB/s |   1.5 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% |  50.9 KiB/s |   4.1 KiB |  00m00s
 Copr repository                        100% |  73.0 MiB/s |   3.2 MiB |  00m00s
Repositories loaded.
Package                           Arch    Version                    Repository                                                         Size
Installing group/module packages:                                                                                                           
 bash                             aarch64 5.2.26-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   8.3 MiB
 bzip2                            aarch64 1.0.8-18.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 427.5 KiB
 coreutils                        aarch64 9.5-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  20.7 MiB
 cpio                             aarch64 2.15-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 diffutils                        aarch64 3.10-5.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.1 MiB
 fedora-release-common            noarch  41-0.6                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  19.2 KiB
 findutils                        aarch64 1:4.9.0-8.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.7 MiB
 gawk                             aarch64 5.3.0-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.2 MiB
 glibc-minimal-langpack           aarch64 2.39.9000-10.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 grep                             aarch64 3.11-7.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 gzip                             aarch64 1.13-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 488.8 KiB
 info                             aarch64 7.1-2.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 613.5 KiB
 patch                            aarch64 2.7.6-24.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 390.5 KiB
 redhat-rpm-config                noarch  288-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183.3 KiB
 rpm-build                        aarch64 4.19.1.1-1.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 sed                              aarch64 4.9-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 shadow-utils                     aarch64 2:4.15.1-2.fc41            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.3 MiB
 tar                              aarch64 2:1.35-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 unzip                            aarch64 6.0-63.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 726.4 KiB
 util-linux                       aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  17.5 MiB
 which                            aarch64 2.21-41.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 248.1 KiB
 xz                               aarch64 1:5.4.6-3.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.3 MiB
Installing dependencies:                                                                                                                    
 alternatives                     aarch64 1.26-3.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 218.2 KiB
 ansible-srpm-macros              noarch  1-14.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  35.7 KiB
 audit-libs                       aarch64 4.0.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 547.2 KiB
 authselect                       aarch64 1.5.0-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309.4 KiB
 authselect-libs                  aarch64 1.5.0-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 931.8 KiB
 basesystem                       noarch  11-20.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 binutils                         aarch64 2.42.50-6.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  33.4 MiB
 binutils-gold                    aarch64 2.42.50-6.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 bzip2-libs                       aarch64 1.0.8-18.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 200.7 KiB
 ca-certificates                  noarch  2023.2.62_v7.0.401-6.fc40  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.3 MiB
 coreutils-common                 aarch64 9.5-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  11.2 MiB
 cracklib                         aarch64 2.9.11-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 934.6 KiB
 crypto-policies                  noarch  20240320-1.git58e3d95.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 119.2 KiB
 curl                             aarch64 8.7.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 886.0 KiB
 cyrus-sasl-lib                   aarch64 2.1.28-19.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 debugedit                        aarch64 5.0-14.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 498.8 KiB
 dwz                              aarch64 0.15-6.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 386.7 KiB
 ed                               aarch64 1.20.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 282.3 KiB
 efi-srpm-macros                  noarch  5-11.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  40.1 KiB
 elfutils                         aarch64 0.191-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.0 MiB
 elfutils-debuginfod-client       aarch64 0.191-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 396.7 KiB
 elfutils-default-yama-scope      noarch  0.191-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.8 KiB
 elfutils-libelf                  aarch64 0.191-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.3 MiB
 elfutils-libs                    aarch64 0.191-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 fedora-gpg-keys                  noarch  41-0.1                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125.0 KiB
 fedora-release                   noarch  41-0.6                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 fedora-release-identity-basic    noarch  41-0.6                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 694.0   B
 fedora-repos                     noarch  41-0.1                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.9 KiB
 fedora-repos-rawhide             noarch  41-0.1                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 KiB
 file                             aarch64 5.45-5.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 267.4 KiB
 file-libs                        aarch64 5.45-5.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  10.0 MiB
 filesystem                       aarch64 3.18-9.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 106.0   B
 fonts-srpm-macros                noarch  1:2.0.5-14.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  55.3 KiB
 forge-srpm-macros                noarch  0.3.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  39.0 KiB
 fpc-srpm-macros                  noarch  1.3-12.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144.0   B
 gdb-minimal                      aarch64 14.2-4.fc41                copr_base                                                      12.7 MiB
 gdbm                             aarch64 1:1.23-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 928.2 KiB
 gdbm-libs                        aarch64 1:1.23-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 425.8 KiB
 ghc-srpm-macros                  noarch  1.9.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 747.0   B
 glibc                            aarch64 2.39.9000-10.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   9.7 MiB
 glibc-common                     aarch64 2.39.9000-10.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.6 MiB
 glibc-gconv-extra                aarch64 2.39.9000-10.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  49.0 MiB
 gmp                              aarch64 1:6.3.0-1.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 721.9 KiB
 gnat-srpm-macros                 noarch  6-5.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 KiB
 go-srpm-macros                   noarch  3.5.0-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  60.6 KiB
 jansson                          aarch64 2.13.1-9.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 220.4 KiB
 kernel-srpm-macros               noarch  1.0-23.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 KiB
 keyutils-libs                    aarch64 1.6.3-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 226.3 KiB
 krb5-libs                        aarch64 1.21.2-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.4 MiB
 libacl                           aarch64 2.3.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.0 KiB
 libarchive                       aarch64 3.7.2-3.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 libattr                          aarch64 2.5.2-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.5 KiB
 libblkid                         aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 418.5 KiB
 libbrotli                        aarch64 1.1.0-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libcap                           aarch64 2.69-8.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.4 MiB
 libcap-ng                        aarch64 0.8.5-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 417.0 KiB
 libcom_err                       aarch64 1.47.0-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 239.2 KiB
 libcurl                          aarch64 8.7.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 921.3 KiB
 libeconf                         aarch64 0.6.2-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 206.0 KiB
 libevent                         aarch64 2.1.12-12.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 libfdisk                         aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482.8 KiB
 libffi                           aarch64 3.4.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 282.3 KiB
 libgcc                           aarch64 14.0.1-0.15.fc41           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 350.2 KiB
 libgomp                          aarch64 14.0.1-0.15.fc41           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 566.9 KiB
 libidn2                          aarch64 2.3.7-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 457.1 KiB
 libmount                         aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 483.8 KiB
 libnghttp2                       aarch64 1.61.0-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.1 KiB
 libnsl2                          aarch64 2.0.1-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 221.9 KiB
 libpkgconf                       aarch64 2.1.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 198.0 KiB
 libpsl                           aarch64 0.21.5-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.5 KiB
 libpwquality                     aarch64 1.4.5-9.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libselinux                       aarch64 3.6-4.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 265.1 KiB
 libsemanage                      aarch64 3.6-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 361.4 KiB
 libsepol                         aarch64 3.6-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 874.0 KiB
 libsmartcols                     aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 288.4 KiB
 libssh                           aarch64 0.10.6-6.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 581.2 KiB
 libssh-config                    noarch  0.10.6-6.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 277.0   B
 libstdc++                        aarch64 14.0.1-0.15.fc41           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.8 MiB
 libtasn1                         aarch64 4.19.0-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 283.7 KiB
 libtirpc                         aarch64 1.3.4-1.rc3.fc41           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274.6 KiB
 libtool-ltdl                     aarch64 2.4.7-10.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 222.2 KiB
 libunistring                     aarch64 1.1-7.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 MiB
 libutempter                      aarch64 1.2.1-13.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 417.6 KiB
 libuuid                          aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.4 KiB
 libverto                         aarch64 0.3.2-8.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.4 KiB
 libxcrypt                        aarch64 4.4.36-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 398.9 KiB
 libxml2                          aarch64 2.12.6-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 libzstd                          aarch64 1.5.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 795.9 KiB
 lua-libs                         aarch64 5.4.6-5.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 393.0 KiB
 lua-srpm-macros                  noarch  1-13.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.3 KiB
 lz4-libs                         aarch64 1.9.4-6.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 261.4 KiB
 mpfr                             aarch64 4.2.1-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 818.7 KiB
 ncurses-base                     noarch  6.4-12.20240127.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.2 KiB
 ncurses-libs                     aarch64 6.4-12.20240127.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 ocaml-srpm-macros                noarch  9-3.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 KiB
 openblas-srpm-macros             noarch  2-17.fc41                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 112.0   B
 openldap                         aarch64 2.6.7-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 openssl-libs                     aarch64 1:3.2.1-6.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.8 MiB
 p11-kit                          aarch64 0.25.3-4.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.8 MiB
 p11-kit-trust                    aarch64 0.25.3-4.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 655.4 KiB
 package-notes-srpm-macros        noarch  0.5-11.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 KiB
 pam                              aarch64 1.6.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  11.0 MiB
 pam-libs                         aarch64 1.6.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 607.0 KiB
 pcre2                            aarch64 10.43-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 905.3 KiB
 pcre2-syntax                     noarch  10.43-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 249.0 KiB
 perl-srpm-macros                 noarch  1-53.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0   B
 pkgconf                          aarch64 2.1.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 238.3 KiB
 pkgconf-m4                       noarch  2.1.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  13.9 KiB
 pkgconf-pkg-config               aarch64 2.1.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 990.0   B
 popt                             aarch64 1.19-6.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 272.8 KiB
 publicsuffix-list-dafsa          noarch  20240107-3.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  67.5 KiB
 pyproject-srpm-macros            noarch  1.12.0-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 KiB
 python-srpm-macros               noarch  3.12-9.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  50.5 KiB
 qt5-srpm-macros                  noarch  5.15.13-1.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 492.0   B
 qt6-srpm-macros                  noarch  6.7.0-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0   B
 readline                         aarch64 8.2-8.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 689.1 KiB
 rpm                              aarch64 4.19.1.1-1.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.0 MiB
 rpm-build-libs                   aarch64 4.19.1.1-1.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.4 KiB
 rpm-libs                         aarch64 4.19.1.1-1.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.6 KiB
 rpm-sequoia                      aarch64 1.6.0-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 rust-srpm-macros                 noarch  26.2-1.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.8 KiB
 setup                            noarch  2.14.5-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.4 KiB
 sqlite-libs                      aarch64 3.45.2-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 systemd-libs                     aarch64 255.4-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.5 MiB
 util-linux-core                  aarch64 2.40-13.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.2 MiB
 xxhash-libs                      aarch64 0.8.2-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 212.2 KiB
 xz-libs                          aarch64 1:5.4.6-3.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 265.6 KiB
 zig-srpm-macros                  noarch  1-2.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 KiB
 zip                              aarch64 3.0-40.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 zlib-ng-compat                   aarch64 2.1.6-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 261.7 KiB
 zstd                             aarch64 1.5.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
Installing groups:                                                                                                                          
 Buildsystem building group                                                                                                                 

Transaction Summary:
 Installing:      153 packages

Total size of inbound packages is 52 MiB. Need to download 0 B.
After this operation 307 MiB will be used (install 307 MiB, remove 0 B).
[  1/153] tar-2:1.35-3.fc40.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
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[  2/153] bzip2-0:1.0.8-18.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[  3/153] redhat-rpm-config-0:288-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
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[  4/153] rpm-build-0:4.19.1.1-1.fc40.a 100% |   0.0   B/s |   0.0   B |  00m00s
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[  5/153] unzip-0:6.0-63.fc40.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
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[  6/153] cpio-0:2.15-1.fc40.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[  7/153] which-0:2.21-41.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[  8/153] bash-0:5.2.26-3.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[  9/153] coreutils-0:9.5-1.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 10/153] grep-0:3.11-7.fc40.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 11/153] patch-0:2.7.6-24.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 12/153] sed-0:4.9-1.fc40.aarch64      100% |   0.0   B/s |   0.0   B |  00m00s
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[ 13/153] shadow-utils-2:4.15.1-2.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 14/153] util-linux-0:2.40-13.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 15/153] diffutils-0:3.10-5.fc40.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 16/153] fedora-release-common-0:41-0. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 17/153] findutils-1:4.9.0-8.fc40.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 18/153] gawk-0:5.3.0-3.fc40.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
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[ 19/153] glibc-minimal-langpack-0:2.39 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 20/153] gzip-0:1.13-1.fc40.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 21/153] info-0:7.1-2.fc40.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
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[ 22/153] xz-1:5.4.6-3.fc41.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
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[ 23/153] glibc-0:2.39.9000-10.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 24/153] xz-libs-1:5.4.6-3.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 25/153] audit-libs-0:4.0.1-1.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 26/153] authselect-libs-0:1.5.0-5.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 27/153] libblkid-0:2.40-13.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 28/153] libcap-ng-0:0.8.5-1.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 31/153] libselinux-0:3.6-4.fc40.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 32/153] libsmartcols-0:2.40-13.fc41.a 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 33/153] libutempter-0:1.2.1-13.fc40.a 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 34/153] libuuid-0:2.40-13.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 35/153] ncurses-libs-0:6.4-12.2024012 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 36/153] pam-0:1.6.1-1.fc41.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 37/153] pam-libs-0:1.6.1-1.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 38/153] readline-0:8.2-8.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 39/153] systemd-libs-0:255.4-1.fc41.a 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 40/153] util-linux-core-0:2.40-13.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 41/153] zlib-ng-compat-0:2.1.6-2.fc40 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 42/153] bzip2-libs-0:1.0.8-18.fc40.aa 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 43/153] libacl-0:2.3.2-1.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 44/153] libcap-0:2.69-8.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[ 45/153] libgcc-0:14.0.1-0.15.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 46/153] libzstd-0:1.5.6-1.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 47/153] lz4-libs-0:1.9.4-6.fc40.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 48/153] libattr-0:2.5.2-3.fc40.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 49/153] libeconf-0:0.6.2-1.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 50/153] libsemanage-0:3.6-3.fc40.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 51/153] libxcrypt-0:4.4.36-5.fc40.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 52/153] setup-0:2.14.5-2.fc40.noarch  100% |   0.0   B/s |   0.0   B |  00m00s
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[ 53/153] binutils-0:2.42.50-6.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 54/153] debugedit-0:5.0-14.fc40.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 55/153] elfutils-0:0.191-5.fc41.aarch 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 57/153] file-0:5.45-5.fc41.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 58/153] pkgconf-pkg-config-0:2.1.0-1. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 59/153] popt-0:1.19-6.fc40.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 60/153] rpm-0:4.19.1.1-1.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 61/153] rpm-build-libs-0:4.19.1.1-1.f 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 62/153] rpm-libs-0:4.19.1.1-1.fc40.aa 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 63/153] zstd-0:1.5.6-1.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
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[ 64/153] curl-0:8.7.1-1.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
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[ 65/153] libarchive-0:3.7.2-3.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 66/153] glibc-gconv-extra-0:2.39.9000 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 67/153] ansible-srpm-macros-0:1-14.fc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 68/153] dwz-0:0.15-6.fc40.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
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[ 69/153] efi-srpm-macros-0:5-11.fc40.n 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 70/153] fonts-srpm-macros-1:2.0.5-14. 100% |   0.0   B/s |   0.0   B |  00m00s
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--------------------------------------------------------------------------------
[153/153] Total                         100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
[  1/155] Verify package files          100% | 735.0   B/s | 153.0   B |  00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-9.fc41.aarch64
>>> Stop pre-transaction scriptlet: filesystem-0:3.18-9.fc41.aarch64
[  2/155] Prepare transaction           100% |   2.5 KiB/s | 153.0   B |  00m00s
[  3/155] Installing libgcc-0:14.0.1-0. 100% | 171.8 MiB/s | 351.9 KiB |  00m00s
>>> Running post-install scriptlet: libgcc-0:14.0.1-0.15.fc41.aarch64
>>> Stop post-install scriptlet: libgcc-0:14.0.1-0.15.fc41.aarch64
[  4/155] Installing crypto-policies-0: 100% |  20.4 MiB/s | 146.2 KiB |  00m00s
>>> Running post-install scriptlet: crypto-policies-0:20240320-1.git58e3d95.fc41
>>> Stop post-install scriptlet: crypto-policies-0:20240320-1.git58e3d95.fc41.no
[  5/155] Installing fedora-release-ide 100% |   0.0   B/s | 952.0   B |  00m00s
[  6/155] Installing fedora-gpg-keys-0: 100% |  33.2 MiB/s | 170.1 KiB |  00m00s
[  7/155] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
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[  9/155] Installing fedora-release-com 100% |  22.7 MiB/s |  23.3 KiB |  00m00s
[ 10/155] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 11/155] Installing setup-0:2.14.5-2.f 100% |  47.3 MiB/s | 725.8 KiB |  00m00s
>>> Running post-install scriptlet: setup-0:2.14.5-2.fc40.noarch
>>> Stop post-install scriptlet: setup-0:2.14.5-2.fc40.noarch
[ 12/155] Installing filesystem-0:3.18- 100% |   2.3 MiB/s | 212.5 KiB |  00m00s
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[ 17/155] Installing coreutils-common-0 100% | 294.5 MiB/s |  11.2 MiB |  00m00s
[ 18/155] Installing ncurses-base-0:6.4 100% |  49.1 MiB/s | 351.6 KiB |  00m00s
[ 19/155] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
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>>> Running pre-install scriptlet: glibc-0:2.39.9000-10.fc41.aarch64
>>> Stop pre-install scriptlet: glibc-0:2.39.9000-10.fc41.aarch64
[ 21/155] Installing glibc-0:2.39.9000- 100% | 277.3 MiB/s |   9.7 MiB |  00m00s
>>> Running post-install scriptlet: glibc-0:2.39.9000-10.fc41.aarch64
>>> Stop post-install scriptlet: glibc-0:2.39.9000-10.fc41.aarch64
[ 22/155] Installing bash-0:5.2.26-3.fc 100% | 307.9 MiB/s |   8.3 MiB |  00m00s
>>> Running post-install scriptlet: bash-0:5.2.26-3.fc40.aarch64
>>> Stop post-install scriptlet: bash-0:5.2.26-3.fc40.aarch64
[ 23/155] Installing glibc-common-0:2.3 100% | 284.7 MiB/s |   2.6 MiB |  00m00s
[ 24/155] Installing glibc-gconv-extra- 100% | 551.1 MiB/s |  49.0 MiB |  00m00s
>>> Running post-install scriptlet: glibc-gconv-extra-0:2.39.9000-10.fc41.aarch6
>>> Stop post-install scriptlet: glibc-gconv-extra-0:2.39.9000-10.fc41.aarch64
[ 25/155] Installing zlib-ng-compat-0:2 100% | 256.4 MiB/s | 262.5 KiB |  00m00s
[ 26/155] Installing xz-libs-1:5.4.6-3. 100% | 260.5 MiB/s | 266.8 KiB |  00m00s
[ 27/155] Installing bzip2-libs-0:1.0.8 100% | 197.0 MiB/s | 201.8 KiB |  00m00s
[ 28/155] Installing libuuid-0:2.40-13. 100% | 193.7 MiB/s | 198.3 KiB |  00m00s
[ 29/155] Installing readline-0:8.2-8.f 100% | 337.5 MiB/s | 691.2 KiB |  00m00s
[ 30/155] Installing libzstd-0:1.5.6-1. 100% | 259.5 MiB/s | 797.2 KiB |  00m00s
[ 31/155] Installing elfutils-libelf-0: 100% | 328.5 MiB/s |   1.3 MiB |  00m00s
[ 32/155] Installing popt-0:1.19-6.fc40 100% |  68.2 MiB/s | 279.4 KiB |  00m00s
[ 33/155] Installing libstdc++-0:14.0.1 100% | 307.8 MiB/s |   2.8 MiB |  00m00s
[ 34/155] Installing libblkid-0:2.40-13 100% | 409.8 MiB/s | 419.6 KiB |  00m00s
[ 35/155] Installing libattr-0:2.5.2-3. 100% | 192.8 MiB/s | 197.4 KiB |  00m00s
[ 36/155] Installing libacl-0:2.3.2-1.f 100% | 192.2 MiB/s | 196.8 KiB |  00m00s
[ 37/155] Installing libxcrypt-0:4.4.36 100% | 196.1 MiB/s | 401.6 KiB |  00m00s
[ 38/155] Installing gmp-1:6.3.0-1.fc41 100% | 235.7 MiB/s | 724.2 KiB |  00m00s
[ 39/155] Installing lz4-libs-0:1.9.4-6 100% | 256.3 MiB/s | 262.5 KiB |  00m00s
[ 40/155] Installing libeconf-0:0.6.2-1 100% | 202.8 MiB/s | 207.6 KiB |  00m00s
[ 41/155] Installing gdbm-libs-1:1.23-6 100% | 417.5 MiB/s | 427.5 KiB |  00m00s
[ 42/155] Installing mpfr-0:4.2.1-3.fc4 100% | 267.0 MiB/s | 820.2 KiB |  00m00s
[ 43/155] Installing gawk-0:5.3.0-3.fc4 100% | 387.5 MiB/s |   4.3 MiB |  00m00s
[ 44/155] Installing dwz-0:0.15-6.fc40. 100% | 189.5 MiB/s | 388.1 KiB |  00m00s
[ 45/155] Installing unzip-0:6.0-63.fc4 100% | 356.4 MiB/s | 729.8 KiB |  00m00s
[ 46/155] Installing file-libs-0:5.45-5 100% | 589.6 MiB/s |  10.0 MiB |  00m00s
[ 47/155] Installing file-0:5.45-5.fc41 100% | 262.6 MiB/s | 268.9 KiB |  00m00s
[ 48/155] Installing libcap-ng-0:0.8.5- 100% | 409.1 MiB/s | 418.9 KiB |  00m00s
[ 49/155] Installing audit-libs-0:4.0.1 100% | 268.2 MiB/s | 549.4 KiB |  00m00s
[ 50/155] Installing pam-libs-0:1.6.1-1 100% | 297.6 MiB/s | 609.4 KiB |  00m00s
[ 51/155] Installing libcap-0:2.69-8.fc 100% | 343.7 MiB/s |   1.4 MiB |  00m00s
[ 52/155] Installing systemd-libs-0:255 100% | 350.9 MiB/s |   2.5 MiB |  00m00s
[ 53/155] Installing libsmartcols-0:2.4 100% | 282.8 MiB/s | 289.6 KiB |  00m00s
[ 54/155] Installing libcom_err-0:1.47. 100% | 234.7 MiB/s | 240.3 KiB |  00m00s
[ 55/155] Installing libsepol-0:3.6-3.f 100% | 284.8 MiB/s | 874.9 KiB |  00m00s
[ 56/155] Installing pcre2-0:10.43-1.fc 100% | 442.7 MiB/s | 906.7 KiB |  00m00s
[ 57/155] Installing libselinux-0:3.6-4 100% | 260.1 MiB/s | 266.3 KiB |  00m00s
[ 58/155] Installing sed-0:4.9-1.fc40.a 100% | 164.3 MiB/s |   1.0 MiB |  00m00s
[ 59/155] Installing grep-0:3.11-7.fc40 100% | 156.7 MiB/s |   1.1 MiB |  00m00s
[ 60/155] Installing findutils-1:4.9.0- 100% | 207.6 MiB/s |   1.7 MiB |  00m00s
[ 61/155] Installing xz-1:5.4.6-3.fc41. 100% | 207.6 MiB/s |   2.3 MiB |  00m00s
[ 62/155] Installing libmount-0:2.40-13 100% | 236.8 MiB/s | 485.0 KiB |  00m00s
[ 63/155] Installing alternatives-0:1.2 100% | 214.7 MiB/s | 219.9 KiB |  00m00s
[ 64/155] Installing jansson-0:2.13.1-9 100% | 216.5 MiB/s | 221.7 KiB |  00m00s
[ 65/155] Installing lua-libs-0:5.4.6-5 100% | 384.9 MiB/s | 394.2 KiB |  00m00s
[ 66/155] Installing libtasn1-0:4.19.0- 100% | 278.8 MiB/s | 285.5 KiB |  00m00s
[ 67/155] Installing libunistring-0:1.1 100% | 311.9 MiB/s |   1.9 MiB |  00m00s
[ 68/155] Installing libidn2-0:2.3.7-1. 100% | 113.0 MiB/s | 463.0 KiB |  00m00s
[ 69/155] Installing libpsl-0:0.21.5-3. 100% | 193.0 MiB/s | 197.6 KiB |  00m00s
[ 70/155] Installing util-linux-core-0: 100% | 442.7 MiB/s |   6.2 MiB |  00m00s
[ 71/155] Installing tar-2:1.35-3.fc40. 100% | 278.8 MiB/s |   3.1 MiB |  00m00s
[ 72/155] Installing libsemanage-0:3.6- 100% | 118.2 MiB/s | 363.2 KiB |  00m00s
[ 73/155] Installing shadow-utils-2:4.1 100% | 179.9 MiB/s |   7.4 MiB |  00m00s
>>> Running pre-install scriptlet: libutempter-0:1.2.1-13.fc40.aarch64
>>> Stop pre-install scriptlet: libutempter-0:1.2.1-13.fc40.aarch64
[ 74/155] Installing libutempter-0:1.2. 100% | 204.9 MiB/s | 419.6 KiB |  00m00s
[ 75/155] Installing zip-0:3.0-40.fc40. 100% | 281.0 MiB/s |   1.1 MiB |  00m00s
[ 76/155] Installing gdbm-1:1.23-6.fc40 100% | 227.8 MiB/s | 933.2 KiB |  00m00s
[ 77/155] Installing cyrus-sasl-lib-0:2 100% | 310.7 MiB/s |   3.1 MiB |  00m00s
[ 78/155] Installing zstd-0:1.5.6-1.fc4 100% | 313.2 MiB/s |   1.6 MiB |  00m00s
[ 79/155] Installing libfdisk-0:2.40-13 100% | 236.2 MiB/s | 483.8 KiB |  00m00s
[ 80/155] Installing bzip2-0:1.0.8-18.f 100% | 210.9 MiB/s | 432.0 KiB |  00m00s
[ 81/155] Installing libxml2-0:2.12.6-1 100% | 314.8 MiB/s |   2.2 MiB |  00m00s
[ 82/155] Installing sqlite-libs-0:3.45 100% | 299.1 MiB/s |   1.5 MiB |  00m00s
[ 83/155] Installing ed-0:1.20.1-1.fc41 100% | 139.0 MiB/s | 284.7 KiB |  00m00s
[ 84/155] Installing patch-0:2.7.6-24.f 100% | 191.4 MiB/s | 392.0 KiB |  00m00s
[ 85/155] Installing elfutils-default-y 100% | 340.5 KiB/s |   2.0 KiB |  00m00s
>>> Running post-install scriptlet: elfutils-default-yama-scope-0:0.191-5.fc41.n
>>> Stop post-install scriptlet: elfutils-default-yama-scope-0:0.191-5.fc41.noar
[ 86/155] Installing cpio-0:2.15-1.fc40 100% | 174.4 MiB/s |   1.2 MiB |  00m00s
[ 87/155] Installing diffutils-0:3.10-5 100% | 263.6 MiB/s |   2.1 MiB |  00m00s
[ 88/155] Installing libpkgconf-0:2.1.0 100% | 194.5 MiB/s | 199.1 KiB |  00m00s
[ 89/155] Installing pkgconf-0:2.1.0-1. 100% | 235.2 MiB/s | 240.8 KiB |  00m00s
[ 90/155] Installing keyutils-libs-0:1. 100% | 222.4 MiB/s | 227.8 KiB |  00m00s
[ 91/155] Installing libverto-0:0.3.2-8 100% | 194.6 MiB/s | 199.2 KiB |  00m00s
[ 92/155] Installing libgomp-0:14.0.1-0 100% | 277.5 MiB/s | 568.3 KiB |  00m00s
[ 93/155] Installing libffi-0:3.4.6-1.f 100% | 277.1 MiB/s | 283.7 KiB |  00m00s
[ 94/155] Installing p11-kit-0:0.25.3-4 100% | 217.8 MiB/s |   2.8 MiB |  00m00s
[ 95/155] Installing p11-kit-trust-0:0. 100% |  71.3 MiB/s | 657.2 KiB |  00m00s
>>> Running post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.aarch64
>>> Stop post-install scriptlet: p11-kit-trust-0:0.25.3-4.fc40.aarch64
[ 96/155] Installing openssl-libs-1:3.2 100% | 310.9 MiB/s |   7.8 MiB |  00m00s
[ 97/155] Installing coreutils-0:9.5-1. 100% | 472.5 MiB/s |  20.8 MiB |  00m00s
>>> Running pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.n
>>> Stop pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noar
[ 98/155] Installing ca-certificates-0: 100% |   2.5 MiB/s |   2.3 MiB |  00m01s
>>> Running post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.
>>> Stop post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40.noa
[ 99/155] Installing krb5-libs-0:1.21.2 100% | 262.0 MiB/s |   3.4 MiB |  00m00s
[100/155] Installing libtirpc-0:1.3.4-1 100% | 135.0 MiB/s | 276.4 KiB |  00m00s
[101/155] Installing gzip-0:1.13-1.fc40 100% | 160.9 MiB/s | 494.3 KiB |  00m00s
[102/155] Installing authselect-libs-0: 100% | 132.1 MiB/s | 946.7 KiB |  00m00s
[103/155] Installing libarchive-0:3.7.2 100% | 254.0 MiB/s |   1.0 MiB |  00m00s
[104/155] Installing authselect-0:1.5.0 100% | 102.1 MiB/s | 313.8 KiB |  00m00s
[105/155] Installing cracklib-0:2.9.11- 100% | 154.0 MiB/s | 946.0 KiB |  00m00s
[106/155] Installing libpwquality-0:1.4 100% | 158.2 MiB/s |   1.1 MiB |  00m00s
[107/155] Installing libnsl2-0:2.0.1-1. 100% | 108.9 MiB/s | 223.0 KiB |  00m00s
[108/155] Installing pam-0:1.6.1-1.fc41 100% | 367.8 MiB/s |  11.0 MiB |  00m00s
[109/155] Installing libssh-0:0.10.6-6. 100% | 189.9 MiB/s | 583.3 KiB |  00m00s
[110/155] Installing rpm-sequoia-0:1.6. 100% | 318.5 MiB/s |   2.2 MiB |  00m00s
[111/155] Installing rpm-libs-0:4.19.1. 100% | 281.0 MiB/s | 863.2 KiB |  00m00s
[112/155] Installing libevent-0:2.1.12- 100% | 380.7 MiB/s |   1.5 MiB |  00m00s
[113/155] Installing xxhash-libs-0:0.8. 100% | 208.6 MiB/s | 213.6 KiB |  00m00s
[114/155] Installing libbrotli-0:1.1.0- 100% | 285.1 MiB/s |   1.1 MiB |  00m00s
[115/155] Installing libnghttp2-0:1.61. 100% | 257.1 MiB/s | 263.2 KiB |  00m00s
[116/155] Installing libtool-ltdl-0:2.4 100% | 218.0 MiB/s | 223.3 KiB |  00m00s
[117/155] Installing openldap-0:2.6.7-1 100% | 248.7 MiB/s |   1.0 MiB |  00m00s
[118/155] Installing libcurl-0:8.7.1-1. 100% | 300.3 MiB/s | 922.4 KiB |  00m00s
[119/155] Installing elfutils-debuginfo 100% | 389.4 MiB/s | 398.8 KiB |  00m00s
[120/155] Installing elfutils-libs-0:0. 100% | 326.8 MiB/s |   1.0 MiB |  00m00s
[121/155] Installing binutils-gold-0:2. 100% | 192.1 MiB/s |   3.1 MiB |  00m00s
>>> Running post-install scriptlet: binutils-gold-0:2.42.50-6.fc41.aarch64
>>> Stop post-install scriptlet: binutils-gold-0:2.42.50-6.fc41.aarch64
[122/155] Installing binutils-0:2.42.50 100% | 356.1 MiB/s |  33.5 MiB |  00m00s
>>> Running post-install scriptlet: binutils-0:2.42.50-6.fc41.aarch64
>>> Stop post-install scriptlet: binutils-0:2.42.50-6.fc41.aarch64
[123/155] Installing elfutils-0:0.191-5 100% | 358.2 MiB/s |   5.0 MiB |  00m00s
[124/155] Installing gdb-minimal-0:14.2 100% | 333.1 MiB/s |  12.7 MiB |  00m00s
[125/155] Installing debugedit-0:5.0-14 100% | 244.9 MiB/s | 501.5 KiB |  00m00s
[126/155] Installing rpm-build-libs-0:4 100% | 257.0 MiB/s | 263.2 KiB |  00m00s
[127/155] Installing curl-0:8.7.1-1.fc4 100% |  72.3 MiB/s | 888.5 KiB |  00m00s
>>> Running pre-install scriptlet: rpm-0:4.19.1.1-1.fc40.aarch64
>>> Stop pre-install scriptlet: rpm-0:4.19.1.1-1.fc40.aarch64
[128/155] Installing rpm-0:4.19.1.1-1.f 100% | 149.3 MiB/s |   3.4 MiB |  00m00s
[129/155] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[130/155] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[131/155] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[132/155] Installing pkgconf-m4-0:2.1.0 100% |   0.0   B/s |  14.3 KiB |  00m00s
[133/155] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[134/155] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[135/155] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[136/155] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 768.0   B |  00m00s
[137/155] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[138/155] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[139/155] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[140/155] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[141/155] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[142/155] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[143/155] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[144/155] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[145/155] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[146/155] Installing fonts-srpm-macros- 100% |  55.1 MiB/s |  56.5 KiB |  00m00s
[147/155] Installing forge-srpm-macros- 100% |  39.4 MiB/s |  40.3 KiB |  00m00s
[148/155] Installing go-srpm-macros-0:3 100% |  60.2 MiB/s |  61.6 KiB |  00m00s
[149/155] Installing python-srpm-macros 100% |  50.5 MiB/s |  51.7 KiB |  00m00s
[150/155] Installing redhat-rpm-config- 100% |  92.6 MiB/s | 189.7 KiB |  00m00s
[151/155] Installing rpm-build-0:4.19.1 100% | 301.1 MiB/s |   1.2 MiB |  00m00s
[152/155] Installing pyproject-srpm-mac 100% |   2.0 MiB/s |   2.1 KiB |  00m00s
[153/155] Installing util-linux-0:2.40- 100% | 373.0 MiB/s |  17.5 MiB |  00m00s
>>> Running post-install scriptlet: util-linux-0:2.40-13.fc41.aarch64
>>> Stop post-install scriptlet: util-linux-0:2.40-13.fc41.aarch64
[154/155] Installing which-0:2.21-41.fc 100% | 122.2 MiB/s | 250.3 KiB |  00m00s
[155/155] Installing info-0:7.1-2.fc40. 100% | 516.3 KiB/s | 613.9 KiB |  00m01s
>>> Running post-transaction scriptlet: filesystem-0:3.18-9.fc41.aarch64
>>> Stop post-transaction scriptlet: filesystem-0:3.18-9.fc41.aarch64
>>> Running post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.f
>>> Stop post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-6.fc40
>>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc41.aarch64
>>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-5.fc41.aarch64
>>> Running post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.aarch64
>>> Stop post-transaction scriptlet: rpm-0:4.19.1.1-1.fc40.aarch64
>>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Running trigger-install scriptlet: info-0:7.1-2.fc40.aarch64
>>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.aarch64
Warning: skipped PGP checks for 153 package(s).
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.26-3.fc40.aarch64
ansible-srpm-macros-1-14.fc40.noarch
audit-libs-4.0.1-1.fc41.aarch64
authselect-1.5.0-5.fc41.aarch64
authselect-libs-1.5.0-5.fc41.aarch64
basesystem-11-20.fc40.noarch
bash-5.2.26-3.fc40.aarch64
binutils-2.42.50-6.fc41.aarch64
binutils-gold-2.42.50-6.fc41.aarch64
bzip2-1.0.8-18.fc40.aarch64
bzip2-libs-1.0.8-18.fc40.aarch64
ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch
coreutils-9.5-1.fc41.aarch64
coreutils-common-9.5-1.fc41.aarch64
cpio-2.15-1.fc40.aarch64
cracklib-2.9.11-5.fc40.aarch64
crypto-policies-20240320-1.git58e3d95.fc41.noarch
curl-8.7.1-1.fc41.aarch64
cyrus-sasl-lib-2.1.28-19.fc40.aarch64
debugedit-5.0-14.fc40.aarch64
diffutils-3.10-5.fc40.aarch64
dwz-0.15-6.fc40.aarch64
ed-1.20.1-1.fc41.aarch64
efi-srpm-macros-5-11.fc40.noarch
elfutils-0.191-5.fc41.aarch64
elfutils-debuginfod-client-0.191-5.fc41.aarch64
elfutils-default-yama-scope-0.191-5.fc41.noarch
elfutils-libelf-0.191-5.fc41.aarch64
elfutils-libs-0.191-5.fc41.aarch64
fedora-gpg-keys-41-0.1.noarch
fedora-release-41-0.6.noarch
fedora-release-common-41-0.6.noarch
fedora-release-identity-basic-41-0.6.noarch
fedora-repos-41-0.1.noarch
fedora-repos-rawhide-41-0.1.noarch
file-5.45-5.fc41.aarch64
file-libs-5.45-5.fc41.aarch64
filesystem-3.18-9.fc41.aarch64
findutils-4.9.0-8.fc40.aarch64
fonts-srpm-macros-2.0.5-14.fc40.noarch
forge-srpm-macros-0.3.1-1.fc41.noarch
fpc-srpm-macros-1.3-12.fc40.noarch
gawk-5.3.0-3.fc40.aarch64
gdb-minimal-14.2-4.fc41.aarch64
gdbm-1.23-6.fc40.aarch64
gdbm-libs-1.23-6.fc40.aarch64
ghc-srpm-macros-1.9.1-1.fc41.noarch
glibc-2.39.9000-10.fc41.aarch64
glibc-common-2.39.9000-10.fc41.aarch64
glibc-gconv-extra-2.39.9000-10.fc41.aarch64
glibc-minimal-langpack-2.39.9000-10.fc41.aarch64
gmp-6.3.0-1.fc41.aarch64
gnat-srpm-macros-6-5.fc40.noarch
go-srpm-macros-3.5.0-1.fc41.noarch
grep-3.11-7.fc40.aarch64
gzip-1.13-1.fc40.aarch64
info-7.1-2.fc40.aarch64
jansson-2.13.1-9.fc40.aarch64
kernel-srpm-macros-1.0-23.fc41.noarch
keyutils-libs-1.6.3-3.fc40.aarch64
krb5-libs-1.21.2-5.fc40.aarch64
libacl-2.3.2-1.fc40.aarch64
libarchive-3.7.2-3.fc41.aarch64
libattr-2.5.2-3.fc40.aarch64
libblkid-2.40-13.fc41.aarch64
libbrotli-1.1.0-3.fc40.aarch64
libcap-2.69-8.fc41.aarch64
libcap-ng-0.8.5-1.fc41.aarch64
libcom_err-1.47.0-5.fc40.aarch64
libcurl-8.7.1-1.fc41.aarch64
libeconf-0.6.2-1.fc41.aarch64
libevent-2.1.12-12.fc40.aarch64
libfdisk-2.40-13.fc41.aarch64
libffi-3.4.6-1.fc41.aarch64
libgcc-14.0.1-0.15.fc41.aarch64
libgomp-14.0.1-0.15.fc41.aarch64
libidn2-2.3.7-1.fc40.aarch64
libmount-2.40-13.fc41.aarch64
libnghttp2-1.61.0-1.fc41.aarch64
libnsl2-2.0.1-1.fc40.aarch64
libpkgconf-2.1.0-1.fc40.aarch64
libpsl-0.21.5-3.fc40.aarch64
libpwquality-1.4.5-9.fc40.aarch64
libselinux-3.6-4.fc40.aarch64
libsemanage-3.6-3.fc40.aarch64
libsepol-3.6-3.fc40.aarch64
libsmartcols-2.40-13.fc41.aarch64
libssh-0.10.6-6.fc41.aarch64
libssh-config-0.10.6-6.fc41.noarch
libstdc++-14.0.1-0.15.fc41.aarch64
libtasn1-4.19.0-6.fc40.aarch64
libtirpc-1.3.4-1.rc3.fc41.aarch64
libtool-ltdl-2.4.7-10.fc40.aarch64
libunistring-1.1-7.fc41.aarch64
libutempter-1.2.1-13.fc40.aarch64
libuuid-2.40-13.fc41.aarch64
libverto-0.3.2-8.fc40.aarch64
libxcrypt-4.4.36-5.fc40.aarch64
libxml2-2.12.6-1.fc41.aarch64
libzstd-1.5.6-1.fc41.aarch64
lua-libs-5.4.6-5.fc40.aarch64
lua-srpm-macros-1-13.fc40.noarch
lz4-libs-1.9.4-6.fc40.aarch64
mpfr-4.2.1-3.fc40.aarch64
ncurses-base-6.4-12.20240127.fc40.noarch
ncurses-libs-6.4-12.20240127.fc40.aarch64
ocaml-srpm-macros-9-3.fc40.noarch
openblas-srpm-macros-2-17.fc41.noarch
openldap-2.6.7-1.fc40.aarch64
openssl-libs-3.2.1-6.fc41.aarch64
p11-kit-0.25.3-4.fc40.aarch64
p11-kit-trust-0.25.3-4.fc40.aarch64
package-notes-srpm-macros-0.5-11.fc40.noarch
pam-1.6.1-1.fc41.aarch64
pam-libs-1.6.1-1.fc41.aarch64
patch-2.7.6-24.fc40.aarch64
pcre2-10.43-1.fc41.aarch64
pcre2-syntax-10.43-1.fc41.noarch
perl-srpm-macros-1-53.fc40.noarch
pkgconf-2.1.0-1.fc40.aarch64
pkgconf-m4-2.1.0-1.fc40.noarch
pkgconf-pkg-config-2.1.0-1.fc40.aarch64
popt-1.19-6.fc40.aarch64
publicsuffix-list-dafsa-20240107-3.fc40.noarch
pyproject-srpm-macros-1.12.0-1.fc40.noarch
python-srpm-macros-3.12-9.fc41.noarch
qt5-srpm-macros-5.15.13-1.fc41.noarch
qt6-srpm-macros-6.7.0-1.fc41.noarch
readline-8.2-8.fc40.aarch64
redhat-rpm-config-288-1.fc41.noarch
rpm-4.19.1.1-1.fc40.aarch64
rpm-build-4.19.1.1-1.fc40.aarch64
rpm-build-libs-4.19.1.1-1.fc40.aarch64
rpm-libs-4.19.1.1-1.fc40.aarch64
rpm-sequoia-1.6.0-2.fc40.aarch64
rust-srpm-macros-26.2-1.fc41.noarch
sed-4.9-1.fc40.aarch64
setup-2.14.5-2.fc40.noarch
shadow-utils-4.15.1-2.fc41.aarch64
sqlite-libs-3.45.2-1.fc41.aarch64
systemd-libs-255.4-1.fc41.aarch64
tar-1.35-3.fc40.aarch64
unzip-6.0-63.fc40.aarch64
util-linux-2.40-13.fc41.aarch64
util-linux-core-2.40-13.fc41.aarch64
which-2.21-41.fc40.aarch64
xxhash-libs-0.8.2-2.fc40.aarch64
xz-5.4.6-3.fc41.aarch64
xz-libs-5.4.6-3.fc41.aarch64
zig-srpm-macros-1-2.fc40.noarch
zip-3.0-40.fc40.aarch64
zlib-ng-compat-2.1.6-2.fc40.aarch64
zstd-1.5.6-1.fc41.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-aarch64-1713009811.077841/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1713009811.077841/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-giklwl1_/python-biopython/python-biopython.spec) Config(child) 0 minutes 27 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/python-biopython-1.83-5.fc41.src.rpm)  Config(fedora-rawhide-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1713009811.077841/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1713009811.077841/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-rawhide-aarch64-1713009811.077841/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-1.fc40.aarch64
  rpm-sequoia-1.6.0-2.fc40.aarch64
  python3-dnf-4.19.2-1.fc41.noarch
  yum-4.19.2-1.fc41.noarch
  dnf5-5.1.17-1.fc41.aarch64
  dnf5-plugins-5.1.17-1.fc41.aarch64
Finish: chroot init
Start: build phase for python-biopython-1.83-5.fc41.src.rpm
Start: build setup for python-biopython-1.83-5.fc41.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.src.rpm
Updating and loading repositories:
 fedora                                 100% |  38.1 KiB/s |   9.6 KiB |  00m00s
 Copr repository                        100% | 109.8 KiB/s |   1.5 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% |  69.9 KiB/s |   4.1 KiB |  00m00s
Repositories loaded.
Package                     Arch    Version             Repository                                                         Size
Installing:                                                                                                                    
 gcc                        aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  93.5 MiB
 pyproject-rpm-macros       noarch  1.12.0-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  98.8 KiB
 python3-devel              aarch64 3.12.3-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 python3-reportlab          noarch  4.1.0-2.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  10.9 MiB
Installing dependencies:                                                                                                       
 abattis-cantarell-vf-fonts noarch  0.301-12.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 192.7 KiB
 annobin-docs               noarch  12.48-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  95.7 KiB
 annobin-plugin-gcc         aarch64 12.48-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 cairo                      aarch64 1.18.0-3.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.0 MiB
 cpp                        aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  31.8 MiB
 default-fonts-core-sans    noarch  4.0-12.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  11.9 KiB
 dejavu-sans-fonts          noarch  2.37-23.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.5 MiB
 expat                      aarch64 2.6.2-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 536.7 KiB
 fontconfig                 aarch64 2.15.0-4.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.4 MiB
 fonts-filesystem           noarch  1:2.0.5-14.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 freetype                   aarch64 2.13.2-5.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 942.9 KiB
 fribidi                    aarch64 1.0.13-4.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 673.1 KiB
 gc                         aarch64 8.2.2-6.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 850.3 KiB
 gcc-plugin-annobin         aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.0 KiB
 glib2                      aarch64 2.80.0-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  16.4 MiB
 glibc-devel                aarch64 2.39.9000-10.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 gnutls                     aarch64 3.8.5-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.4 MiB
 google-noto-fonts-common   noarch  20240401-1.fc41     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  17.5 KiB
 google-noto-sans-vf-fonts  noarch  20240401-1.fc41     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 graphite2                  aarch64 1.3.14-15.fc40      copr_base                                                     495.7 KiB
 guile30                    aarch64 3.0.7-12.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  52.0 MiB
 harfbuzz                   aarch64 8.4.0-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.9 MiB
 jbigkit-libs               aarch64 2.1-29.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 437.5 KiB
 kernel-headers             aarch64 6.9.0-0.rc3.30.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.1 MiB
 lcms2                      aarch64 2.16-3.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 484.8 KiB
 libX11                     aarch64 1.8.9-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.3 MiB
 libX11-common              noarch  1.8.9-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libXau                     aarch64 1.0.11-6.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 242.8 KiB
 libXext                    aarch64 1.3.6-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 209.9 KiB
 libXrender                 aarch64 0.9.11-6.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 198.1 KiB
 libasan                    aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
 libatomic                  aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.9 KiB
 libb2                      aarch64 0.98.1-11.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 202.1 KiB
 libimagequant              aarch64 4.0.3-3.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 730.5 KiB
 libjpeg-turbo              aarch64 3.0.2-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 792.4 KiB
 liblerc                    aarch64 4.0.0-6.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 610.4 KiB
 libmpc                     aarch64 1.3.1-5.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 280.7 KiB
 libpng                     aarch64 2:1.6.40-3.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 333.6 KiB
 libraqm                    aarch64 0.8.0-7.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.6 KiB
 libtiff                    aarch64 4.6.0-2.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.7 MiB
 libubsan                   aarch64 14.0.1-0.15.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 539.1 KiB
 libwebp                    aarch64 1.3.2-5.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 libxcb                     aarch64 1.16.1-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.0 MiB
 libxcrypt-devel            aarch64 4.4.36-5.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  30.3 KiB
 make                       aarch64 1:4.4.1-6.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.8 MiB
 mpdecimal                  aarch64 2.5.1-9.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 328.7 KiB
 nettle                     aarch64 3.9.1-6.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 953.6 KiB
 openjpeg2                  aarch64 2.5.2-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 537.6 KiB
 pixman                     aarch64 0.43.4-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 718.3 KiB
 python-pip-wheel           noarch  24.0-2.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 python-rpm-macros          noarch  3.12-9.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  22.1 KiB
 python3                    aarch64 3.12.3-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 211.4 KiB
 python3-chardet            noarch  5.2.0-8.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.1 MiB
 python3-libs               aarch64 3.12.3-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  51.2 MiB
 python3-olefile            noarch  0.47-3.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 343.2 KiB
 python3-packaging          noarch  24.0-1.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 424.8 KiB
 python3-pillow             aarch64 10.3.0-1.fc41       copr_base                                                       4.3 MiB
 python3-rpm-generators     noarch  14-10.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  81.7 KiB
 python3-rpm-macros         noarch  3.12-9.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.4 KiB
 tzdata                     noarch  2024a-5.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
 xml-common                 noarch  0.6.3-63.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  78.4 KiB

Transaction Summary:
 Installing:       65 packages

Total size of inbound packages is 85 MiB. Need to download 999 KiB.
After this operation 320 MiB will be used (install 320 MiB, remove 0 B).
[ 1/65] gcc-0:14.0.1-0.15.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 2/65] pyproject-rpm-macros-0:1.12.0-1 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 3/65] python3-devel-0:3.12.3-1.fc41.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 4/65] python3-reportlab-0:4.1.0-2.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 5/65] cpp-0:14.0.1-0.15.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 6/65] gcc-plugin-annobin-0:14.0.1-0.1 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 7/65] dejavu-sans-fonts-0:2.37-23.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 8/65] python3-0:3.12.3-1.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[ 9/65] python3-chardet-0:5.2.0-8.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[10/65] python-rpm-macros-0:3.12-9.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[11/65] python3-rpm-generators-0:14-10. 100% |   0.0   B/s |   0.0   B |  00m00s
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[12/65] python3-rpm-macros-0:3.12-9.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
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[13/65] python3-libs-0:3.12.3-1.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
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[14/65] annobin-plugin-gcc-0:12.48-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
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[15/65] glibc-devel-0:2.39.9000-10.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[16/65] libasan-0:14.0.1-0.15.fc41.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[17/65] libatomic-0:14.0.1-0.15.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[18/65] libmpc-0:1.3.1-5.fc40.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[19/65] libubsan-0:14.0.1-0.15.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[20/65] make-1:4.4.1-6.fc40.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[21/65] fonts-filesystem-1:2.0.5-14.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[22/65] annobin-docs-0:12.48-1.fc41.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[23/65] freetype-0:2.13.2-5.fc40.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
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[24/65] lcms2-0:2.16-3.fc40.aarch64     100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[25/65] libimagequant-0:4.0.3-3.fc40.aa 100% |   0.0   B/s |   0.0   B |  00m00s
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[26/65] libjpeg-turbo-0:3.0.2-1.fc40.aa 100% |   0.0   B/s |   0.0   B |  00m00s
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[27/65] libraqm-0:0.8.0-7.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[28/65] libtiff-0:4.6.0-2.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[29/65] libwebp-0:1.3.2-5.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[30/65] libxcb-0:1.16.1-1.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[31/65] openjpeg2-0:2.5.2-1.fc41.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[32/65] python3-olefile-0:0.47-3.fc40.n 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[33/65] python3-packaging-0:24.0-1.fc41 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[34/65] expat-0:2.6.2-1.fc41.aarch64    100% |   0.0   B/s |   0.0   B |  00m00s
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[35/65] libb2-0:0.98.1-11.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[36/65] mpdecimal-0:2.5.1-9.fc40.aarch6 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[37/65] python-pip-wheel-0:24.0-2.fc41. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[38/65] tzdata-0:2024a-5.fc41.noarch    100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[39/65] guile30-0:3.0.7-12.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
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[40/65] libXau-0:1.0.11-6.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[41/65] jbigkit-libs-0:2.1-29.fc40.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
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[42/65] liblerc-0:4.0.0-6.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
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[43/65] fribidi-0:1.0.13-4.fc40.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[44/65] harfbuzz-0:8.4.0-1.fc41.aarch64 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[45/65] cairo-0:1.18.0-3.fc40.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[46/65] glib2-0:2.80.0-1.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[47/65] gc-0:8.2.2-6.fc40.aarch64       100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[48/65] kernel-headers-0:6.9.0-0.rc3.30 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[49/65] libxcrypt-devel-0:4.4.36-5.fc40 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[50/65] gnutls-0:3.8.5-1.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[51/65] libpng-2:1.6.40-3.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[52/65] fontconfig-0:2.15.0-4.fc40.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[53/65] libX11-0:1.8.9-1.fc41.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[54/65] libXext-0:1.3.6-1.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[55/65] libXrender-0:0.9.11-6.fc40.aarc 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[56/65] pixman-0:0.43.4-1.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[57/65] libX11-common-0:1.8.9-1.fc41.no 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[58/65] nettle-0:3.9.1-6.fc40.aarch64   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[59/65] default-fonts-core-sans-0:4.0-1 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[60/65] xml-common-0:0.6.3-63.fc40.noar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[61/65] abattis-cantarell-vf-fonts-0:0. 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[62/65] google-noto-sans-vf-fonts-0:202 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[63/65] google-noto-fonts-common-0:2024 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[64/65] graphite2-0:1.3.14-15.fc40.aarc 100% |   5.7 MiB/s |  92.6 KiB |  00m00s
[65/65] python3-pillow-0:10.3.0-1.fc41. 100% |  27.7 MiB/s | 906.1 KiB |  00m00s
--------------------------------------------------------------------------------
[65/65] Total                           100% |   8.5 MiB/s | 998.7 KiB |  00m00s
Running transaction
[ 1/67] Verify package files            100% | 218.0   B/s |  65.0   B |  00m00s
[ 2/67] Prepare transaction             100% | 955.0   B/s |  65.0   B |  00m00s
[ 3/67] Installing fonts-filesystem-1:2 100% |   0.0   B/s | 788.0   B |  00m00s
[ 4/67] Installing python-rpm-macros-0: 100% |   0.0   B/s |  22.8 KiB |  00m00s
[ 5/67] Installing python3-rpm-macros-0 100% |   0.0   B/s |   6.7 KiB |  00m00s
[ 6/67] Installing libpng-2:1.6.40-3.fc 100% | 163.5 MiB/s | 334.9 KiB |  00m00s
[ 7/67] Installing libwebp-0:1.3.2-5.fc 100% | 309.3 MiB/s |   1.2 MiB |  00m00s
[ 8/67] Installing libjpeg-turbo-0:3.0. 100% | 258.5 MiB/s | 794.1 KiB |  00m00s
[ 9/67] Installing libmpc-0:1.3.1-5.fc4 100% | 275.6 MiB/s | 282.2 KiB |  00m00s
[10/67] Installing cpp-0:14.0.1-0.15.fc 100% | 311.7 MiB/s |  31.8 MiB |  00m00s
[11/67] Installing pyproject-rpm-macros 100% |  98.4 MiB/s | 100.8 KiB |  00m00s
[12/67] Installing dejavu-sans-fonts-0: 100% | 367.2 MiB/s |   5.5 MiB |  00m00s
[13/67] Installing abattis-cantarell-vf 100% | 189.9 MiB/s | 194.4 KiB |  00m00s
[14/67] Installing google-noto-fonts-co 100% |   0.0   B/s |  18.3 KiB |  00m00s
[15/67] Installing google-noto-sans-vf- 100% | 249.8 MiB/s |   1.2 MiB |  00m00s
[16/67] Installing default-fonts-core-s 100% |   2.5 MiB/s |  18.2 KiB |  00m00s
>>> Running pre-install scriptlet: xml-common-0:0.6.3-63.fc40.noarch
>>> Stop pre-install scriptlet: xml-common-0:0.6.3-63.fc40.noarch
[17/67] Installing xml-common-0:0.6.3-6 100% |  39.6 MiB/s |  81.1 KiB |  00m00s
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[41/67] Installing freetype-0:2.13.2-5. 100% | 230.6 MiB/s | 944.6 KiB |  00m00s
[42/67] Installing fontconfig-0:2.15.0- 100% |   2.3 MiB/s |   2.4 MiB |  00m01s
>>> Running post-install scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
>>> Stop post-install scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
[43/67] Installing libraqm-0:0.8.0-7.fc 100% |  48.3 MiB/s | 197.7 KiB |  00m00s
[44/67] Installing tzdata-0:2024a-5.fc4 100% |  35.9 MiB/s |   1.9 MiB |  00m00s
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[55/67] Installing openjpeg2-0:2.5.2-1. 100% | 175.7 MiB/s | 539.6 KiB |  00m00s
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[57/67] Installing lcms2-0:2.16-3.fc40. 100% | 158.3 MiB/s | 486.4 KiB |  00m00s
[58/67] Installing python3-pillow-0:10. 100% | 228.5 MiB/s |   4.3 MiB |  00m00s
[59/67] Installing annobin-docs-0:12.48 100% |  94.4 MiB/s |  96.7 KiB |  00m00s
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[61/67] Installing libatomic-0:14.0.1-0 100% | 193.0 MiB/s | 197.6 KiB |  00m00s
[62/67] Installing libasan-0:14.0.1-0.1 100% | 267.1 MiB/s |   1.6 MiB |  00m00s
[63/67] Installing gcc-0:14.0.1-0.15.fc 100% | 350.2 MiB/s |  93.5 MiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
[64/67] Installing gcc-plugin-annobin-0 100% |  13.9 MiB/s | 198.6 KiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
[65/67] Installing annobin-plugin-gcc-0 100% |  57.1 MiB/s |   1.1 MiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:288-1.fc41.noarch
[66/67] Installing python3-reportlab-0: 100% | 220.3 MiB/s |  11.0 MiB |  00m00s
[67/67] Installing python3-devel-0:3.12 100% |   6.5 MiB/s |   1.3 MiB |  00m00s
>>> Running post-transaction scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
>>> Stop post-transaction scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
>>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Running trigger-install scriptlet: info-0:7.1-2.fc40.aarch64
>>> Stop trigger-install scriptlet: info-0:7.1-2.fc40.aarch64
>>> Running trigger-install scriptlet: glib2-0:2.80.0-1.fc41.aarch64
>>> Stop trigger-install scriptlet: glib2-0:2.80.0-1.fc41.aarch64
>>> Running trigger-install scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
>>> Stop trigger-install scriptlet: fontconfig-0:2.15.0-4.fc40.aarch64
Warning: skipped PGP checks for 65 package(s).
Finish: build setup for python-biopython-1.83-5.fc41.src.rpm
Start: rpmbuild python-biopython-1.83-5.fc41.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.xBisFG
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf biopython-1.83
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.83.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd biopython-1.83
+ rm -rf /builddir/build/BUILD/biopython-1.83-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/biopython-1.83-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/4683.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f
+ /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/4696.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.5Hzmzk
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ echo pyproject-rpm-macros
+ echo python3-devel
+ echo 'python3dist(pip) >= 19'
+ echo 'python3dist(packaging)'
+ '[' -f pyproject.toml ']'
+ '[' -f setup.py ']'
+ echo 'python3dist(setuptools) >= 40.8'
+ echo 'python3dist(wheel)'
+ rm -rfv '*.dist-info/'
+ '[' -f /usr/bin/python3 ']'
+ mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ echo -n
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ RPM_TOXENV=py312
+ HOSTNAME=rpmbuild
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires -x tests
Handling setuptools >= 40.8 from default build backend
Requirement not satisfied: setuptools >= 40.8
Handling wheel from default build backend
Requirement not satisfied: wheel
Exiting dependency generation pass: build backend
+ cat /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires
+ rm -rfv '*.dist-info/'
+ RPM_EC=0
++ jobs -p
+ exit 0
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.buildreqs.nosrc.rpm
INFO: Going to install missing dynamic buildrequires
Updating and loading repositories:
 fedora                                 100% |  99.7 KiB/s |   9.6 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% |  48.5 KiB/s |   4.1 KiB |  00m00s
 Copr repository                        100% | 118.2 KiB/s |   1.5 KiB |  00m00s
 Copr repository                        100% |  60.6 MiB/s |   3.2 MiB |  00m00s
Repositories loaded.
Package "gcc-14.0.1-0.15.fc41.aarch64" is already installed.
Package "pyproject-rpm-macros-1.12.0-1.fc40.noarch" is already installed.
Package "python3-devel-3.12.3-1.fc41.aarch64" is already installed.
Package "python3-packaging-24.0-1.fc41.noarch" is already installed.
Package "python3-reportlab-4.1.0-2.fc41.noarch" is already installed.

Package             Arch   Version         Repository                                                         Size
Installing:                                                                                                       
 python3-pip        noarch 24.0-2.fc41     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  14.2 MiB
 python3-setuptools noarch 69.2.0-1.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.2 MiB
 python3-wheel      noarch 1:0.43.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 513.0 KiB

Transaction Summary:
 Installing:        3 packages

Total size of inbound packages is 4 MiB. Need to download 0 B.
After this operation 22 MiB will be used (install 22 MiB, remove 0 B).
[1/3] python3-pip-0:24.0-2.fc41.noarch  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[2/3] python3-setuptools-0:69.2.0-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[3/3] python3-wheel-1:0.43.0-1.fc41.noa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[3/3] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
[1/5] Verify package files              100% | 187.0   B/s |   3.0   B |  00m00s
[2/5] Prepare transaction               100% | 103.0   B/s |   3.0   B |  00m00s
[3/5] Installing python3-wheel-1:0.43.0 100% |  86.6 MiB/s | 532.0 KiB |  00m00s
[4/5] Installing python3-setuptools-0:6 100% | 174.2 MiB/s |   7.3 MiB |  00m00s
[5/5] Installing python3-pip-0:24.0-2.f 100% | 135.8 MiB/s |  14.5 MiB |  00m00s
>>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
Warning: skipped PGP checks for 3 package(s).
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.8pcZz9
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ echo pyproject-rpm-macros
+ echo python3-devel
+ echo 'python3dist(pip) >= 19'
+ echo 'python3dist(packaging)'
+ '[' -f pyproject.toml ']'
+ '[' -f setup.py ']'
+ echo 'python3dist(setuptools) >= 40.8'
+ echo 'python3dist(wheel)'
+ rm -rfv '*.dist-info/'
+ '[' -f /usr/bin/python3 ']'
+ mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ echo -n
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ RPM_TOXENV=py312
+ HOSTNAME=rpmbuild
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires -x tests
Handling setuptools >= 40.8 from default build backend
Requirement satisfied: setuptools >= 40.8
   (installed: setuptools 69.2.0)
Handling wheel from default build backend
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Handling wheel from get_requires_for_build_wheel
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running dist_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info'
Handling numpy from hook generated metadata: Requires-Dist (biopython)
Requirement not satisfied: numpy
+ cat /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires
+ rm -rfv biopython-1.83.dist-info/
removed 'biopython-1.83.dist-info/LICENSE.rst'
removed 'biopython-1.83.dist-info/LICENSE'
removed 'biopython-1.83.dist-info/METADATA'
removed 'biopython-1.83.dist-info/top_level.txt'
removed directory 'biopython-1.83.dist-info/'
+ RPM_EC=0
++ jobs -p
+ exit 0
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.buildreqs.nosrc.rpm
INFO: Going to install missing dynamic buildrequires
Updating and loading repositories:
 fedora                                 100% |  33.8 KiB/s |   9.6 KiB |  00m00s
 Copr repository                        100% | 118.2 KiB/s |   1.5 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% |  65.5 KiB/s |   4.1 KiB |  00m00s
Repositories loaded.
Package "gcc-14.0.1-0.15.fc41.aarch64" is already installed.
Package "pyproject-rpm-macros-1.12.0-1.fc40.noarch" is already installed.
Package "python3-devel-3.12.3-1.fc41.aarch64" is already installed.
Package "python3-packaging-24.0-1.fc41.noarch" is already installed.
Package "python3-pip-24.0-2.fc41.noarch" is already installed.
Package "python3-reportlab-4.1.0-2.fc41.noarch" is already installed.
Package "python3-setuptools-69.2.0-1.fc41.noarch" is already installed.
Package "python3-wheel-1:0.43.0-1.fc41.noarch" is already installed.

Package                    Arch    Version          Repository                                                         Size
Installing:                                                                                                                
 python3-numpy             aarch64 1:1.26.4-2.fc41  copr_base                                                      41.5 MiB
Installing dependencies:                                                                                                   
 flexiblas                 aarch64 3.4.2-1.fc41     copr_base                                                      46.9 KiB
 flexiblas-netlib          aarch64 3.4.2-1.fc41     copr_base                                                       9.6 MiB
 flexiblas-openblas-openmp aarch64 3.4.2-1.fc41     copr_base                                                     195.3 KiB
 libgfortran               aarch64 14.0.1-0.15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 openblas                  aarch64 0.3.26-4.fc40    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  96.0 KiB
 openblas-openmp           aarch64 0.3.26-4.fc40    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  19.5 MiB

Transaction Summary:
 Installing:        7 packages

Total size of inbound packages is 14 MiB. Need to download 0 B.
After this operation 72 MiB will be used (install 72 MiB, remove 0 B).
[1/7] python3-numpy-1:1.26.4-2.fc41.aar 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[2/7] flexiblas-netlib-0:3.4.2-1.fc41.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[3/7] flexiblas-0:3.4.2-1.fc41.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[4/7] flexiblas-openblas-openmp-0:3.4.2 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[5/7] libgfortran-0:14.0.1-0.15.fc41.aa 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[6/7] openblas-openmp-0:0.3.26-4.fc40.a 100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
[7/7] openblas-0:0.3.26-4.fc40.aarch64  100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded
--------------------------------------------------------------------------------
[7/7] Total                             100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
[1/9] Verify package files              100% | 132.0   B/s |   7.0   B |  00m00s
[2/9] Prepare transaction               100% | 212.0   B/s |   7.0   B |  00m00s
[3/9] Installing libgfortran-0:14.0.1-0 100% | 304.3 MiB/s |   1.5 MiB |  00m00s
[4/9] Installing openblas-0:0.3.26-4.fc 100% |  95.5 MiB/s |  97.8 KiB |  00m00s
[5/9] Installing openblas-openmp-0:0.3. 100% | 405.3 MiB/s |  19.5 MiB |  00m00s
[6/9] Installing flexiblas-0:3.4.2-1.fc 100% |  47.0 MiB/s |  48.1 KiB |  00m00s
[7/9] Installing flexiblas-openblas-ope 100% | 191.6 MiB/s | 196.2 KiB |  00m00s
[8/9] Installing flexiblas-netlib-0:3.4 100% | 311.3 MiB/s |   9.7 MiB |  00m00s
[9/9] Installing python3-numpy-1:1.26.4 100% | 256.4 MiB/s |  41.8 MiB |  00m00s
>>> Running trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.39.9000-10.fc41.aarch64
Warning: skipped PGP checks for 7 package(s).
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.4Wtmok
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ echo pyproject-rpm-macros
+ echo python3-devel
+ echo 'python3dist(pip) >= 19'
+ echo 'python3dist(packaging)'
+ '[' -f pyproject.toml ']'
+ '[' -f setup.py ']'
+ echo 'python3dist(setuptools) >= 40.8'
+ echo 'python3dist(wheel)'
+ rm -rfv '*.dist-info/'
+ '[' -f /usr/bin/python3 ']'
+ mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ echo -n
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ RPM_TOXENV=py312
+ HOSTNAME=rpmbuild
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires -x tests
Handling setuptools >= 40.8 from default build backend
Requirement satisfied: setuptools >= 40.8
   (installed: setuptools 69.2.0)
Handling wheel from default build backend
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Handling wheel from get_requires_for_build_wheel
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running dist_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info'
Handling numpy from hook generated metadata: Requires-Dist (biopython)
Requirement satisfied: numpy
   (installed: numpy 1.26.4)
+ cat /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires
+ rm -rfv biopython-1.83.dist-info/
removed 'biopython-1.83.dist-info/LICENSE.rst'
removed 'biopython-1.83.dist-info/LICENSE'
removed 'biopython-1.83.dist-info/METADATA'
removed 'biopython-1.83.dist-info/top_level.txt'
removed directory 'biopython-1.83.dist-info/'
+ RPM_EC=0
++ jobs -p
+ exit 0
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.buildreqs.nosrc.rpm
INFO: Going to install missing dynamic buildrequires
Updating and loading repositories:
 fedora                                 100% | 110.1 KiB/s |   9.6 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% |  71.1 KiB/s |   4.1 KiB |  00m00s
 Copr repository                        100% | 109.8 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package "gcc-14.0.1-0.15.fc41.aarch64" is already installed.
Package "pyproject-rpm-macros-1.12.0-1.fc40.noarch" is already installed.
Package "python3-devel-3.12.3-1.fc41.aarch64" is already installed.
Package "python3-numpy-1:1.26.4-2.fc41.aarch64" is already installed.
Package "python3-packaging-24.0-1.fc41.noarch" is already installed.
Package "python3-pip-24.0-2.fc41.noarch" is already installed.
Package "python3-reportlab-4.1.0-2.fc41.noarch" is already installed.
Package "python3-setuptools-69.2.0-1.fc41.noarch" is already installed.
Package "python3-wheel-1:0.43.0-1.fc41.noarch" is already installed.
Nothing to do.

Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1712966400
Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.nkDJF5
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ echo pyproject-rpm-macros
+ echo python3-devel
+ echo 'python3dist(pip) >= 19'
+ echo 'python3dist(packaging)'
+ '[' -f pyproject.toml ']'
+ '[' -f setup.py ']'
+ echo 'python3dist(setuptools) >= 40.8'
+ echo 'python3dist(wheel)'
+ rm -rfv '*.dist-info/'
+ '[' -f /usr/bin/python3 ']'
+ mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ echo -n
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ RPM_TOXENV=py312
+ HOSTNAME=rpmbuild
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires -x tests
Handling setuptools >= 40.8 from default build backend
Requirement satisfied: setuptools >= 40.8
   (installed: setuptools 69.2.0)
Handling wheel from default build backend
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running egg_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
Handling wheel from get_requires_for_build_wheel
Requirement satisfied: wheel
   (installed: wheel 0.43.0)
running dist_info
writing biopython.egg-info/PKG-INFO
writing dependency_links to biopython.egg-info/dependency_links.txt
writing requirements to biopython.egg-info/requires.txt
writing top-level names to biopython.egg-info/top_level.txt
reading manifest file 'biopython.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.py{}' found anywhere in distribution
warning: no previously-included files matching '*.py-e' found anywhere in distribution
warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
adding license file 'LICENSE'
adding license file 'LICENSE.rst'
writing manifest file 'biopython.egg-info/SOURCES.txt'
creating '/builddir/build/BUILD/biopython-1.83/biopython-1.83.dist-info'
Handling numpy from hook generated metadata: Requires-Dist (biopython)
Requirement satisfied: numpy
   (installed: numpy 1.26.4)
+ cat /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-buildrequires
+ rm -rfv biopython-1.83.dist-info/
removed 'biopython-1.83.dist-info/LICENSE.rst'
removed 'biopython-1.83.dist-info/LICENSE'
removed 'biopython-1.83.dist-info/METADATA'
removed 'biopython-1.83.dist-info/top_level.txt'
removed directory 'biopython-1.83.dist-info/'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.RM44rH
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd biopython-1.83
+ mkdir -p /builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir
Processing /builddir/build/BUILD/biopython-1.83
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  running dist_info
  creating /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info
  writing /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/PKG-INFO
  writing dependency_links to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/dependency_links.txt
  writing requirements to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/requires.txt
  writing top-level names to /builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/top_level.txt
  writing manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/SOURCES.txt'
  reading manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '*.pyo' found anywhere in distribution
  warning: no previously-included files matching '*.py{}' found anywhere in distribution
  warning: no previously-included files matching '*.py-e' found anywhere in distribution
  warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
  adding license file 'LICENSE'
  adding license file 'LICENSE.rst'
  writing manifest file '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython.egg-info/SOURCES.txt'
  creating '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-modern-metadata-jx1e6wtu/biopython-1.83.dist-info'
  Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: biopython
  Building wheel for biopython (pyproject.toml): started
  Running command Building wheel for biopython (pyproject.toml)
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-aarch64-cpython-312
  creating build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/pairwise2.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/kNN.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/bgzf.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/_utils.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/SeqRecord.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/SeqFeature.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/Seq.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/NaiveBayes.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/MaxEntropy.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/MarkovModel.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/LogisticRegression.py -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/File.py -> build/lib.linux-aarch64-cpython-312/Bio
  creating build/lib.linux-aarch64-cpython-312/Bio/Affy
  copying Bio/Affy/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Affy
  copying Bio/Affy/CelFile.py -> build/lib.linux-aarch64-cpython-312/Bio/Affy
  creating build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/tabular.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/stockholm.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/sam.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/psl.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/phylip.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/nexus.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/msf.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/mauve.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/maf.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/interfaces.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/hhr.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/fasta.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/exonerate.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/emboss.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/clustal.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/chain.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/bigpsl.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/bigmaf.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/bigbed.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/bed.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/analysis.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/a2m.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/AlignInfo.py -> build/lib.linux-aarch64-cpython-312/Bio/Align
  creating build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Prank.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/Applications
  creating build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices
  copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices
  creating build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/NexusIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/MsfIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/MauveIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/MafIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/Interfaces.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/FastaIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-aarch64-cpython-312/Bio/AlignIO
  creating build/lib.linux-aarch64-cpython-312/Bio/Alphabet
  copying Bio/Alphabet/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Alphabet
  creating build/lib.linux-aarch64-cpython-312/Bio/Application
  copying Bio/Application/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Application
  creating build/lib.linux-aarch64-cpython-312/Bio/Blast
  copying Bio/Blast/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Blast
  copying Bio/Blast/Record.py -> build/lib.linux-aarch64-cpython-312/Bio/Blast
  copying Bio/Blast/NCBIXML.py -> build/lib.linux-aarch64-cpython-312/Bio/Blast
  copying Bio/Blast/NCBIWWW.py -> build/lib.linux-aarch64-cpython-312/Bio/Blast
  copying Bio/Blast/Applications.py -> build/lib.linux-aarch64-cpython-312/Bio/Blast
  creating build/lib.linux-aarch64-cpython-312/Bio/CAPS
  copying Bio/CAPS/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/CAPS
  creating build/lib.linux-aarch64-cpython-312/Bio/Cluster
  copying Bio/Cluster/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Cluster
  creating build/lib.linux-aarch64-cpython-312/Bio/codonalign
  copying Bio/codonalign/codonseq.py -> build/lib.linux-aarch64-cpython-312/Bio/codonalign
  copying Bio/codonalign/codonalignment.py -> build/lib.linux-aarch64-cpython-312/Bio/codonalign
  copying Bio/codonalign/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/codonalign
  creating build/lib.linux-aarch64-cpython-312/Bio/Compass
  copying Bio/Compass/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Compass
  creating build/lib.linux-aarch64-cpython-312/Bio/Data
  copying Bio/Data/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Data
  copying Bio/Data/PDBData.py -> build/lib.linux-aarch64-cpython-312/Bio/Data
  copying Bio/Data/IUPACData.py -> build/lib.linux-aarch64-cpython-312/Bio/Data
  copying Bio/Data/CodonTable.py -> build/lib.linux-aarch64-cpython-312/Bio/Data
  creating build/lib.linux-aarch64-cpython-312/Bio/Emboss
  copying Bio/Emboss/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Emboss
  copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-aarch64-cpython-312/Bio/Emboss
  copying Bio/Emboss/Primer3.py -> build/lib.linux-aarch64-cpython-312/Bio/Emboss
  copying Bio/Emboss/Applications.py -> build/lib.linux-aarch64-cpython-312/Bio/Emboss
  creating build/lib.linux-aarch64-cpython-312/Bio/Entrez
  copying Bio/Entrez/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Entrez
  copying Bio/Entrez/Parser.py -> build/lib.linux-aarch64-cpython-312/Bio/Entrez
  creating build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/Prosite.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/Prodoc.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  copying Bio/ExPASy/Enzyme.py -> build/lib.linux-aarch64-cpython-312/Bio/ExPASy
  creating build/lib.linux-aarch64-cpython-312/Bio/GenBank
  copying Bio/GenBank/utils.py -> build/lib.linux-aarch64-cpython-312/Bio/GenBank
  copying Bio/GenBank/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/GenBank
  copying Bio/GenBank/Scanner.py -> build/lib.linux-aarch64-cpython-312/Bio/GenBank
  copying Bio/GenBank/Record.py -> build/lib.linux-aarch64-cpython-312/Bio/GenBank
  creating build/lib.linux-aarch64-cpython-312/Bio/Geo
  copying Bio/Geo/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Geo
  copying Bio/Geo/Record.py -> build/lib.linux-aarch64-cpython-312/Bio/Geo
  creating build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/KGML_vis.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/Distribution.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/Comparative.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics
  creating build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram
  creating build/lib.linux-aarch64-cpython-312/Bio/HMM
  copying Bio/HMM/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/HMM
  copying Bio/HMM/Utilities.py -> build/lib.linux-aarch64-cpython-312/Bio/HMM
  copying Bio/HMM/Trainer.py -> build/lib.linux-aarch64-cpython-312/Bio/HMM
  copying Bio/HMM/MarkovModel.py -> build/lib.linux-aarch64-cpython-312/Bio/HMM
  copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-aarch64-cpython-312/Bio/HMM
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG
  copying Bio/KEGG/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG
  copying Bio/KEGG/REST.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG/Compound
  copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/Compound
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG/Enzyme
  copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/Enzyme
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG/Gene
  copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/Gene
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG/Map
  copying Bio/KEGG/Map/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/Map
  creating build/lib.linux-aarch64-cpython-312/Bio/PDB
  creating build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf
  copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf
  creating build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML
  copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML
  creating build/lib.linux-aarch64-cpython-312/Bio/Medline
  copying Bio/Medline/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Medline
  creating build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/xms.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/transfac.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/thresholds.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/pfm.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/minimal.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/meme.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/matrix.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/mast.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/clusterbuster.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/alignace.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/motifs/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  creating build/lib.linux-aarch64-cpython-312/Bio/motifs/applications
  copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs/applications
  copying Bio/motifs/applications/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs/applications
  creating build/lib.linux-aarch64-cpython-312/Bio/motifs/jaspar
  copying Bio/motifs/jaspar/db.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs/jaspar
  copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/motifs/jaspar
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  copying Bio/Nexus/Trees.py -> build/lib.linux-aarch64-cpython-312/Bio/Nexus
  copying Bio/Nexus/StandardData.py -> build/lib.linux-aarch64-cpython-312/Bio/Nexus
  copying Bio/Nexus/Nodes.py -> build/lib.linux-aarch64-cpython-312/Bio/Nexus
  copying Bio/Nexus/Nexus.py -> build/lib.linux-aarch64-cpython-312/Bio/Nexus
  creating build/lib.linux-aarch64-cpython-312/Bio/NMR
  copying Bio/NMR/xpktools.py -> build/lib.linux-aarch64-cpython-312/Bio/NMR
  copying Bio/NMR/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/NMR
  copying Bio/NMR/NOEtools.py -> build/lib.linux-aarch64-cpython-312/Bio/NMR
  creating build/lib.linux-aarch64-cpython-312/Bio/Pathway
  copying Bio/Pathway/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Pathway
  creating build/lib.linux-aarch64-cpython-312/Bio/Pathway/Rep
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  copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-aarch64-cpython-312/Bio/Pathway/Rep
  copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-aarch64-cpython-312/Bio/Pathway/Rep
  copying Bio/PDB/vectors.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/qcprot.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/mmcifio.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/internal_coords.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/ic_rebuild.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/ic_data.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/cealign.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Superimposer.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/StructureBuilder.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/StructureAlignment.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Structure.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Selection.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/SCADIO.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/SASA.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/ResidueDepth.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Residue.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Polypeptide.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PSEA.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PICIO.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PDBParser.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PDBList.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PDBIO.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/PDBExceptions.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/NeighborSearch.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/NACCESS.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Model.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/MMCIFParser.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/HSExposure.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/FragmentMapper.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Entity.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Dice.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/DSSP.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Chain.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/Atom.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  creating build/lib.linux-aarch64-cpython-312/Bio/phenotype
  copying Bio/phenotype/pm_fitting.py -> build/lib.linux-aarch64-cpython-312/Bio/phenotype
  copying Bio/phenotype/phen_micro.py -> build/lib.linux-aarch64-cpython-312/Bio/phenotype
  copying Bio/phenotype/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/phenotype
  creating build/lib.linux-aarch64-cpython-312/Bio/PopGen
  copying Bio/PopGen/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen
  creating build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-aarch64-cpython-312/Bio/PopGen/GenePop
  creating build/lib.linux-aarch64-cpython-312/Bio/Restriction
  copying Bio/Restriction/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Restriction
  copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-aarch64-cpython-312/Bio/Restriction
  copying Bio/Restriction/Restriction.py -> build/lib.linux-aarch64-cpython-312/Bio/Restriction
  copying Bio/Restriction/PrintFormat.py -> build/lib.linux-aarch64-cpython-312/Bio/Restriction
  creating build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Residues.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Raf.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Hie.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Dom.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Des.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  copying Bio/SCOP/Cla.py -> build/lib.linux-aarch64-cpython-312/Bio/SCOP
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  copying Bio/SearchIO/_utils.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  copying Bio/SearchIO/_index.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  copying Bio/SearchIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  copying Bio/SearchIO/FastaIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  copying Bio/SearchIO/BlatIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/query.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/hit.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/_base.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/_model
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/BlastIO
  copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/BlastIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HHsuiteIO
  copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HHsuiteIO
  copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HHsuiteIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/HmmerIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/ExonerateIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SearchIO/InterproscanIO
  copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/InterproscanIO
  copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SearchIO/InterproscanIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/_index.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/TabIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/SwissIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/SffIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/QualityIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/PirIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/PhdIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/PdbIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/NibIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/Interfaces.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/IgIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/GckIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/FastaIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/AceIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying Bio/SeqIO/AbiIO.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  creating build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/lcc.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-aarch64-cpython-312/Bio/SeqUtils
  creating build/lib.linux-aarch64-cpython-312/Bio/Sequencing
  copying Bio/Sequencing/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing
  copying Bio/Sequencing/Phd.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing
  copying Bio/Sequencing/Ace.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing
  creating build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications
  copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications
  creating build/lib.linux-aarch64-cpython-312/Bio/SVDSuperimposer
  copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SVDSuperimposer
  creating build/lib.linux-aarch64-cpython-312/Bio/SwissProt
  copying Bio/SwissProt/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/SwissProt
  copying Bio/SwissProt/KeyWList.py -> build/lib.linux-aarch64-cpython-312/Bio/SwissProt
  creating build/lib.linux-aarch64-cpython-312/Bio/TogoWS
  copying Bio/TogoWS/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/TogoWS
  creating build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/_utils.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/_io.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/PhyloXML.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/NexusIO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/NewickIO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/Newick.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/NeXML.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/Consensus.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/CDAOIO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/CDAO.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  copying Bio/Phylo/BaseTree.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo
  creating build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications
  copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications
  creating build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML
  creating build/lib.linux-aarch64-cpython-312/Bio/UniGene
  copying Bio/UniGene/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/UniGene
  creating build/lib.linux-aarch64-cpython-312/Bio/UniProt
  copying Bio/UniProt/__init__.py -> build/lib.linux-aarch64-cpython-312/Bio/UniProt
  copying Bio/UniProt/GOA.py -> build/lib.linux-aarch64-cpython-312/Bio/UniProt
  creating build/lib.linux-aarch64-cpython-312/BioSQL
  copying BioSQL/__init__.py -> build/lib.linux-aarch64-cpython-312/BioSQL
  copying BioSQL/Loader.py -> build/lib.linux-aarch64-cpython-312/BioSQL
  copying BioSQL/DBUtils.py -> build/lib.linux-aarch64-cpython-312/BioSQL
  copying BioSQL/BioSeqDatabase.py -> build/lib.linux-aarch64-cpython-312/BioSQL
  copying BioSQL/BioSeq.py -> build/lib.linux-aarch64-cpython-312/BioSQL
  running egg_info
  writing biopython.egg-info/PKG-INFO
  writing dependency_links to biopython.egg-info/dependency_links.txt
  writing requirements to biopython.egg-info/requires.txt
  writing top-level names to biopython.egg-info/top_level.txt
  reading manifest file 'biopython.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip'
  warning: no previously-included files matching '*.pyc' found anywhere in distribution
  warning: no previously-included files matching '*.pyo' found anywhere in distribution
  warning: no previously-included files matching '*.py{}' found anywhere in distribution
  warning: no previously-included files matching '*.py-e' found anywhere in distribution
  warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt'
  adding license file 'LICENSE'
  adding license file 'LICENSE.rst'
  writing manifest file 'biopython.egg-info/SOURCES.txt'
  /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration.
  !!

          ********************************************************************************
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.

          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added
          to the `packages` configuration field.

          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).

          You can read more about "package discovery" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

          If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are
          already explicitly excluding 'Bio.Align.substitution_matrices.data' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.

          You can read more about "package data files" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************

  !!
    check.warn(importable)
  /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration.
  !!

          ********************************************************************************
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.

          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'Bio.Entrez.DTDs' is explicitly added
          to the `packages` configuration field.

          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).

          You can read more about "package discovery" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

          If you don't want 'Bio.Entrez.DTDs' to be distributed and are
          already explicitly excluding 'Bio.Entrez.DTDs' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.

          You can read more about "package data files" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************

  !!
    check.warn(importable)
  /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration.
  !!

          ********************************************************************************
          ############################
          # Package would be ignored #
          ############################
          Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1],
          but it is absent from setuptools' `packages` configuration.

          This leads to an ambiguous overall configuration. If you want to distribute this
          package, please make sure that 'Bio.Entrez.XSDs' is explicitly added
          to the `packages` configuration field.

          Alternatively, you can also rely on setuptools' discovery methods
          (for example by using `find_namespace_packages(...)`/`find_namespace:`
          instead of `find_packages(...)`/`find:`).

          You can read more about "package discovery" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

          If you don't want 'Bio.Entrez.XSDs' to be distributed and are
          already explicitly excluding 'Bio.Entrez.XSDs' via
          `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
          you can try to use `exclude_package_data`, or `include-package-data=False` in
          combination with a more fine grained `package-data` configuration.

          You can read more about "package data files" on setuptools documentation page:

          - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


          [^1]: For Python, any directory (with suitable naming) can be imported,
                even if it does not contain any `.py` files.
                On the other hand, currently there is no concept of package data
                directory, all directories are treated like packages.
          ********************************************************************************

  !!
    check.warn(importable)
  copying Bio/cpairwise2module.c -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/py.typed -> build/lib.linux-aarch64-cpython-312/Bio
  copying Bio/Align/_codonaligner.c -> build/lib.linux-aarch64-cpython-312/Bio/Align
  copying Bio/Align/_pairwisealigner.c -> build/lib.linux-aarch64-cpython-312/Bio/Align
  creating build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data
  copying Bio/Cluster/cluster.c -> build/lib.linux-aarch64-cpython-312/Bio/Cluster
  copying Bio/Cluster/cluster.h -> build/lib.linux-aarch64-cpython-312/Bio/Cluster
  copying Bio/Cluster/clustermodule.c -> build/lib.linux-aarch64-cpython-312/Bio/Cluster
  creating build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
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  copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs
  creating build/lib.linux-aarch64-cpython-312/Bio/Entrez/XSDs
  copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-aarch64-cpython-312/Bio/Entrez/XSDs
  copying Bio/motifs/_pwm.c -> build/lib.linux-aarch64-cpython-312/Bio/motifs
  copying Bio/Nexus/cnexus.c -> build/lib.linux-aarch64-cpython-312/Bio/Nexus
  copying Bio/PDB/ccealignmodule.c -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/PDB/kdtrees.c -> build/lib.linux-aarch64-cpython-312/Bio/PDB
  copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-aarch64-cpython-312/Bio/SeqIO
  copying BioSQL/py.typed -> build/lib.linux-aarch64-cpython-312/BioSQL
  running build_ext
  building 'Bio.Align._codonaligner' extension
  creating build/temp.linux-aarch64-cpython-312
  creating build/temp.linux-aarch64-cpython-312/Bio
  creating build/temp.linux-aarch64-cpython-312/Bio/Align
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Align/_codonaligner.c -o build/temp.linux-aarch64-cpython-312/Bio/Align/_codonaligner.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/Align/_codonaligner.cpython-312-aarch64-linux-gnu.so
  building 'Bio.Align._pairwisealigner' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-aarch64-cpython-312/Bio/Align/_pairwisealigner.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/Align/_pairwisealigner.cpython-312-aarch64-linux-gnu.so
  building 'Bio.cpairwise2' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-aarch64-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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/cpairwise2.cpython-312-aarch64-linux-gnu.so
  building 'Bio.Nexus.cnexus' extension
  creating build/temp.linux-aarch64-cpython-312/Bio/Nexus
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-aarch64-cpython-312/Bio/Nexus/cnexus.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/Nexus/cnexus.cpython-312-aarch64-linux-gnu.so
  building 'Bio.motifs._pwm' extension
  creating build/temp.linux-aarch64-cpython-312/Bio/motifs
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-aarch64-cpython-312/Bio/motifs/_pwm.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/motifs/_pwm.cpython-312-aarch64-linux-gnu.so
  building 'Bio.Cluster._cluster' extension
  creating build/temp.linux-aarch64-cpython-312/Bio/Cluster
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-aarch64-cpython-312/Bio/Cluster/cluster.o
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-aarch64-cpython-312/Bio/Cluster/clustermodule.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/Cluster/cluster.o build/temp.linux-aarch64-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/Cluster/_cluster.cpython-312-aarch64-linux-gnu.so
  building 'Bio.PDB.kdtrees' extension
  creating build/temp.linux-aarch64-cpython-312/Bio/PDB
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-aarch64-cpython-312/Bio/PDB/kdtrees.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/PDB/kdtrees.cpython-312-aarch64-linux-gnu.so
  building 'Bio.PDB.ccealign' extension
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-aarch64-cpython-312/Bio/PDB/ccealignmodule.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/PDB/ccealign.cpython-312-aarch64-linux-gnu.so
  building 'Bio.SeqIO._twoBitIO' extension
  creating build/temp.linux-aarch64-cpython-312/Bio/SeqIO
  gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-aarch64-cpython-312/Bio/SeqIO/_twoBitIO.o
  gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-aarch64-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-aarch64-linux-gnu.so
  installing to build/bdist.linux-aarch64/wheel
  running install
  running install_lib
  creating build/bdist.linux-aarch64
  creating build/bdist.linux-aarch64/wheel
  creating build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/py.typed -> build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/BioSeq.py -> build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/BioSeqDatabase.py -> build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/DBUtils.py -> build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/Loader.py -> build/bdist.linux-aarch64/wheel/BioSQL
  copying build/lib.linux-aarch64-cpython-312/BioSQL/__init__.py -> build/bdist.linux-aarch64/wheel/BioSQL
  creating build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/cpairwise2.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/py.typed -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/cpairwise2module.c -> build/bdist.linux-aarch64/wheel/Bio
  creating build/bdist.linux-aarch64/wheel/Bio/UniProt
  copying build/lib.linux-aarch64-cpython-312/Bio/UniProt/GOA.py -> build/bdist.linux-aarch64/wheel/Bio/UniProt
  copying build/lib.linux-aarch64-cpython-312/Bio/UniProt/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/UniProt
  creating build/bdist.linux-aarch64/wheel/Bio/UniGene
  copying build/lib.linux-aarch64-cpython-312/Bio/UniGene/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/UniGene
  creating build/bdist.linux-aarch64/wheel/Bio/Phylo
  creating build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/PAML
  creating build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/BaseTree.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/CDAO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/CDAOIO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Consensus.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/NeXML.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/Newick.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/NewickIO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/NexusIO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PhyloXML.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
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  copying build/lib.linux-aarch64-cpython-312/Bio/Phylo/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Phylo
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  copying build/lib.linux-aarch64-cpython-312/Bio/SwissProt/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/SwissProt
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  copying build/lib.linux-aarch64-cpython-312/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Sequencing/Applications
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  copying build/lib.linux-aarch64-cpython-312/Bio/Sequencing/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Sequencing
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  copying build/lib.linux-aarch64-cpython-312/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-aarch64/wheel/Bio/SeqIO
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  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/MMCIFParser.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Model.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/NACCESS.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/NeighborSearch.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PDBExceptions.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PDBIO.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PDBList.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PDBParser.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PICIO.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/PSEA.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Polypeptide.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Residue.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/ResidueDepth.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/SASA.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/SCADIO.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Selection.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Structure.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/StructureAlignment.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/StructureBuilder.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/Superimposer.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/cealign.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/ic_data.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/ic_rebuild.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/internal_coords.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/mmcifio.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/qcprot.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/vectors.py -> build/bdist.linux-aarch64/wheel/Bio/PDB
  creating build/bdist.linux-aarch64/wheel/Bio/PDB/mmtf
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-aarch64/wheel/Bio/PDB/mmtf
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/PDB/mmtf
  copying build/lib.linux-aarch64-cpython-312/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-aarch64/wheel/Bio/PDB/mmtf
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG/KGML
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/KGML
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/KGML
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/KGML
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Map
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/Map/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/Map
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Gene
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/Gene
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Enzyme
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/Enzyme
  creating build/bdist.linux-aarch64/wheel/Bio/KEGG/Compound
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG/Compound
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/REST.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG
  copying build/lib.linux-aarch64-cpython-312/Bio/KEGG/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/KEGG
  creating build/bdist.linux-aarch64/wheel/Bio/HMM
  copying build/lib.linux-aarch64-cpython-312/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-aarch64/wheel/Bio/HMM
  copying build/lib.linux-aarch64-cpython-312/Bio/HMM/MarkovModel.py -> build/bdist.linux-aarch64/wheel/Bio/HMM
  copying build/lib.linux-aarch64-cpython-312/Bio/HMM/Trainer.py -> build/bdist.linux-aarch64/wheel/Bio/HMM
  copying build/lib.linux-aarch64-cpython-312/Bio/HMM/Utilities.py -> build/bdist.linux-aarch64/wheel/Bio/HMM
  copying build/lib.linux-aarch64-cpython-312/Bio/HMM/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/HMM
  creating build/bdist.linux-aarch64/wheel/Bio/Graphics
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  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics/GenomeDiagram
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/Comparative.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/Distribution.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/KGML_vis.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  copying build/lib.linux-aarch64-cpython-312/Bio/Graphics/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Graphics
  creating build/bdist.linux-aarch64/wheel/Bio/Geo
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  copying build/lib.linux-aarch64-cpython-312/Bio/Geo/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Geo
  creating build/bdist.linux-aarch64/wheel/Bio/GenBank
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  copying build/lib.linux-aarch64-cpython-312/Bio/GenBank/Scanner.py -> build/bdist.linux-aarch64/wheel/Bio/GenBank
  copying build/lib.linux-aarch64-cpython-312/Bio/GenBank/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/GenBank
  copying build/lib.linux-aarch64-cpython-312/Bio/GenBank/utils.py -> build/bdist.linux-aarch64/wheel/Bio/GenBank
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  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/Enzyme.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/Prodoc.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/Prosite.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  copying build/lib.linux-aarch64-cpython-312/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-aarch64/wheel/Bio/ExPASy
  creating build/bdist.linux-aarch64/wheel/Bio/Entrez
  creating build/bdist.linux-aarch64/wheel/Bio/Entrez/XSDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/XSDs
  creating build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-aarch64/wheel/Bio/Entrez/DTDs
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  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices/data
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Align/substitution_matrices
  creating build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Prank.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/Applications/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Align/Applications
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/AlignInfo.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/a2m.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/analysis.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/bed.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/bigbed.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/bigmaf.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/bigpsl.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/chain.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/clustal.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/emboss.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/exonerate.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/fasta.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/hhr.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/interfaces.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/maf.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/mauve.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/msf.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/nexus.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/phylip.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/psl.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/sam.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/stockholm.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  copying build/lib.linux-aarch64-cpython-312/Bio/Align/tabular.py -> build/bdist.linux-aarch64/wheel/Bio/Align
  creating build/bdist.linux-aarch64/wheel/Bio/Affy
  copying build/lib.linux-aarch64-cpython-312/Bio/Affy/CelFile.py -> build/bdist.linux-aarch64/wheel/Bio/Affy
  copying build/lib.linux-aarch64-cpython-312/Bio/Affy/__init__.py -> build/bdist.linux-aarch64/wheel/Bio/Affy
  copying build/lib.linux-aarch64-cpython-312/Bio/File.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/LogisticRegression.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/MarkovModel.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/MaxEntropy.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/NaiveBayes.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/Seq.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/SeqFeature.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/SeqRecord.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/__init__.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/_utils.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/bgzf.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/kNN.py -> build/bdist.linux-aarch64/wheel/Bio
  copying build/lib.linux-aarch64-cpython-312/Bio/pairwise2.py -> build/bdist.linux-aarch64/wheel/Bio
  running install_egg_info
  Copying biopython.egg-info to build/bdist.linux-aarch64/wheel/biopython-1.83-py3.12.egg-info
  running install_scripts
  creating build/bdist.linux-aarch64/wheel/biopython-1.83.dist-info/WHEEL
  creating '/builddir/build/BUILD/biopython-1.83/.pyproject-builddir/pip-wheel-f3puv9bm/.tmp-ejaymsp8/biopython-1.83-cp312-cp312-linux_aarch64.whl' and adding 'build/bdist.linux-aarch64/wheel' to it
  adding 'Bio/File.py'
  adding 'Bio/LogisticRegression.py'
  adding 'Bio/MarkovModel.py'
  adding 'Bio/MaxEntropy.py'
  adding 'Bio/NaiveBayes.py'
  adding 'Bio/Seq.py'
  adding 'Bio/SeqFeature.py'
  adding 'Bio/SeqRecord.py'
  adding 'Bio/__init__.py'
  adding 'Bio/_utils.py'
  adding 'Bio/bgzf.py'
  adding 'Bio/cpairwise2.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/cpairwise2module.c'
  adding 'Bio/kNN.py'
  adding 'Bio/pairwise2.py'
  adding 'Bio/py.typed'
  adding 'Bio/Affy/CelFile.py'
  adding 'Bio/Affy/__init__.py'
  adding 'Bio/Align/AlignInfo.py'
  adding 'Bio/Align/__init__.py'
  adding 'Bio/Align/_codonaligner.c'
  adding 'Bio/Align/_codonaligner.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/Align/_pairwisealigner.c'
  adding 'Bio/Align/_pairwisealigner.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/Align/a2m.py'
  adding 'Bio/Align/analysis.py'
  adding 'Bio/Align/bed.py'
  adding 'Bio/Align/bigbed.py'
  adding 'Bio/Align/bigmaf.py'
  adding 'Bio/Align/bigpsl.py'
  adding 'Bio/Align/chain.py'
  adding 'Bio/Align/clustal.py'
  adding 'Bio/Align/emboss.py'
  adding 'Bio/Align/exonerate.py'
  adding 'Bio/Align/fasta.py'
  adding 'Bio/Align/hhr.py'
  adding 'Bio/Align/interfaces.py'
  adding 'Bio/Align/maf.py'
  adding 'Bio/Align/mauve.py'
  adding 'Bio/Align/msf.py'
  adding 'Bio/Align/nexus.py'
  adding 'Bio/Align/phylip.py'
  adding 'Bio/Align/psl.py'
  adding 'Bio/Align/sam.py'
  adding 'Bio/Align/stockholm.py'
  adding 'Bio/Align/tabular.py'
  adding 'Bio/Align/Applications/_ClustalOmega.py'
  adding 'Bio/Align/Applications/_Clustalw.py'
  adding 'Bio/Align/Applications/_Dialign.py'
  adding 'Bio/Align/Applications/_MSAProbs.py'
  adding 'Bio/Align/Applications/_Mafft.py'
  adding 'Bio/Align/Applications/_Muscle.py'
  adding 'Bio/Align/Applications/_Prank.py'
  adding 'Bio/Align/Applications/_Probcons.py'
  adding 'Bio/Align/Applications/_TCoffee.py'
  adding 'Bio/Align/Applications/__init__.py'
  adding 'Bio/Align/substitution_matrices/__init__.py'
  adding 'Bio/Align/substitution_matrices/data/BENNER22'
  adding 'Bio/Align/substitution_matrices/data/BENNER6'
  adding 'Bio/Align/substitution_matrices/data/BENNER74'
  adding 'Bio/Align/substitution_matrices/data/BLASTN'
  adding 'Bio/Align/substitution_matrices/data/BLASTP'
  adding 'Bio/Align/substitution_matrices/data/BLOSUM45'
  adding 'Bio/Align/substitution_matrices/data/BLOSUM50'
  adding 'Bio/Align/substitution_matrices/data/BLOSUM62'
  adding 'Bio/Align/substitution_matrices/data/BLOSUM80'
  adding 'Bio/Align/substitution_matrices/data/BLOSUM90'
  adding 'Bio/Align/substitution_matrices/data/DAYHOFF'
  adding 'Bio/Align/substitution_matrices/data/FENG'
  adding 'Bio/Align/substitution_matrices/data/GENETIC'
  adding 'Bio/Align/substitution_matrices/data/GONNET1992'
  adding 'Bio/Align/substitution_matrices/data/HOXD70'
  adding 'Bio/Align/substitution_matrices/data/JOHNSON'
  adding 'Bio/Align/substitution_matrices/data/JONES'
  adding 'Bio/Align/substitution_matrices/data/LEVIN'
  adding 'Bio/Align/substitution_matrices/data/MCLACHLAN'
  adding 'Bio/Align/substitution_matrices/data/MDM78'
  adding 'Bio/Align/substitution_matrices/data/MEGABLAST'
  adding 'Bio/Align/substitution_matrices/data/NUC.4.4'
  adding 'Bio/Align/substitution_matrices/data/PAM250'
  adding 'Bio/Align/substitution_matrices/data/PAM30'
  adding 'Bio/Align/substitution_matrices/data/PAM70'
  adding 'Bio/Align/substitution_matrices/data/RAO'
  adding 'Bio/Align/substitution_matrices/data/RISLER'
  adding 'Bio/Align/substitution_matrices/data/SCHNEIDER'
  adding 'Bio/Align/substitution_matrices/data/STR'
  adding 'Bio/Align/substitution_matrices/data/TRANS'
  adding 'Bio/AlignIO/ClustalIO.py'
  adding 'Bio/AlignIO/EmbossIO.py'
  adding 'Bio/AlignIO/FastaIO.py'
  adding 'Bio/AlignIO/Interfaces.py'
  adding 'Bio/AlignIO/MafIO.py'
  adding 'Bio/AlignIO/MauveIO.py'
  adding 'Bio/AlignIO/MsfIO.py'
  adding 'Bio/AlignIO/NexusIO.py'
  adding 'Bio/AlignIO/PhylipIO.py'
  adding 'Bio/AlignIO/StockholmIO.py'
  adding 'Bio/AlignIO/__init__.py'
  adding 'Bio/Alphabet/__init__.py'
  adding 'Bio/Application/__init__.py'
  adding 'Bio/Blast/Applications.py'
  adding 'Bio/Blast/NCBIWWW.py'
  adding 'Bio/Blast/NCBIXML.py'
  adding 'Bio/Blast/Record.py'
  adding 'Bio/Blast/__init__.py'
  adding 'Bio/CAPS/__init__.py'
  adding 'Bio/Cluster/__init__.py'
  adding 'Bio/Cluster/_cluster.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/Cluster/cluster.c'
  adding 'Bio/Cluster/cluster.h'
  adding 'Bio/Cluster/clustermodule.c'
  adding 'Bio/Compass/__init__.py'
  adding 'Bio/Data/CodonTable.py'
  adding 'Bio/Data/IUPACData.py'
  adding 'Bio/Data/PDBData.py'
  adding 'Bio/Data/__init__.py'
  adding 'Bio/Emboss/Applications.py'
  adding 'Bio/Emboss/Primer3.py'
  adding 'Bio/Emboss/PrimerSearch.py'
  adding 'Bio/Emboss/__init__.py'
  adding 'Bio/Entrez/Parser.py'
  adding 'Bio/Entrez/__init__.py'
  adding 'Bio/Entrez/DTDs/BITS-embedded-index2.ent'
  adding 'Bio/Entrez/DTDs/BITS-question-answer2.ent'
  adding 'Bio/Entrez/DTDs/Docsum_3_0.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_0.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_1.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_1.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_2.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_2.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_3.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_3.mod.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_4.dtd'
  adding 'Bio/Entrez/DTDs/Docsum_3_4.mod.dtd'
  adding 'Bio/Entrez/DTDs/EMBL_General.dtd'
  adding 'Bio/Entrez/DTDs/EMBL_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/GenBank_General.dtd'
  adding 'Bio/Entrez/DTDs/GenBank_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/HomoloGene.dtd'
  adding 'Bio/Entrez/DTDs/HomoloGene.mod.dtd'
  adding 'Bio/Entrez/DTDs/INSD_INSDSeq.dtd'
  adding 'Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd'
  adding 'Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-articlemeta1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-backmatter1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-chars1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-common-atts1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-common1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-default-classes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-default-mixes1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-display1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-format1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-funding1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-journalmeta1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-link1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-list1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-math1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-modules1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-notat1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-para1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-phrase1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-references1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-related-object1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-section1-3.ent'
  adding 'Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent'
  adding 'Bio/Entrez/DTDs/MMDB.dtd'
  adding 'Bio/Entrez/DTDs/MMDB.mod.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Features.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Features.mod.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Structural_model.dtd'
  adding 'Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Access.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Access.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Biblio.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BioSource.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BioTree.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Blast4.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastDL.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cdd.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cn3d.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Entity.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Entrez2.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Entrezgene.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_FeatDef.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_GBSeq.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Gene.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Gene.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_General.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_General.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ID1Access.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ID2Access.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_MedArchive.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medlars.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medline.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Medline.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Mim.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Mim.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Mime.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Mime.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ObjPrt.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Organism.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Organism.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PCAssay.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PCSubstance.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Project.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Project.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Protein.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Protein.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Pub.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Pub.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PubMed.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_RNA.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_RNA.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Remap.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Remap.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Rsite.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ScoreMat.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_SeqCode.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_SeqTable.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Seq_split.dtd'
  adding 'Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd'
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  adding 'Bio/ExPASy/ScanProsite.py'
  adding 'Bio/ExPASy/__init__.py'
  adding 'Bio/ExPASy/cellosaurus.py'
  adding 'Bio/GenBank/Record.py'
  adding 'Bio/GenBank/Scanner.py'
  adding 'Bio/GenBank/__init__.py'
  adding 'Bio/GenBank/utils.py'
  adding 'Bio/Geo/Record.py'
  adding 'Bio/Geo/__init__.py'
  adding 'Bio/Graphics/BasicChromosome.py'
  adding 'Bio/Graphics/ColorSpiral.py'
  adding 'Bio/Graphics/Comparative.py'
  adding 'Bio/Graphics/DisplayRepresentation.py'
  adding 'Bio/Graphics/Distribution.py'
  adding 'Bio/Graphics/KGML_vis.py'
  adding 'Bio/Graphics/__init__.py'
  adding 'Bio/Graphics/GenomeDiagram/_AbstractDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_CircularDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_Colors.py'
  adding 'Bio/Graphics/GenomeDiagram/_CrossLink.py'
  adding 'Bio/Graphics/GenomeDiagram/_Diagram.py'
  adding 'Bio/Graphics/GenomeDiagram/_Feature.py'
  adding 'Bio/Graphics/GenomeDiagram/_FeatureSet.py'
  adding 'Bio/Graphics/GenomeDiagram/_Graph.py'
  adding 'Bio/Graphics/GenomeDiagram/_GraphSet.py'
  adding 'Bio/Graphics/GenomeDiagram/_LinearDrawer.py'
  adding 'Bio/Graphics/GenomeDiagram/_Track.py'
  adding 'Bio/Graphics/GenomeDiagram/__init__.py'
  adding 'Bio/HMM/DynamicProgramming.py'
  adding 'Bio/HMM/MarkovModel.py'
  adding 'Bio/HMM/Trainer.py'
  adding 'Bio/HMM/Utilities.py'
  adding 'Bio/HMM/__init__.py'
  adding 'Bio/KEGG/REST.py'
  adding 'Bio/KEGG/__init__.py'
  adding 'Bio/KEGG/Compound/__init__.py'
  adding 'Bio/KEGG/Enzyme/__init__.py'
  adding 'Bio/KEGG/Gene/__init__.py'
  adding 'Bio/KEGG/KGML/KGML_parser.py'
  adding 'Bio/KEGG/KGML/KGML_pathway.py'
  adding 'Bio/KEGG/KGML/__init__.py'
  adding 'Bio/KEGG/Map/__init__.py'
  adding 'Bio/Medline/__init__.py'
  adding 'Bio/NMR/NOEtools.py'
  adding 'Bio/NMR/__init__.py'
  adding 'Bio/NMR/xpktools.py'
  adding 'Bio/Nexus/Nexus.py'
  adding 'Bio/Nexus/Nodes.py'
  adding 'Bio/Nexus/StandardData.py'
  adding 'Bio/Nexus/Trees.py'
  adding 'Bio/Nexus/__init__.py'
  adding 'Bio/Nexus/cnexus.c'
  adding 'Bio/Nexus/cnexus.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/PDB/AbstractPropertyMap.py'
  adding 'Bio/PDB/Atom.py'
  adding 'Bio/PDB/Chain.py'
  adding 'Bio/PDB/DSSP.py'
  adding 'Bio/PDB/Dice.py'
  adding 'Bio/PDB/Entity.py'
  adding 'Bio/PDB/FragmentMapper.py'
  adding 'Bio/PDB/HSExposure.py'
  adding 'Bio/PDB/MMCIF2Dict.py'
  adding 'Bio/PDB/MMCIFParser.py'
  adding 'Bio/PDB/Model.py'
  adding 'Bio/PDB/NACCESS.py'
  adding 'Bio/PDB/NeighborSearch.py'
  adding 'Bio/PDB/PDBExceptions.py'
  adding 'Bio/PDB/PDBIO.py'
  adding 'Bio/PDB/PDBList.py'
  adding 'Bio/PDB/PDBParser.py'
  adding 'Bio/PDB/PICIO.py'
  adding 'Bio/PDB/PSEA.py'
  adding 'Bio/PDB/Polypeptide.py'
  adding 'Bio/PDB/Residue.py'
  adding 'Bio/PDB/ResidueDepth.py'
  adding 'Bio/PDB/SASA.py'
  adding 'Bio/PDB/SCADIO.py'
  adding 'Bio/PDB/Selection.py'
  adding 'Bio/PDB/Structure.py'
  adding 'Bio/PDB/StructureAlignment.py'
  adding 'Bio/PDB/StructureBuilder.py'
  adding 'Bio/PDB/Superimposer.py'
  adding 'Bio/PDB/__init__.py'
  adding 'Bio/PDB/ccealign.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/PDB/ccealignmodule.c'
  adding 'Bio/PDB/cealign.py'
  adding 'Bio/PDB/ic_data.py'
  adding 'Bio/PDB/ic_rebuild.py'
  adding 'Bio/PDB/internal_coords.py'
  adding 'Bio/PDB/kdtrees.c'
  adding 'Bio/PDB/kdtrees.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/PDB/mmcifio.py'
  adding 'Bio/PDB/parse_pdb_header.py'
  adding 'Bio/PDB/qcprot.py'
  adding 'Bio/PDB/vectors.py'
  adding 'Bio/PDB/mmtf/DefaultParser.py'
  adding 'Bio/PDB/mmtf/__init__.py'
  adding 'Bio/PDB/mmtf/mmtfio.py'
  adding 'Bio/Pathway/__init__.py'
  adding 'Bio/Pathway/Rep/Graph.py'
  adding 'Bio/Pathway/Rep/MultiGraph.py'
  adding 'Bio/Pathway/Rep/__init__.py'
  adding 'Bio/Phylo/BaseTree.py'
  adding 'Bio/Phylo/CDAO.py'
  adding 'Bio/Phylo/CDAOIO.py'
  adding 'Bio/Phylo/Consensus.py'
  adding 'Bio/Phylo/NeXML.py'
  adding 'Bio/Phylo/NeXMLIO.py'
  adding 'Bio/Phylo/Newick.py'
  adding 'Bio/Phylo/NewickIO.py'
  adding 'Bio/Phylo/NexusIO.py'
  adding 'Bio/Phylo/PhyloXML.py'
  adding 'Bio/Phylo/PhyloXMLIO.py'
  adding 'Bio/Phylo/TreeConstruction.py'
  adding 'Bio/Phylo/__init__.py'
  adding 'Bio/Phylo/_cdao_owl.py'
  adding 'Bio/Phylo/_io.py'
  adding 'Bio/Phylo/_utils.py'
  adding 'Bio/Phylo/Applications/_Fasttree.py'
  adding 'Bio/Phylo/Applications/_Phyml.py'
  adding 'Bio/Phylo/Applications/_Raxml.py'
  adding 'Bio/Phylo/Applications/__init__.py'
  adding 'Bio/Phylo/PAML/__init__.py'
  adding 'Bio/Phylo/PAML/_paml.py'
  adding 'Bio/Phylo/PAML/_parse_baseml.py'
  adding 'Bio/Phylo/PAML/_parse_codeml.py'
  adding 'Bio/Phylo/PAML/_parse_yn00.py'
  adding 'Bio/Phylo/PAML/baseml.py'
  adding 'Bio/Phylo/PAML/chi2.py'
  adding 'Bio/Phylo/PAML/codeml.py'
  adding 'Bio/Phylo/PAML/yn00.py'
  adding 'Bio/PopGen/__init__.py'
  adding 'Bio/PopGen/GenePop/Controller.py'
  adding 'Bio/PopGen/GenePop/EasyController.py'
  adding 'Bio/PopGen/GenePop/FileParser.py'
  adding 'Bio/PopGen/GenePop/LargeFileParser.py'
  adding 'Bio/PopGen/GenePop/__init__.py'
  adding 'Bio/Restriction/PrintFormat.py'
  adding 'Bio/Restriction/Restriction.py'
  adding 'Bio/Restriction/Restriction_Dictionary.py'
  adding 'Bio/Restriction/__init__.py'
  adding 'Bio/SCOP/Cla.py'
  adding 'Bio/SCOP/Des.py'
  adding 'Bio/SCOP/Dom.py'
  adding 'Bio/SCOP/Hie.py'
  adding 'Bio/SCOP/Raf.py'
  adding 'Bio/SCOP/Residues.py'
  adding 'Bio/SCOP/__init__.py'
  adding 'Bio/SVDSuperimposer/__init__.py'
  adding 'Bio/SearchIO/BlatIO.py'
  adding 'Bio/SearchIO/FastaIO.py'
  adding 'Bio/SearchIO/__init__.py'
  adding 'Bio/SearchIO/_index.py'
  adding 'Bio/SearchIO/_utils.py'
  adding 'Bio/SearchIO/BlastIO/__init__.py'
  adding 'Bio/SearchIO/BlastIO/blast_tab.py'
  adding 'Bio/SearchIO/BlastIO/blast_xml.py'
  adding 'Bio/SearchIO/ExonerateIO/__init__.py'
  adding 'Bio/SearchIO/ExonerateIO/_base.py'
  adding 'Bio/SearchIO/ExonerateIO/exonerate_cigar.py'
  adding 'Bio/SearchIO/ExonerateIO/exonerate_text.py'
  adding 'Bio/SearchIO/ExonerateIO/exonerate_vulgar.py'
  adding 'Bio/SearchIO/HHsuiteIO/__init__.py'
  adding 'Bio/SearchIO/HHsuiteIO/hhsuite2_text.py'
  adding 'Bio/SearchIO/HmmerIO/__init__.py'
  adding 'Bio/SearchIO/HmmerIO/_base.py'
  adding 'Bio/SearchIO/HmmerIO/hmmer2_text.py'
  adding 'Bio/SearchIO/HmmerIO/hmmer3_domtab.py'
  adding 'Bio/SearchIO/HmmerIO/hmmer3_tab.py'
  adding 'Bio/SearchIO/HmmerIO/hmmer3_text.py'
  adding 'Bio/SearchIO/InterproscanIO/__init__.py'
  adding 'Bio/SearchIO/InterproscanIO/interproscan_xml.py'
  adding 'Bio/SearchIO/_model/__init__.py'
  adding 'Bio/SearchIO/_model/_base.py'
  adding 'Bio/SearchIO/_model/hit.py'
  adding 'Bio/SearchIO/_model/hsp.py'
  adding 'Bio/SearchIO/_model/query.py'
  adding 'Bio/SeqIO/AbiIO.py'
  adding 'Bio/SeqIO/AceIO.py'
  adding 'Bio/SeqIO/FastaIO.py'
  adding 'Bio/SeqIO/GckIO.py'
  adding 'Bio/SeqIO/IgIO.py'
  adding 'Bio/SeqIO/InsdcIO.py'
  adding 'Bio/SeqIO/Interfaces.py'
  adding 'Bio/SeqIO/NibIO.py'
  adding 'Bio/SeqIO/PdbIO.py'
  adding 'Bio/SeqIO/PhdIO.py'
  adding 'Bio/SeqIO/PirIO.py'
  adding 'Bio/SeqIO/QualityIO.py'
  adding 'Bio/SeqIO/SeqXmlIO.py'
  adding 'Bio/SeqIO/SffIO.py'
  adding 'Bio/SeqIO/SnapGeneIO.py'
  adding 'Bio/SeqIO/SwissIO.py'
  adding 'Bio/SeqIO/TabIO.py'
  adding 'Bio/SeqIO/TwoBitIO.py'
  adding 'Bio/SeqIO/UniprotIO.py'
  adding 'Bio/SeqIO/XdnaIO.py'
  adding 'Bio/SeqIO/__init__.py'
  adding 'Bio/SeqIO/_index.py'
  adding 'Bio/SeqIO/_twoBitIO.c'
  adding 'Bio/SeqIO/_twoBitIO.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/SeqUtils/CheckSum.py'
  adding 'Bio/SeqUtils/IsoelectricPoint.py'
  adding 'Bio/SeqUtils/MeltingTemp.py'
  adding 'Bio/SeqUtils/ProtParam.py'
  adding 'Bio/SeqUtils/ProtParamData.py'
  adding 'Bio/SeqUtils/__init__.py'
  adding 'Bio/SeqUtils/lcc.py'
  adding 'Bio/Sequencing/Ace.py'
  adding 'Bio/Sequencing/Phd.py'
  adding 'Bio/Sequencing/__init__.py'
  adding 'Bio/Sequencing/Applications/_Novoalign.py'
  adding 'Bio/Sequencing/Applications/__init__.py'
  adding 'Bio/Sequencing/Applications/_bwa.py'
  adding 'Bio/Sequencing/Applications/_samtools.py'
  adding 'Bio/SwissProt/KeyWList.py'
  adding 'Bio/SwissProt/__init__.py'
  adding 'Bio/TogoWS/__init__.py'
  adding 'Bio/UniGene/__init__.py'
  adding 'Bio/UniProt/GOA.py'
  adding 'Bio/UniProt/__init__.py'
  adding 'Bio/codonalign/__init__.py'
  adding 'Bio/codonalign/codonalignment.py'
  adding 'Bio/codonalign/codonseq.py'
  adding 'Bio/motifs/__init__.py'
  adding 'Bio/motifs/_pwm.c'
  adding 'Bio/motifs/_pwm.cpython-312-aarch64-linux-gnu.so'
  adding 'Bio/motifs/alignace.py'
  adding 'Bio/motifs/clusterbuster.py'
  adding 'Bio/motifs/mast.py'
  adding 'Bio/motifs/matrix.py'
  adding 'Bio/motifs/meme.py'
  adding 'Bio/motifs/minimal.py'
  adding 'Bio/motifs/pfm.py'
  adding 'Bio/motifs/thresholds.py'
  adding 'Bio/motifs/transfac.py'
  adding 'Bio/motifs/xms.py'
  adding 'Bio/motifs/applications/__init__.py'
  adding 'Bio/motifs/applications/_xxmotif.py'
  adding 'Bio/motifs/jaspar/__init__.py'
  adding 'Bio/motifs/jaspar/db.py'
  adding 'Bio/phenotype/__init__.py'
  adding 'Bio/phenotype/phen_micro.py'
  adding 'Bio/phenotype/pm_fitting.py'
  adding 'BioSQL/BioSeq.py'
  adding 'BioSQL/BioSeqDatabase.py'
  adding 'BioSQL/DBUtils.py'
  adding 'BioSQL/Loader.py'
  adding 'BioSQL/__init__.py'
  adding 'BioSQL/py.typed'
  adding 'biopython-1.83.dist-info/LICENSE'
  adding 'biopython-1.83.dist-info/LICENSE.rst'
  adding 'biopython-1.83.dist-info/METADATA'
  adding 'biopython-1.83.dist-info/WHEEL'
  adding 'biopython-1.83.dist-info/top_level.txt'
  adding 'biopython-1.83.dist-info/RECORD'
  removing build/bdist.linux-aarch64/wheel
  Building wheel for biopython (pyproject.toml): finished with status 'done'
  Created wheel for biopython: filename=biopython-1.83-cp312-cp312-linux_aarch64.whl size=3074940 sha256=7cd7d3fad17d9aeeaf67a061ee42eb9a7b422d65fed54246e0e705a2bcf7f15d
  Stored in directory: /builddir/.cache/pip/wheels/8f/13/4d/5683b29d5ae933c1f9b0d0a504ae17c8e39ba4601c20249b2d
Successfully built biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ZrEWD8
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64
++ dirname /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd biopython-1.83
++ ls /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir/biopython-1.83-cp312-cp312-linux_aarch64.whl
++ xargs basename --multiple
++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/'
+ specifier=biopython==1.83
+ '[' -z biopython==1.83 ']'
+ TMPDIR=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir
+ /usr/bin/python3 -m pip install --root /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64 --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir biopython==1.83
Using pip 24.0 from /usr/lib/python3.12/site-packages/pip (python 3.12)
Looking in links: /builddir/build/BUILD/biopython-1.83/pyproject-wheeldir
Processing ./pyproject-wheeldir/biopython-1.83-cp312-cp312-linux_aarch64.whl
Installing collected packages: biopython
Successfully installed biopython-1.83
+ '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin ']'
+ rm -f /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-ghost-distinfo
+ site_dirs=()
+ '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages ']'
+ '[' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages '!=' /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages ']'
+ '[' -d /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages ']'
+ site_dirs+=("/usr/lib64/python3.12/site-packages")
+ for site_dir in ${site_dirs[@]}
+ for distinfo in /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64$site_dir/*.dist-info
+ echo '%ghost /usr/lib64/python3.12/site-packages/biopython-1.83.dist-info'
+ sed -i s/pip/rpm/ /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/INSTALLER
+ PYTHONPATH=/usr/lib/rpm/redhat
+ /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64 --record /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD --output /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-record
+ rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD
removed '/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/RECORD'
+ rm -fv /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/REQUESTED
removed '/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/biopython-1.83.dist-info/REQUESTED'
++ wc -l /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-ghost-distinfo
++ cut -f1 '-d '
+ lines=1
+ '[' 1 -ne 1 ']'
+ RPM_PERCENTAGES_COUNT=2
+ /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-modules --buildroot /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64 --sitelib /usr/lib/python3.12/site-packages --sitearch /usr/lib64/python3.12/site-packages --python-version 3.12 --pyproject-record /builddir/build/BUILD/python-biopython-1.83-5.fc41.aarch64-pyproject-record --prefix /usr Bio BioSQL
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.83-5.fc41 --unique-debug-suffix -1.83-5.fc41.aarch64 --unique-debug-src-base python-biopython-1.83-5.fc41.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/biopython-1.83
find-debuginfo: starting
Extracting debug info from 9 files
DWARF-compressing 9 files
sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/python-biopython-1.83-5.fc41.aarch64
1246 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/debug/usr/lib64/python3.12 using python3.12
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12 using python3.12
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.P3Pmu4
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd biopython-1.83
+ pushd Tests
~/build/BUILD/biopython-1.83/Tests ~/build/BUILD/biopython-1.83
++ grep -v test_Align_bigbed.py
++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_chain.py test_Align_clustal.py test_Align_codonalign.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCPSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hhsuite2_text.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_interproscan_xml.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_XXmotif_tool.py test_align.py test_align_substitution_matrices.py test_bgzf.py test_cellosaurus.py test_codonalign.py test_geo.py test_kNN.py test_mmtf.py test_mmtf_online.py test_motifs.py test_motifs_online.py test_pairwise2.py test_pairwise2_no_C.py test_pairwise_aligner.py test_pairwise_alignment_map.py test_phenotype.py test_phenotype_fit.py test_phyml_tool.py test_prodoc.py test_prosite.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py
++ grep -v test_Tutorial.py
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.039 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Affy.py
test_Affy ... ok
testAffy3 (test_Affy.AffyTest.testAffy3) ... ok
testAffy4 (test_Affy.AffyTest.testAffy4) ... ok
testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok
testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok
testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.017 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO.py
test_AlignIO ... ok
test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files)
Check that parsing an empty file returns an empty list. ... ok
test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate)
Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok
test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files)
Check that writers can cope with no alignments. ... ok
test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments)
Check that writers reject records that are not alignments. ... ok
test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok
test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok
test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok
test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok
test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok
test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok
test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok
test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok
test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok
test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok
test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok
test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok
test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok
test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok
test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok
test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok
test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok
test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok
test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok
test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok
test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok
test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok
test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok
test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok
test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok
test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok
test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok
test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok
test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok
test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok
test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok
test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok
test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok
test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok
test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok
test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok
test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok
test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok
test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok
test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok
test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok
test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok
test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok
test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok
test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok
test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.586 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
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
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
----------------------------------------------------------------------
Ran 1 test in 0.044 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
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 0.043 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
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 0.051 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_MauveIO.py
test_AlignIO_MauveIO ... ok
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 0.063 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok
test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
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 0.140 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignInfo.py
test_AlignInfo ... ok
test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok
test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok
test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_Alignment.py
test_Align_Alignment ... ok
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 0.272 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_a2m.py
test_Align_a2m ... ok
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 0.070 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bed.py
test_Align_bed ... ok
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 0.137 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigmaf.py
test_Align_bigmaf ... ok
test_reading (test_Align_bigmaf.TestAlign_bundle_without_target.test_reading)
Test parsing bundle_without_target.bb. ... ok
test_writing (test_Align_bigmaf.TestAlign_bundle_without_target.test_writing)
Test writing bundle_without_target.bb. ... ok
test_declaration (test_Align_bigmaf.TestAlign_declaration.test_declaration) ... ok
test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok
test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok
test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok
test_reading (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_reading)
Test parsing file ucsc_mm9_chr10.bb. ... ok
test_writing (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_writing)
Test writing file ucsc_mm9_chr10.bb. ... ok
test_reading (test_Align_bigmaf.TestAlign_ucsc_test.test_reading)
Test reading ucsc_test.bb. ... ok
test_writing (test_Align_bigmaf.TestAlign_ucsc_test.test_writing)
Test writing ucsc_test.bb. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.433 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigpsl.py
test_Align_bigpsl ... ok
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 0.420 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_chain.py
test_Align_chain ... ok
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 0.145 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_clustal.py
test_Align_clustal ... ok
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 0.067 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_codonalign.py
test_Align_codonalign ... ok
test_aligner (test_Align_codonalign.TestBasic.test_aligner) ... ok
test_alignments (test_Align_codonalign.TestBasic.test_alignments) ... ok
test1 (test_Align_codonalign.TestBuildAndIO.test1) ... ok
test2 (test_Align_codonalign.TestBuildAndIO.test2) ... ok
test3 (test_Align_codonalign.TestBuildAndIO.test3) ... ok
test4 (test_Align_codonalign.TestBuildAndIO.test4) ... ok
test5 (test_Align_codonalign.TestBuildAndIO.test5) ... ok
test_mk (test_Align_codonalign.Test_MK.test_mk) ... ok
test_build1 (test_Align_codonalign.Test_build.test_build1) ... ok
test_build2 (test_Align_codonalign.Test_build.test_build2) ... ok
test_build3 (test_Align_codonalign.Test_build.test_build3) ... ok
test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.804 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_emboss.py
test_Align_emboss ... ok
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 0.075 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_exonerate.py
test_Align_exonerate ... ok
test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar)
Test parsing exn_22_m_affine_local_cigar.exn. ... ok
test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar)
Test parsing exn_22_m_affine_local_vulgar.exn. ... ok
test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar)
Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok
test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar)
Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok
test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar)
Test parsing exn_22_m_coding2coding_cigar.exn. ... ok
test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar)
Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok
test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar)
Test parsing exn_22_m_cigar_fshifts.exn). ... ok
test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar)
Test parsing exn_22_o_vulgar_fshifts.exn. ... ok
test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar)
Test parsing exn_22_m_coding2genome_cigar.exn. ... ok
test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar)
Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok
test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar)
Test parsing exn_22_m_dna2protein_cigar.exn. ... ok
test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar)
Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok
test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar)
Test parsing exn_22_m_est2genome_cigar.exn. ... ok
test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar)
Test parsing exn_22_m_est2genome_vulgar.exn. ... ok
test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar)
Test parsing exn_22_o_vulgar_cigar.exn. ... ok
test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar)
Test parsing exn_22_o_vulgar.exn. ... ok
test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar)
Test parsing exn_22_q_multiple_cigar.exn. ... ok
test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar)
Test parsing exn_22_q_multiple_vulgar.exn. ... ok
test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar)
Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok
test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar)
Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok
test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none)
Test parsing exonerate output (exn_22_q_none.exn). ... ok
test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar)
Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok
test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar)
Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok
test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar)
Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok
test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar)
Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok
test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar)
Test parsing exn_22_m_protein2genome_cigar.exn. ... ok
test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar)
Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok
test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar)
Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok
test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar)
Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok
test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar)
Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok
test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar)
Test parsing exn_22_m_ungapped_cigar.exn. ... ok
test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar)
Test parsing exn_22_m_ungapped_vulgar.exn. ... ok
test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar)
Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok
test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar)
Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_fasta.py
test_Align_fasta ... ok
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 0.066 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_hhr.py
test_Align_hhr ... ok
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 0.267 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_maf.py
test_Align_maf ... ok
test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453)
Test parsing bug2453.maf. ... ok
test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target)
Test parsing bundle_without_target.maf. ... ok
test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch)
Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok
test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature)
Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok
test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10)
Test parsing MAF file ucsc_mm9_chr10.maf. ... ok
test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad)
Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok
test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test)
Test parsing ucsc_test.maf. ... ok
test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453)
Test reading and writing bug2453.maf. ... ok
test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target)
Test reading and writing bundle_without_target.maf. ... ok
test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10)
Test reading and writing ucsc_mm9_chr10.maf. ... ok
test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test)
Test reading and writing ucsc_test.maf. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.363 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_mauve.py
test_Align_mauve ... ok
test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok
test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok
test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok
test_parse (test_Align_mauve.TestSeparateFiles.test_parse) ... ok
test_write_read (test_Align_mauve.TestSeparateFiles.test_write_read) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.079 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_msf.py
test_Align_msf ... ok
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 0.049 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_nexus.py
test_Align_nexus ... ok
test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok
test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok
test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.082 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_phylip.py
test_Align_phylip ... ok
test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok
test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok
test_interlaced (test_Align_phylip.TestPhylipReading.test_interlaced) ... ok
test_interlaced2 (test_Align_phylip.TestPhylipReading.test_interlaced2) ... ok
test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok
test_sequential (test_Align_phylip.TestPhylipReading.test_sequential) ... ok
test_sequential2 (test_Align_phylip.TestPhylipReading.test_sequential2) ... ok
test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.094 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_psl.py
test_Align_psl ... ok
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 0.357 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_sam.py
test_Align_sam ... ok
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 0.292 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_stockholm.py
test_Align_stockholm ... ok
test_io_nonstandard_annotations (test_Align_stockholm.TestStockholm_reading.test_io_nonstandard_annotations)
Test input and output of nonstandard GC, GS and GR annotation lines. ... ok
test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1)
Test parsing CATH record 3.30.160.60/FF/004774. ... ok
test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2)
Test parsing CATH record 2.105.10.10/FF/000002. ... ok
test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3)
Test parsing CATH record 1.10.275.10/FF/000026. ... ok
test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example)
Test parsing Pfam record HAT as the docstring example. ... ok
test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45)
Test parsing hmmalign output. ... ok
test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1)
Test parsing Pfam record 120_Rick_ant. ... ok
test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2)
Test parsing Pfam record 7kD_DNA_binding. ... ok
test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3)
Test parsing Pfam record 12TM_1. ... ok
test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4)
Test parsing Pfam record 3Beta_HSD. ... ok
test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5)
Test parsing Pfam record ArsP_1. ... ok
test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6)
Test parsing Pfam record COX2_TM. ... ok
test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7)
Test parsing Pfam record Alpha_E1_glycop. ... ok
test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8)
Test parsing Pfam record Cyclin_N. ... ok
test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9)
Test parsing Pfam record SH3_11. ... ok
test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1)
Test parsing Rfam record BTnc005. ... ok
test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2)
Test parsing Rfam record SraC_RyeA. ... ok
test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3)
Test parsing Rfam record McaS. ... ok
test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4)
Test parsing Rfam record IRES_KSHV. ... ok
test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5)
Test parsing Rfam record BMV3_UPD-PK3. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.427 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_tabular.py
test_Align_tabular ... ok
test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok
test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok
test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok
test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok
test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok
test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok
test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok
test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok
test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok
test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok
test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok
test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok
test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok
test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok
test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok
test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok
test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.350 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp.test_echo) ... ok
test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok
test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok
test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok
test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok
test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok
test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok
test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok
test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.021 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BWA_tool.py
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.012 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.111 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_MySQLdb_online.py
test_BioSQL_MySQLdb_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.109 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_mysql_connector_online.py
test_BioSQL_mysql_connector_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample)
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_psycopg2_online.py
test_BioSQL_psycopg2_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932)
From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816)
From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265)
From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1)
From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6)
From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref)
From GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest.test_one_of)
From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2)
From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items)
Check all associated data is deleted from an item. ... ok
test_server (common_BioSQL.DeleteTest.test_server)
Check BioSeqDatabase methods. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest.test_reload)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest.test_transfer)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest.test_load_database)
Load SeqRecord objects into a BioSQL database. ... ok
test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items)
Test that valid ids can't be retrieved between namespaces. ... ok
test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_server (common_BioSQL.MultiReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_get_db_items (common_BioSQL.ReadTest.test_get_db_items)
Check list, keys, length etc. ... ok
test_lookup_items (common_BioSQL.ReadTest.test_lookup_items)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest.test_server)
Check BioSeqDatabase methods. ... ok
test_addition (common_BioSQL.SeqInterfaceTest.test_addition)
Check can add Seq objects from BioSQL together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest.test_convert)
Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok
test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok
test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok
test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok
test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok
test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok
test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication)
Check can multiply Seq objects from BioSQL by integers. ... ok
test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok
test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing)
Check that slices of DBSeqRecord are retrieved properly. ... ok
test_seq (common_BioSQL.SeqInterfaceTest.test_seq)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing)
Check that slices of sequences are retrieved properly. ... ok
test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location)
Loaded uniprot-xml with ambiguous location in BioSQL. ... ok
test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok
test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok
test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok
test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok
test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok
test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok
test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok
test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok
test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok
test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok
test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok
test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok
test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok
test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok
test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok
test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok
test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok
test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok
test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok
test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok
test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok
test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok
test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932)
From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816)
From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265)
From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest.test_arab1)
From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6)
From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest.test_no_ref)
From GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest.test_one_of)
From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2)
From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 3.631 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_BioSQL_sqlite3_online.py
test_BioSQL_sqlite3_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Blast_Record.py
test_Blast_Record ... ok
test_str (test_Blast_Record.TestHsp.test_str) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.037 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_CAPS.py
test_CAPS ... ok
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 0.119 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Chi2.py
test_Chi2 ... ok
test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok
test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok
test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.060 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.065 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Cluster.py
test_Cluster ... ok
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 0.038 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_CodonTable.py
test_CodonTable ... ok
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 0.039 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_ColorSpiral.py
test_ColorSpiral ... ok
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 0.049 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok
testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok
testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok
testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok
testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok
test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok
test_bootstrap_consensus_msa (test_Consensus.BootstrapTest.test_bootstrap_consensus_msa) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok
test_bootstrap_trees_msa (test_Consensus.BootstrapTest.test_bootstrap_trees_msa) ... ok
test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok
test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok
test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok
test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok
test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.109 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.040 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
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 0.060 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.071 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_EmbossPhylipNew.py
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse)
Make sure we can parse an internal oligo file correctly. ... ok
test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full)
Test parsing multiple primer sets (NirK full). ... ok
test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd)
Test parsing multiple primer sets (NirK forward). ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez.py
test_Entrez ... ok
test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok
test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok
test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok
test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo)
Test constructed url for request to Entrez. ... ok
test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok
test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2)
Commas: Link from protein to gene. ... ok
test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3)
Multiple ID entries: Find one-to-one links from protein to gene. ... ok
test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok
test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok
test_default_params (test_Entrez.TestURLConstruction.test_default_params)
Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok
test_email_warning (test_Entrez.TestURLConstruction.test_email_warning)
Test issuing warning when user does not specify email address. ... ok
test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok
test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key)
Test checking whether a Request object specifies an API key. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.149 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Entrez_parser.py
test_Entrez_parser ... ok
test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas)
Test parsing XML using Schemas. ... ok
test_fasta (test_Entrez_parser.EFetchTest.test_fasta)
Test error handling when presented with Fasta non-XML data. ... ok
test_genbank (test_Entrez_parser.EFetchTest.test_genbank)
Test error handling when presented with GenBank non-XML data. ... ok
test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1)
Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok
test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2)
Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok
test_omim (test_Entrez_parser.EFetchTest.test_omim)
Test parsing XML returned by EFetch, OMIM database. ... ok
test_pmc (test_Entrez_parser.EFetchTest.test_pmc)
Test parsing XML returned by EFetch from PubMed Central. ... ok
test_protein (test_Entrez_parser.EFetchTest.test_protein)
Test parsing XML returned by EFetch, Protein database. ... ok
test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1)
Test parsing XML returned by EFetch, PubMed database (first test). ... ok
test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2)
Test parsing XML returned by EFetch, PubMed database (second test). ... ok
test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html)
Test error handling when presented with HTML (so XML-like) data. ... ok
test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping)
Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok
test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok
test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags)
Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok
test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags)
Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok
test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy)
Test parsing XML returned by EFetch, Taxonomy database. ... ok
test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml)
Test error handling for a truncated XML declaration. ... ok
test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration)
Test error handling for a missing XML declaration. ... ok
test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition)
Test error handling for a missing DTD or XML Schema. ... ok
test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1)
Test parsing XML output returned by EGQuery (first test). ... ok
test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2)
Test parsing XML output returned by EGQuery (second test). ... ok
test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted)
Test if corrupted XML is handled correctly. ... ok
test_list (test_Entrez_parser.EInfoTest.test_list)
Test parsing database list returned by EInfo. ... ok
test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1)
Test parsing database info returned by EInfo. ... ok
test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2)
Test validating the XML against the DTD. ... ok
test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3)
Test non-validating parser on XML with an inconsistent DTD. ... ok
test_medline (test_Entrez_parser.ELinkTest.test_medline)
Test parsing medline indexed articles returned by ELink. ... ok
test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide)
Test parsing Nucleotide to Protein links returned by ELink. ... ok
test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1)
Test parsing pubmed links returned by ELink (first test). ... ok
test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2)
Test parsing pubmed links returned by ELink (second test). ... ok
test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3)
Test parsing pubmed link returned by ELink (third test). ... ok
test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4)
Test parsing pubmed links returned by ELink (fourth test). ... ok
test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5)
Test parsing pubmed links returned by ELink (fifth test). ... ok
test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6)
Test parsing pubmed links returned by ELink (sixth test). ... ok
test_epost (test_Entrez_parser.EPostTest.test_epost)
Test parsing XML returned by EPost. ... ok
test_invalid (test_Entrez_parser.EPostTest.test_invalid)
Test parsing XML returned by EPost with invalid id (overflow tag). ... ok
test_wrong (test_Entrez_parser.EPostTest.test_wrong)
Test parsing XML returned by EPost with incorrect arguments. ... ok
test_journals (test_Entrez_parser.ESearchTest.test_journals)
Test parsing XML returned by ESearch from the Journals database. ... ok
test_notfound (test_Entrez_parser.ESearchTest.test_notfound)
Test parsing XML returned by ESearch when no items were found. ... ok
test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide)
Test parsing XML returned by ESearch from the Nucleotide database. ... ok
test_pmc (test_Entrez_parser.ESearchTest.test_pmc)
Test parsing XML returned by ESearch from PubMed Central. ... ok
test_protein (test_Entrez_parser.ESearchTest.test_protein)
Test parsing XML returned by ESearch from the Protein database. ... ok
test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1)
Test parsing XML returned by ESearch from PubMed (first test). ... ok
test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2)
Test parsing XML returned by ESearch from PubMed (second test). ... ok
test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3)
Test parsing XML returned by ESearch from PubMed (third test). ... ok
test_espell (test_Entrez_parser.ESpellTest.test_espell)
Test parsing XML output returned by ESpell. ... ok
test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none)
Test parsing ESummary XML where an Integer is not defined. ... ok
test_journals (test_Entrez_parser.ESummaryTest.test_journals)
Test parsing XML returned by ESummary from the Journals database. ... ok
test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide)
Test parsing XML returned by ESummary from the Nucleotide database. ... ok
test_protein (test_Entrez_parser.ESummaryTest.test_protein)
Test parsing XML returned by ESummary from the Protein database. ... ok
test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed)
Test parsing XML returned by ESummary from PubMed. ... ok
test_structure (test_Entrez_parser.ESummaryTest.test_structure)
Test parsing XML returned by ESummary from the Structure database. ... ok
test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy)
Test parsing XML returned by ESummary from the Taxonomy database. ... ok
test_unists (test_Entrez_parser.ESummaryTest.test_unists)
Test parsing XML returned by ESummary from the UniSTS database. ... ok
test_wrong (test_Entrez_parser.ESummaryTest.test_wrong)
Test parsing XML returned by ESummary with incorrect arguments. ... ok
test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO)
Test parsing a BytesIO stream (bytes not string). ... ok
test_closed_file (test_Entrez_parser.GeneralTests.test_closed_file)
Test parsing closed file fails gracefully. ... ok
test_parse_bytes_stream (test_Entrez_parser.GeneralTests.test_parse_bytes_stream)
Test parsing a file opened in binary mode. ... ok
test_parse_text_file (test_Entrez_parser.GeneralTests.test_parse_text_file)
Test parsing a file opened in text mode. ... ok
test_pickle (test_Entrez_parser.GeneralTests.test_pickle)
Test if records created by the parser can be pickled. ... ok
test_read_bytes_stream (test_Entrez_parser.GeneralTests.test_read_bytes_stream)
Test reading a file opened in binary mode. ... ok
test_read_text_file (test_Entrez_parser.GeneralTests.test_read_text_file)
Test reading a file opened in text mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.410 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme.test_lactate)
Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok
test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok
test_parse_many (test_Enzyme.TestEnzyme.test_parse_many)
Check parse function with multiple records. ... ok
test_parse_one (test_Enzyme.TestEnzyme.test_parse_one)
Check parse function with one record. ... ok
test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok
test_proline (test_Enzyme.TestEnzyme.test_proline)
Parsing ENZYME record for proline racemase (5.1.1.4). ... ok
test_valine (test_Enzyme.TestEnzyme.test_valine)
Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_ExPASy.py
test_ExPASy ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.070 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_File.py
test_File ... ok
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: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GenBank.py
test_GenBank ... ok
test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction)
Test EMBL CDS interaction, parse CDS features on embl files. ... ok
test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction)
Test EMBL Record interaction on embl files. ... ok
test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction)
Test CDS interaction, parse CDS features on gb(k) files. ... ok
test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction)
Test GenBank records interaction on gbk files. ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning)
Feature line wrapping warning. ... ok
test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location)
Bad origin wrapping. ... ok
test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix)
Attempt to fix implied origin wrapping. ... ok
test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning)
Un-parsable feature location warning. ... ok
test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap)
Test the attempts to fix compound complex origin wrapping. ... ok
test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb)
Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok
test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl)
Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok
test_dblink (test_GenBank.GenBankTests.test_dblink)
Parse GenBank record with old DBLINK project entry. ... ok
test_dblink_two (test_GenBank.GenBankTests.test_dblink_two)
Parse GenBank record with old and new DBLINK project entries. ... ok
test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage)
Missing taxonomy lineage. ... ok
test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence)
Tests if extremely long sequences can be read. ... ok
test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap)
Test features that wrap an origin, and have fuzzy location. ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing)
Bad location wrapping. ... ok
test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct)
Check if user provided date is inserted correctly. ... ok
test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime)
Check if datetime objects are handled correctly. ... ok
test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default)
Check if default date is handled correctly. ... ok
test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid)
Check if invalid dates are treated as default. ... ok
test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list)
Check if date lists are handled correctly. ... ok
test_genbank_read (test_GenBank.GenBankTests.test_genbank_read)
GenBank.read(...) simple test. ... ok
test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid)
GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok
test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord)
GenBank.read(...) error on multiple record input. ... ok
test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end)
GenBank.read(...) error on malformed file. ... ok
test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate)
Test that features wrapped around origin give expected data. ... ok
test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error)
Parsing invalid product line. ... ok
test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly)
Test if chromosome topology is conserved. ... ok
test_long_names (test_GenBank.GenBankTests.test_long_names)
Various GenBank names which push the column based LOCUS line. ... ok
test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line)
Check that we can read and write files with longer locus lines. ... ok
test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing)
Test malformed structured comment gives warning. ... ok
test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing)
Multiline structured comment parsing. ... ok
test_negative_location (test_GenBank.GenBankTests.test_negative_location)
Negative feature locations. ... ok
test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read)
Check qualifier escaping is preserved when parsing. ... ok
test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write)
Check qualifier escaping is preserved when writing. ... ok
test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order)
Check the qualifier order is preserved. ... ok
test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing)
Structured comment parsing. ... ok
test_tsa (test_GenBank.GenBankTests.test_tsa)
Test TSA annotation parsing. ... ok
test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt)
Check IMGT ID line parsing. ... ok
test_topology_embl (test_GenBank.LineOneTests.test_topology_embl)
Check EMBL ID line parsing. ... ok
test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank)
Check GenBank LOCUS line parsing. ... ok
test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line)
Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok
test_mad_dots (test_GenBank.OutputTests.test_mad_dots)
Writing and reading back accesssion.version variants. ... ok
test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description)
Read in file using SeqRecord default description. ... ok
test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division)
Make sure we don't kill the TSA data_file_division for TSA files. ... ok
test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features)
Test the ability to clean up feature values. ... ok
test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus)
Test the ENSEMBL locus line. ... ok
test_write_format (test_GenBank.TestBasics.test_write_format)
Test writing to the difference formats. ... ok
test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok
test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok
test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok
test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok
test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok
test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok
test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok
test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok
test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok
test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok
test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok
test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok
test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok
test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok
test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok
test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok
test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok
test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok
test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok
test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok
test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin)
Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok
test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok
test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok
test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok
test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok
test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok
test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok
test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok
test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok
test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok
test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok
test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok
test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok
test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok
test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok
test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok
test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok
test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok
test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok
test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok
test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok
test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok
test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.247 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GenomeDiagram.py
test_GenomeDiagram ... ok
test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions)
Test color translations. ... ok
test_add_track (test_GenomeDiagram.DiagramTest.test_add_track)
Add track. ... ok
test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error)
Test adding unspecified track. ... ok
test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level)
Add track to occupied level. ... ok
test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks)
Delete track. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf)
Construct and draw PDF using object approach. ... ok
test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks)
Get track. ... ok
test_move_track (test_GenomeDiagram.DiagramTest.test_move_track)
Move a track. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram)
Construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_renumber (test_GenomeDiagram.DiagramTest.test_renumber)
Test renumbering tracks. ... ok
test_str (test_GenomeDiagram.DiagramTest.test_str)
Test diagram's info as string. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest.test_limits)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest.test_slicing)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest.test_label_default)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest.test_labels)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads)
Feature ARROW sigil heads within bounding box. ... ok
test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads)
Feature BIGARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads)
Feature OCTO sigil heads within bounding box. ... ok
test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow)
Feature arrow sigil heads within bounding box. ... ok
test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow)
Feature big-arrow sigil heads within bounding box. ... ok
test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy)
Feature arrow sigil heads within bounding box. ... ok
test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo)
Feature big-arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.259 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... skipping. Reportlab module rlPyCairo unavailable
cannot import desired renderPM backend rlPyCairo
Seek advice at the users list see
https://pairlist2.pair.net/mailman/listinfo/reportlab-users
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.743 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.156 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1)
Test creation of a simple ScatterPlot with one list. ... ok
test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7)
Test creation of a simple ScatterPlot with more lists. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.736 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_HMMCasino.py
test_HMMCasino ... ok
test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard)
Standard Training with known states. ... ok
test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without)
Baum-Welch training without known state sequences. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.259 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_HMMGeneral.py
test_HMMGeneral ... ok
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 0.038 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG.py
test_KEGG ... ok
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 0.075 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_graphics.py
test_KGML_graphics ... ok
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 4.259 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.040 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KGML_nographics.py
test_KGML_nographics ... ok
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 0.587 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_KeyWList.py
test_KeyWList ... ok
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 0.037 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_LogisticRegression.py
test_LogisticRegression ... ok
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 0.036 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_MafIO_index.py
test_MafIO_index ... ok
test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok
test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok
test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok
test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok
test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok
test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok
test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok
test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok
test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok
test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok
test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok
test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok
test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok
test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok
test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok
test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok
test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok
test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary)
Following issues 504 and 1086. ... ok
test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length)
Following issues 504 and 1086. ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok
test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3)
Following issue 1083. ... ok
test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1)
Checking that spliced sequences are correct. ... ok
test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2)
Checking that spliced sequences are correct. ... ok
test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok
test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok
test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok
test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok
test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok
test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok
test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1)
Correct retrieval of Cnksr3 in mouse. ... ok
test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok
test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.776 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.041 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_MarkovModel.py
test_MarkovModel ... ok
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 0.146 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Medline.py
test_Medline ... ok
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: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.065 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok
test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok
test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok
test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok
test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok
test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok
test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok
test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok
test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok
test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok
test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.460 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBI_BLAST_tools.py
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_NCBI_qblast.py
test_NCBI_qblast ... ok
test_blastp_nr_actin (test_NCBI_qblast.TestQblast.test_blastp_nr_actin) ... ok
test_discomegablast (test_NCBI_qblast.TestQblast.test_discomegablast) ... ok
test_error_conditions (test_NCBI_qblast.TestQblast.test_error_conditions)
Test if exceptions were properly handled. ... ok
test_orchid_est (test_NCBI_qblast.TestQblast.test_orchid_est) ... ok
test_parse_qblast_ref_page (test_NCBI_qblast.TestQblast.test_parse_qblast_ref_page) ... ok
test_pcr_primers (test_NCBI_qblast.TestQblast.test_pcr_primers) ... ok
test_short_query (test_NCBI_qblast.TestQblast.test_short_query)
Test SHORT_QUERY_ADJUST parameter. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_NMR.py
test_NMR ... ok
test_noetools (test_NMR.NmrTests.test_noetools)
Self test for NMR.NOEtools. ... ok
test_xpktools (test_NMR.NmrTests.test_xpktools)
Self test for NMR.xpktools. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_NaiveBayes.py
test_NaiveBayes ... ok
test_car_data (test_NaiveBayes.CarTest.test_car_data)
Simple example using car data. ... ok
test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok
test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok
test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok
test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok
test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok
test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok
test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Nexus.py
test_Nexus ... ok
test_NexusComments (test_Nexus.NexusTest1.test_NexusComments)
Test the ability to parse nexus comments at internal and leaf nodes. ... ok
test_NexusTest1 (test_Nexus.NexusTest1.test_NexusTest1)
Test Nexus module. ... ok
test_TreeTest1 (test_Nexus.NexusTest1.test_TreeTest1)
Test Tree module. ... ok
test_TreeTest2 (test_Nexus.NexusTest1.test_TreeTest2)
Handle text labels on internal nodes. ... ok
test_WriteToFileName (test_Nexus.NexusTest1.test_WriteToFileName)
Test writing to a given filename. ... ok
test_large_newick (test_Nexus.NexusTest1.test_large_newick) ... ok
test_merge_with_support (test_Nexus.NexusTest1.test_merge_with_support)
Test merge_with_support and consensus method. ... ok
test_to_string (test_Nexus.NexusTest1.test_to_string)
Test to_string method. ... ok
test_write_alignment (test_Nexus.NexusTest1.test_write_alignment) ... ok
test_write_alignment_msa (test_Nexus.NexusTest1.test_write_alignment_msa) ... ok
test_write_with_dups (test_Nexus.NexusTest1.test_write_with_dups) ... ok
test_data_and_codons_block (test_Nexus.OldSelfTests.test_data_and_codons_block)
Simple sequence data file with DATA and CODONS block. ... ok
test_data_sets_trees_unknown_block (test_Nexus.OldSelfTests.test_data_sets_trees_unknown_block)
Sequence data file with DATA, SETS, TREES and an unknown block. ... ok
test_taxa_and_characters_block (test_Nexus.OldSelfTests.test_taxa_and_characters_block)
Taxa and characters multi-state block. ... ok
test_taxa_and_characters_with_many_codings_one_without_state (test_Nexus.OldSelfTests.test_taxa_and_characters_with_many_codings_one_without_state)
Taxa and chr blocks, over 9 codings, 1 character without states. ... ok
test_taxa_and_characters_with_many_codings_two_without_state (test_Nexus.OldSelfTests.test_taxa_and_characters_with_many_codings_two_without_state)
Taxa and chr blocks, over 9 codings, 2 character without states. ... ok
test_trees_and_taxa_block (test_Nexus.OldSelfTests.test_trees_and_taxa_block)
Basic tree file with TREES and TAXA block. ... ok
test_empty_file_read (test_Nexus.TestSelf.test_empty_file_read) ... ok
test_empty_file_read_msa (test_Nexus.TestSelf.test_empty_file_read_msa) ... ok
test_multiple_output (test_Nexus.TestSelf.test_multiple_output) ... ok
test_multiple_output_msa (test_Nexus.TestSelf.test_multiple_output_msa) ... ok
test_repeated_names_no_taxa (test_Nexus.TestSelf.test_repeated_names_no_taxa) ... ok
test_repeated_names_no_taxa_msa (test_Nexus.TestSelf.test_repeated_names_no_taxa_msa) ... ok
test_repeated_names_with_taxa (test_Nexus.TestSelf.test_repeated_names_with_taxa) ... ok
test_repeated_names_with_taxa_msa (test_Nexus.TestSelf.test_repeated_names_with_taxa_msa) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.370 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_baseml.py
test_PAML_baseml ... ok
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 0.108 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_codeml.py
test_PAML_codeml ... ok
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 0.644 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PAML_yn00.py
test_PAML_yn00 ... ok
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 0.065 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDBList.py
test_PDBList ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.048 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_CEAligner.py
test_PDB_CEAligner ... ok
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 2.015 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_DSSP.py
test_PDB_DSSP ... ok
test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA)
Tests the usage of different ASA tables. ... ok
test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file)
Test parsing of pregenerated DSSP. ... ok
test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj)
All elements correctly added to xtra attribute of input model object. ... ok
test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file)
Test parsing of pregenerated DSSP missing header information. ... ok
setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.'
----------------------------------------------------------------------
Ran 1 test in 0.145 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Dice.py
test_PDB_Dice ... ok
test_dice (test_PDB_Dice.DiceTests.test_dice)
Self test for PDB.Dice module. ... ok
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.064 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Disordered.py
test_PDB_Disordered ... ok
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 0.071 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Exposure.py
test_PDB_Exposure ... ok
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 0.261 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_FragmentMapper.py
test_PDB_FragmentMapper ... ok
test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper)
Self test for FragmentMapper module. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
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
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 1.330 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIF2Dict.py
test_PDB_MMCIF2Dict ... ok
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 0.075 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIFIO.py
test_PDB_MMCIFIO ... ok
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 0.203 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_MMCIFParser.py
test_PDB_MMCIFParser ... ok
test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion)
Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok
test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering)
Convert mmCIF to PDB and renumber atom serials. ... ok
test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering)
Convert mmCIF to PDB and preserve original serial numbering. ... ok
testModels (test_PDB_MMCIFParser.ParseReal.testModels)
Test file with multiple models. ... ok
test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle)
Test if the parser can handle file handle as well as filename. ... ok
test_header (test_PDB_MMCIFParser.ParseReal.test_header)
Test if the parser populates header data. ... ok
test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions)
Test file with residue insertion codes. ... ok
test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers)
Extract polypeptides from 1A80. ... ok
test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast)
Test if FastMMCIFParser can parse point mutations correctly. ... ok
test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main)
Test if MMCIFParser parse point mutations correctly. ... ok
test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.055 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_NACCESS.py
test_PDB_NACCESS ... ok
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 0.049 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PDBIO.py
test_PDB_PDBIO ... ok
test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering)
Preserve model serial numbers during I/O. ... ok
test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy)
Write PDB file with missing occupancy. ... ok
test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits)
Test raising error when structure cannot meet PDB format limits. ... ok
test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select)
Write a selection of the structure using a Select subclass. ... ok
test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering)
Test writing PDB and do not preserve atom numbering. ... ok
test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue)
Write a chainless residue using PDBIO. ... ok
test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering)
Test writing PDB and preserve atom numbering. ... ok
test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue)
Write a single residue using PDBIO. ... ok
test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain)
Write a single residue (chain id == X) using PDBIO. ... ok
test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain)
Write a single orphan residue using PDBIO. ... ok
test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure)
Write a full structure using PDBIO. ... ok
test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated)
Test parsing of truncated lines. ... ok
test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element)
PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok
test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element)
Write a structure with atomic element X with PDBIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.184 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PDBParser.py
test_PDB_PDBParser ... ok
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 0.083 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_PSEA.py
test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path
----------------------------------------------------------------------
Ran 1 test in 0.048 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Polypeptide.py
test_PDB_Polypeptide ... ok
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 0.072 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_QCPSuperimposer.py
test_PDB_QCPSuperimposer ... ok
test_compare_to_svd (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_compare_to_svd)
Compare results of QCP to SVD. ... ok
test_get_init_rms (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_get_init_rms)
Test initial RMS calculation. ... ok
test_get_transformed (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_get_transformed)
Test transformation of coordinates after QCP. ... ok
test_on_pdb (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_on_pdb)
Align a PDB to itself. ... ok
test_run (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_run)
Test QCP on dummy data. ... ok
test_set (test_PDB_QCPSuperimposer.QCPSuperimposerTest.test_set)
Test setting of initial parameters. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.069 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_ResidueDepth.py
test_PDB_ResidueDepth ... ok
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 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SASA.py
test_PDB_SASA ... ok
test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii)
Run Shrake-Rupley with custom radii. ... ok
test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm)
Run Shrake-Rupley with default parameters. ... ok
test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level)
Raise exception on input Atom entity. ... ok
test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type)
Raise exception on unsupported entity type. ... ok
test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1)
Raise exception on invalid level parameter: X. ... ok
test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity)
Raise exception on invalid level parameter: S > C. ... ok
test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points)
Raise exception on bad n_points parameter. ... ok
test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius)
Raise exception on bad probe_radius parameter. ... ok
test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution)
Run Shrake-Rupley with 960 points per sphere. ... ok
test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C)
Run Shrake-Rupley with level C. ... ok
test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R)
Run Shrake-Rupley with level R. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.782 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_SMCRA.py
test_PDB_SMCRA ... ok
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 0.285 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Selection.py
test_PDB_Selection ... ok
test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok
test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level)
Unfold from lowest level to all levels. ... ok
test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level)
Unfold from chain level to all levels. ... ok
test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level)
Unfold from model to all levels. ... ok
test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level)
Unfold from chain level to all levels. ... ok
test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level)
Unfold from highest level to all levels. ... ok
test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_StructureAlignment.py
test_PDB_StructureAlignment ... ok
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 0.201 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_Superimposer.py
test_PDB_Superimposer ... ok
test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer)
Test on module that superimpose two protein structures. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_internal_coords.py
test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)

----------------------------------------------------------------------
Ran 1 test in 0.072 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_parse_pdb_header.py
test_PDB_parse_pdb_header ... ok
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 0.081 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PDB_vectors.py
test_PDB_vectors ... ok
test_Vector (test_PDB_vectors.VectorTests.test_Vector)
Test Vector object. ... ok
test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles)
Test Vector angles. ... ok
test_coord_space (test_PDB_vectors.VectorTests.test_coord_space)
Confirm can generate coordinate space transform for 3 points. ... ok
test_division (test_PDB_vectors.VectorTests.test_division)
Confirm division works. ... ok
test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates)
Test spherical coordinates. ... ok
test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0)
Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok
test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180)
Test 180 deg rotation. ... ok
test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90)
Test 90 deg rotation. ... ok
test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space)
Confirm multi_coord_space computes forward, reverse transforms. ... ok
test_normalization (test_PDB_vectors.VectorTests.test_normalization)
Test Vector normalization. ... ok
test_refmat (test_PDB_vectors.VectorTests.test_refmat)
Test refmat can mirror one matrix to another. ... ok
test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0)
Test rotmat when the rotation is 0 deg (singularity). ... ok
test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180)
Test rotmat when the rotation is 180 deg (singularity). ... ok
test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90)
Test regular 90 deg rotation. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.053 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PQR.py
test_PQR ... ok
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 0.078 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Pathway.py
test_Pathway ... ok
testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok
testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok
test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok
test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok
test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok
test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok
test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok
test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.069 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo.py
test_Phylo ... ok
test_convert (test_Phylo.IOTests.test_convert)
Convert a tree between all supported formats. ... ok
test_convert_phyloxml_binary (test_Phylo.IOTests.test_convert_phyloxml_binary)
Try writing phyloxml to a binary handle; fail on Py3. ... ok
test_convert_phyloxml_filename (test_Phylo.IOTests.test_convert_phyloxml_filename)
Write phyloxml to a given filename. ... ok
test_convert_phyloxml_text (test_Phylo.IOTests.test_convert_phyloxml_text)
Write phyloxml to a text handle. ... ok
test_format_branch_length (test_Phylo.IOTests.test_format_branch_length)
Custom format string for Newick branch length serialization. ... ok
test_int_labels (test_Phylo.IOTests.test_int_labels)
Read newick formatted tree with numeric labels. ... ok
test_newick_read_multiple (test_Phylo.IOTests.test_newick_read_multiple)
Parse a Nexus file with multiple trees. ... ok
test_newick_read_scinot (test_Phylo.IOTests.test_newick_read_scinot)
Parse Newick branch lengths in scientific notation. ... ok
test_newick_read_single1 (test_Phylo.IOTests.test_newick_read_single1)
Read first Newick file with one tree. ... ok
test_newick_read_single2 (test_Phylo.IOTests.test_newick_read_single2)
Read second Newick file with one tree. ... ok
test_newick_read_single3 (test_Phylo.IOTests.test_newick_read_single3)
Read Nexus file with one tree. ... ok
test_newick_write (test_Phylo.IOTests.test_newick_write)
Parse a Nexus file with multiple trees. ... ok
test_phylo_read_extra (test_Phylo.IOTests.test_phylo_read_extra)
Additional tests to check correct parsing. ... ok
test_unicode_exception (test_Phylo.IOTests.test_unicode_exception)
Read a Newick file with a unicode byte order mark (BOM). ... ok
test_collapse (test_Phylo.MixinTests.test_collapse)
TreeMixin: collapse() method. ... ok
test_collapse_all (test_Phylo.MixinTests.test_collapse_all)
TreeMixin: collapse_all() method. ... ok
test_common_ancestor (test_Phylo.MixinTests.test_common_ancestor)
TreeMixin: common_ancestor() method. ... ok
test_depths (test_Phylo.MixinTests.test_depths)
TreeMixin: depths() method. ... ok
test_distance (test_Phylo.MixinTests.test_distance)
TreeMixin: distance() method. ... ok
test_find_clades (test_Phylo.MixinTests.test_find_clades)
TreeMixin: find_clades() method. ... ok
test_find_elements (test_Phylo.MixinTests.test_find_elements)
TreeMixin: find_elements() method. ... ok
test_find_terminal (test_Phylo.MixinTests.test_find_terminal)
TreeMixin: find_elements() with terminal argument. ... ok
test_get_path (test_Phylo.MixinTests.test_get_path)
TreeMixin: get_path() method. ... ok
test_is_bifurcating (test_Phylo.MixinTests.test_is_bifurcating)
TreeMixin: is_bifurcating() method. ... ok
test_is_monophyletic (test_Phylo.MixinTests.test_is_monophyletic)
TreeMixin: is_monophyletic() method. ... ok
test_ladderize (test_Phylo.MixinTests.test_ladderize)
TreeMixin: ladderize() method. ... ok
test_prune (test_Phylo.MixinTests.test_prune)
TreeMixin: prune() method. ... ok
test_split (test_Phylo.MixinTests.test_split)
TreeMixin: split() method. ... ok
test_total_branch_length (test_Phylo.MixinTests.test_total_branch_length)
TreeMixin: total_branch_length() method. ... ok
test_trace (test_Phylo.MixinTests.test_trace)
TreeMixin: trace() method. ... ok
test_randomized (test_Phylo.TreeTests.test_randomized)
Tree.randomized: generate a new randomized tree. ... ok
test_root_at_midpoint (test_Phylo.TreeTests.test_root_at_midpoint)
Tree.root_at_midpoint: reroot at the tree's midpoint. ... ok
test_root_with_outgroup (test_Phylo.TreeTests.test_root_with_outgroup)
Tree.root_with_outgroup: reroot at a given clade. ... ok
test_str (test_Phylo.TreeTests.test_str)
Tree.__str__: pretty-print to a string. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.457 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PhyloXML.py
test_PhyloXML ... ok
test_alignment (test_PhyloXML.MethodTests.test_alignment) ... ok
test_clade_getitem (test_PhyloXML.MethodTests.test_clade_getitem)
Clade.__getitem__: get sub-clades by extended indexing. ... ok
test_clade_to_phylogeny (test_PhyloXML.MethodTests.test_clade_to_phylogeny)
Convert a Clade object to a new Phylogeny. ... ok
test_color_hex (test_PhyloXML.MethodTests.test_color_hex)
BranchColor: to_hex() method. ... ok
test_events (test_PhyloXML.MethodTests.test_events)
Events: Mapping-type behavior. ... ok
test_phylogeny_to_phyloxml (test_PhyloXML.MethodTests.test_phylogeny_to_phyloxml)
Convert a Phylogeny object to a new Phyloxml. ... ok
test_phyloxml_getitem (test_PhyloXML.MethodTests.test_phyloxml_getitem)
Phyloxml.__getitem__: get phylogenies by name or index. ... ok
test_sequence_conversion (test_PhyloXML.MethodTests.test_sequence_conversion) ... ok
test_singlular (test_PhyloXML.MethodTests.test_singlular)
Clade, Phylogeny: Singular properties for plural attributes. ... ok
test_to_alignment (test_PhyloXML.MethodTests.test_to_alignment) ... ok
test_parse_apaf (test_PhyloXML.ParseTests.test_parse_apaf)
Parse the phylogenies in apaf.xml. ... ok
test_parse_bcl2 (test_PhyloXML.ParseTests.test_parse_bcl2)
Parse the phylogenies in bcl_2.xml. ... ok
test_parse_dollo (test_PhyloXML.ParseTests.test_parse_dollo)
Parse the phylogenies in o_tol_332_d_dollo.xml. ... ok
test_parse_made (test_PhyloXML.ParseTests.test_parse_made)
Parse the phylogenies in made_up.xml. ... ok
test_parse_phylo (test_PhyloXML.ParseTests.test_parse_phylo)
Parse the phylogenies in phyloxml_examples.xml. ... ok
test_read_apaf (test_PhyloXML.ParseTests.test_read_apaf)
Read apaf.xml to produce a phyloXML object. ... ok
test_read_bcl2 (test_PhyloXML.ParseTests.test_read_bcl2)
Read bcl_2.xml to produce a phyloXML object. ... ok
test_read_dollo (test_PhyloXML.ParseTests.test_read_dollo)
Read o_tol_332_d_dollo.xml to produce a phyloXML object. ... ok
test_read_made (test_PhyloXML.ParseTests.test_read_made)
Read made_up.xml to produce a phyloXML object. ... ok
test_read_phylo (test_PhyloXML.ParseTests.test_read_phylo)
Read phyloxml_examples.xml to produce a phyloXML object. ... ok
test_shape_apaf (test_PhyloXML.ParseTests.test_shape_apaf)
Check the branching structure of apaf.xml. ... ok
test_shape_bcl2 (test_PhyloXML.ParseTests.test_shape_bcl2)
Check the branching structure of bcl_2.xml. ... ok
test_shape_dollo (test_PhyloXML.ParseTests.test_shape_dollo)
Check the branching structure of o_tol_332_d_dollo.xml. ... ok
test_shape_phylo (test_PhyloXML.ParseTests.test_shape_phylo)
Check the branching structure of phyloxml_examples.xml. ... ok
test_Annotation (test_PhyloXML.TreeTests.test_Annotation)
Instantiation of Annotation objects. ... ok
test_BinaryCharacters (test_PhyloXML.TreeTests.test_BinaryCharacters)
Instantiation of BinaryCharacters objects. ... ok
test_Clade (test_PhyloXML.TreeTests.test_Clade)
Instantiation of Clade objects. ... ok
test_CladeRelation (test_PhyloXML.TreeTests.test_CladeRelation)
Instantiation of CladeRelation objects. ... ok
test_Confidence (test_PhyloXML.TreeTests.test_Confidence)
Instantiation of Confidence objects. ... ok
test_Date (test_PhyloXML.TreeTests.test_Date)
Instantiation of Date objects. ... ok
test_Distribution (test_PhyloXML.TreeTests.test_Distribution)
Instantiation of Distribution objects. ... ok
test_DomainArchitecture (test_PhyloXML.TreeTests.test_DomainArchitecture)
Instantiation of DomainArchitecture objects. ... ok
test_Events (test_PhyloXML.TreeTests.test_Events)
Instantiation of Events objects. ... ok
test_Other (test_PhyloXML.TreeTests.test_Other)
Instantiation of Other objects. ... ok
test_Phylogeny (test_PhyloXML.TreeTests.test_Phylogeny)
Instantiation of Phylogeny objects. ... ok
test_Phyloxml (test_PhyloXML.TreeTests.test_Phyloxml)
Instantiation of Phyloxml objects. ... ok
test_Polygon (test_PhyloXML.TreeTests.test_Polygon)
Instantiation of Polygon objects. ... ok
test_Property (test_PhyloXML.TreeTests.test_Property)
Instantiation of Property objects. ... ok
test_Reference (test_PhyloXML.TreeTests.test_Reference)
Instantiation of Reference objects. ... ok
test_Sequence (test_PhyloXML.TreeTests.test_Sequence)
Instantiation of Sequence objects. ... ok
test_SequenceRelation (test_PhyloXML.TreeTests.test_SequenceRelation)
Instantiation of SequenceRelation objects. ... ok
test_Taxonomy (test_PhyloXML.TreeTests.test_Taxonomy)
Instantiation of Taxonomy objects. ... ok
test_Uri (test_PhyloXML.TreeTests.test_Uri)
Instantiation of Uri objects. ... ok
test_apaf (test_PhyloXML.WriterTests.test_apaf)
Round-trip parsing and serialization of apaf.xml. ... ok
test_bcl2 (test_PhyloXML.WriterTests.test_bcl2)
Round-trip parsing and serialization of bcl_2.xml. ... ok
test_dollo (test_PhyloXML.WriterTests.test_dollo)
Round-trip parsing and serialization of o_tol_332_d_dollo.xml. ... ok
test_made (test_PhyloXML.WriterTests.test_made)
Round-trip parsing and serialization of made_up.xml. ... ok
test_phylo (test_PhyloXML.WriterTests.test_phylo)
Round-trip parsing and serialization of phyloxml_examples.xml. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.347 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_CDAO.py
test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format.
----------------------------------------------------------------------
Ran 1 test in 0.055 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_NeXML.py
test_Phylo_NeXML ... ok
test_parse (test_Phylo_NeXML.ParseTests.test_parse)
Extract and count phylogenetic trees using Phylo.parse. ... ok
test_write (test_Phylo_NeXML.WriterTests.test_write)
Test for serialization of objects to NeXML format. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.136 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_matplotlib.py
test_Phylo_matplotlib ... skipping. Install matplotlib if you want to use Bio.Phylo._utils.
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Phylo_networkx.py
test_Phylo_networkx ... skipping. Install networkx if you wish to use it with Bio.Phylo
----------------------------------------------------------------------
Ran 1 test in 0.054 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.010 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
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 0.017 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.065 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.063 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity)
Calculate protein aromaticity. ... ok
test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH)
Test charge_at_pH function. ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids)
Calculate amino acid counts. ... ok
test_flexibility (test_ProtParam.ProtParamTest.test_flexibility)
Calculate protein flexibility. ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent)
Calculate amino acid percentages. ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight)
Calculate protein molecular weight. ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight)
Calculate monoisotopic molecular weight. ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical)
Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok
test_gravy (test_ProtParam.ProtParamTest.test_gravy)
Calculate gravy. Tests all pre-defined scales. ... ok
test_instability_index (test_ProtParam.ProtParamTest.test_instability_index)
Calculate protein instability index. ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point)
Calculate the isoelectric point. ... ok
test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient)
Molar extinction coefficient. ... ok
test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale)
Calculate the Kite Doolittle scale. ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction)
Calculate secondary structure fractions. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.050 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_RCSBFormats.py
test_RCSBFormats ... ok
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 0.409 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Restriction.py
test_Restriction ... ok
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 0.141 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
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 0.062 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
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 0.058 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Des.py
test_SCOP_Des ... ok
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
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.057 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
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 0.058 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests.testError)
Test if a corrupt record raises the appropriate exception. ... ok
testParse (test_SCOP_Hie.HieTests.testParse)
Test if all records in a HIE file are being read. ... ok
testStr (test_SCOP_Hie.HieTests.testStr)
Test if we can convert each record to a string correctly. ... ok
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.056 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
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 0.060 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
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 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok
testParse (test_SCOP_Scop.ScopTests.testParse) ... ok
testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents)
Test getDescendents method. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok
test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab.py
test_SearchIO_blast_tab ... ok
test_tab_2226_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_001)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_001). ... ok
test_tab_2226_tblastn_002 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_002)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_002). ... ok
test_tab_2226_tblastn_003 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_003)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_003). ... ok
test_tab_2226_tblastn_004 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_004)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_004). ... ok
test_tab_2226_tblastn_005 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_005)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005). ... ok
test_tab_2226_tblastn_005_comments_false (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_005_comments_false)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005). ... ok
test_tab_2226_tblastn_006 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_006)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_006). ... ok
test_tab_2226_tblastn_007 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_007)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_007). ... ok
test_tab_2226_tblastn_008 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_008)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_008). ... ok
test_tab_2226_tblastn_009 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_009)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_009). ... ok
test_tab_2226_tblastn_010 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_010)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_010). ... ok
test_tab_2226_tblastn_011 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_011)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_011). ... ok
test_tab_2226_tblastn_012 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_012)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_012). ... ok
test_tab_2226_tblastn_013 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2226_tblastn_013)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_013). ... ok
test_tab_2228_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2228_tblastn_001)
Test parsing TBLASTN 2.2.28+ tabular output (tab_2228_tblastn_001). ... ok
test_tab_2228_tblastx_001 (test_SearchIO_blast_tab.BlastTabCases.test_tab_2228_tblastx_001)
Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.084 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_tab_index.py
test_SearchIO_blast_tab_index ... ok
test_blasttab_2226_tblastn_001 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_001)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries. ... ok
test_blasttab_2226_tblastn_002 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_002)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits. ... ok
test_blasttab_2226_tblastn_004 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_004)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits. ... ok
test_blasttab_2226_tblastn_005 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_005)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries, commented. ... ok
test_blasttab_2226_tblastn_006 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_006)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits, commented. ... ok
test_blasttab_2226_tblastn_009 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_009)
Test blast-tab indexing, BLAST 2.2.26+, custom columns. ... ok
test_blasttab_2226_tblastn_010 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_010)
Test blast-tab indexing, BLAST 2.2.26+, custom columns, commented. ... ok
test_blasttab_2226_tblastn_011 (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_2226_tblastn_011)
Test blast-tab indexing, BLAST 2.2.26+, all columns, commented. ... ok
test_blasttab_comment_sing (test_SearchIO_blast_tab_index.BlastTabIndexCases.test_blasttab_comment_sing)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits, commented. ... ok
test_blasttab_2226_multiple_first (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_first)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first (tab_2226_tblastn_001.txt). ... ok
test_blasttab_2226_multiple_first_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_first_commented)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first, commented (tab_2226_tblastn_005.txt). ... ok
test_blasttab_2226_multiple_last (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_last)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last (tab_2226_tblastn_001.txt). ... ok
test_blasttab_2226_multiple_last_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_last_commented)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last, commented (tab_2226_tblastn_005.txt). ... ok
test_blasttab_2226_multiple_middle_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_multiple_middle_commented)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, middle, commented (tab_2226_tblastn_005.txt). ... ok
test_blasttab_2226_single (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_single)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
test_blasttab_2226_single_commented (test_SearchIO_blast_tab_index.BlastTabRawCases.test_blasttab_2226_single_commented)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query, commented (tab_2226_tblastn_008.txt). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.080 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml.py
test_SearchIO_blast_xml ... ok
test_xml_2226_blastn_006 (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006) ... ok
test_xml_2226_blastn_006_use_raw_hit_ids (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006_use_raw_hit_ids) ... ok
test_xml_2226_blastn_006_use_raw_query_ids (test_SearchIO_blast_xml.BlastXmlSpecialCases.test_xml_2226_blastn_006_use_raw_query_ids) ... ok
test_xml_2212L_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2212L_blastn_001) ... ok
test_xml_2226_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_001) ... ok
test_xml_2226_blastn_002 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_002) ... ok
test_xml_2226_blastn_003 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_003) ... ok
test_xml_2226_blastn_004 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_004) ... ok
test_xml_2226_blastn_005 (test_SearchIO_blast_xml.BlastnXmlCases.test_xml_2226_blastn_005) ... ok
test_xml_2212L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2212L_blastp_001) ... ok
test_xml_2218L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218L_blastp_001) ... ok
test_xml_2218_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218_blastp_001) ... ok
test_xml_2218_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2218_blastp_002) ... ok
test_xml_2222_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2222_blastp_001) ... ok
test_xml_2226_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_001) ... ok
test_xml_2226_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_002) ... ok
test_xml_2226_blastp_003 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_003) ... ok
test_xml_2226_blastp_004 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_004) ... ok
test_xml_2226_blastp_005 (test_SearchIO_blast_xml.BlastpXmlCases.test_xml_2226_blastp_005) ... ok
test_xml_2212L_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2212L_blastx_001) ... ok
test_xml_2222_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2222_blastx_001) ... ok
test_xml_2226_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_001) ... ok
test_xml_2226_blastx_002 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_002) ... ok
test_xml_2226_blastx_003 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_003) ... ok
test_xml_2226_blastx_004 (test_SearchIO_blast_xml.BlastxXmlCases.test_xml_2226_blastx_004) ... ok
test_xml_2212L_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2212L_tblastn_001) ... ok
test_xml_2226_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_001) ... ok
test_xml_2226_tblastn_002 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_002) ... ok
test_xml_2226_tblastn_003 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_003) ... ok
test_xml_2226_tblastn_004 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_004) ... ok
test_xml_2226_tblastn_005 (test_SearchIO_blast_xml.TblastnXmlCases.test_xml_2226_tblastn_005) ... ok
test_xml_2212L_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2212L_tblastx_001) ... ok
test_xml_2226_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_001) ... ok
test_xml_2226_tblastx_002 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_002) ... ok
test_xml_2226_tblastx_003 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_003) ... ok
test_xml_2226_tblastx_004 (test_SearchIO_blast_xml.TblastxXmlCases.test_xml_2226_tblastx_004) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.172 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blast_xml_index.py
test_SearchIO_blast_xml_index ... ok
test_blastxml_2212L_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2212L_blastp_001)
Test blast-xml indexing, BLAST 2.2.12. ... ok
test_blastxml_2218_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2218_blastp_001)
Test blast-xml indexing, BLAST 2.2.18+. ... ok
test_blastxml_2222_blastx_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2222_blastx_001)
Test blast-xml indexing, BLAST 2.2.22+. ... ok
test_blastxml_2226_tblastn_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_001)
Test blast-xml indexing, BLAST 2.2.26+, multiple queries. ... ok
test_blastxml_2226_tblastn_002 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_002)
Test blast-xml indexing, BlAST 2.2.26+, single query, no hits. ... ok
test_blastxml_2226_tblastn_004 (test_SearchIO_blast_xml_index.BlastXmlIndexCases.test_blastxml_2226_tblastn_004)
Test blast-xml indexing, BLAST 2.2.26+, single query, multiple hits. ... ok
test_blastxml_2226_multiple_first (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_first)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, first (xml_2226_blastp_001.xml). ... ok
test_blastxml_2226_multiple_last (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_last)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, last (xml_2226_blastp_001.xml). ... ok
test_blastxml_2226_multiple_middle (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_multiple_middle)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, middle (xml_2226_blastp_001.xml). ... ok
test_blastxml_2226_single (test_SearchIO_blast_xml_index.BlastXmlRawCases.test_blastxml_2226_single)
Test blast-xml raw string retrieval, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
----------------------------------------------------------------------
Ran 1 test in 1.177 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
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
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.072 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001)
Test blat-psl indexing, multiple queries. ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002)
Test blat-psl indexing, single query, no hits. ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003)
Test blat-psl indexing, single query, single hit. ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004)
Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005)
Test blat-psl indexing, multiple queries, no header. ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006)
Test blat-pslx indexing, multiple queries. ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007)
Test blat-pslx indexing, single query, no hits. ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008)
Test blat-pslx indexing, single query, single hit. ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009)
Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010)
Test blat-pslx indexing, multiple queries, no header. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.094 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
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 0.105 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome)
Test exonerate-text indexing, single. ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple)
Test exonerate-text indexing, single. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.061 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
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 0.051 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002)
Test parsing fasta34 output (output002.m10). ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003)
Test parsing fasta34 output (output003.m10). ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001)
Test parsing fasta35 output (output001.m10). ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004)
Test parsing fasta35 output (output004.m10). ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005)
Test parsing ssearch35 output (output005.m10). ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006)
Test parsing fasta35 output (output006.m10). ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007)
Test parsing fasta36 output (output007.m10). ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008)
Test parsing tfastx36 output (output008.m10). ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009)
Test parsing fasta36 output (output009.m10). ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010)
Test parsing fasta36 output (output010.m10). ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011)
Test parsing fasta36 output (output011.m10). ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012)
Test parsing fasta36 output (output012.m10). ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013)
Test parsing fasta36 output (output013.m10). ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014)
Test parsing fasta36 output (output014.m10). ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015)
Test parsing fasta36 output (output015.m10). ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016)
Test parsing fasta36 output (output016.m10). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_fasta_m10_index.py
test_SearchIO_fasta_m10_index ... ok
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 0.089 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hhsuite2_text.py
test_SearchIO_hhsuite2_text ... ok
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 0.090 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text ... ok
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 0.119 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
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 0.094 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001)
Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002)
Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004)
Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001)
Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.051 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_domtab_index.py
test_SearchIO_hmmer3_domtab_index ... ok
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 0.060 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab.py
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.047 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_tab_index ... ok
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 0.053 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001)
Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002)
Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003)
Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004)
Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005)
Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok
test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok
test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002)
Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001)
Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002)
Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003)
Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004)
Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005)
Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006)
Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007)
Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008)
Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009)
Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010)
Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok
test_30_hmmscan_011 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_011)
Parsing hmmscan 3.0 (text_30_hmmscan_011). ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001)
Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001)
Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.128 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
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 0.079 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_interproscan_xml.py
test_SearchIO_interproscan_xml ... ok
test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.043 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_model.py
test_SearchIO_model ... ok
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 0.077 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SearchIO_write.py
test_SearchIO_write ... ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok
test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query)
Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok
test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query)
Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.202 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqFeature.py
test_SeqFeature ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/Bio/SeqFeature.py:1040: BiopythonParserWarning: Attempting to fix invalid location '3..2' as it looks like incorrect origin wrapping. Please fix input file, this could have unintended behavior.
  warnings.warn(
ok
test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_origin_spanning_location (test_SeqFeature.TestExtract.test_origin_spanning_location)
Test location spanning origin. ... ok
test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record)
Test compound location with reference to another record. ... ok
test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence)
Test compound location with reference to another sequence. ... ok
test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record)
Test location with reference to another record. ... ok
test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence)
Test location with reference to another sequence. ... ok
test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy)
Test fuzzy representations. ... ok
test_pickle (test_SeqFeature.TestPositions.test_pickle)
Test pickle behaviour of position instances. ... ok
test_eq_identical (test_SeqFeature.TestReference.test_eq_identical)
Test two identical references eq() to True. ... ok
test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok
test_location_aliases (test_SeqFeature.TestSeqFeature.test_location_aliases) ... ok
test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds)
Test that a CDS feature is subject to respective checks. ... ok
test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical)
Test two identical locations are equal. ... ok
test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical)
Test two different locations are not equal. ... ok
test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets)
Test adding and subtracting integer offsets. ... ok
test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO.py
test_SeqIO ... ok
test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok
test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok
test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok
test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok
test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok
test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok
test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok
test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok
test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok
test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok
test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok
test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok
test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok
test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok
test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type)
Convert Clustal to NEXUS with molecule type. ... ok
test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type)
Convert Clustal to NEXUS without molecule type. ... ok
test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok
test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok
test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok
test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok
test_embl13 (test_SeqIO.TestSeqIO.test_embl13)
Test parsing embl file with wrapped locations and unspecified type. ... ok
test_embl14 (test_SeqIO.TestSeqIO.test_embl14)
Test parsing file with features over-indented for EMBL. ... ok
test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok
test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok
test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok
test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok
test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok
test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok
test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok
test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok
test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok
test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok
test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok
test_empty_file (test_SeqIO.TestSeqIO.test_empty_file)
Check parsers can cope with an empty file. ... ok
test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok
test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok
test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok
test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok
test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok
test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok
test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok
test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok
test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok
test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok
test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok
test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok
test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok
test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok
test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok
test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok
test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok
test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok
test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok
test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok
test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok
test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok
test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok
test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok
test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok
test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type)
Convert FASTA to SeqXML with molecule type. ... ok
test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type)
Convert FASTA to SeqXML without molecule type. ... ok
test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok
test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok
test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok
test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok
test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok
test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok
test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok
test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok
test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok
test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok
test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok
test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok
test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok
test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok
test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok
test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16)
Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok
test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok
test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok
test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok
test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok
test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20)
Test parsing GenPept file with nasty bond locations. ... ok
test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok
test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22)
Test that genbank format write doesn't destroy db_source in annotations. ... ok
test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23)
Test that peptide genbank files can be written with long names. ... ok
test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok
test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok
test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok
test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok
test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok
test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok
test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok
test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok
test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok
test_ig3 (test_SeqIO.TestSeqIO.test_ig3)
Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok
test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1)
Test parsing file with features over-indented for EMBL. ... ok
test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok
test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok
test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok
test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok
test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok
test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok
test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok
test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok
test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok
test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok
test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok
test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok
test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok
test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok
test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok
test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok
test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok
test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok
test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok
test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok
test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok
test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok
test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok
test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok
test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok
test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok
test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok
test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok
test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok
test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok
test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok
test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok
test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok
test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok
test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok
test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok
test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok
test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok
test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok
test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok
test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok
test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok
test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok
test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok
test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok
test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok
test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok
test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok
test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok
test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok
test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok
test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok
test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok
test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok
test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok
test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok
test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok
test_uniprot_xml_namespace (test_SeqIO.TestSeqIO.test_uniprot_xml_namespace) ... ok
test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok
test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta)
Testing FASTA with gzip. ... ok
test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq)
Testing FASTQ with gzip. ... ok
test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank)
Testing GenBank with gzip. ... ok
----------------------------------------------------------------------
Ran 1 test in 14.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_AbiIO.py
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type)
Test if filetype is ABIF. ... ok
test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1)
Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi.test_raw)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi.test_trim)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type)
Test if error is raised if filetype is not ABIF. ... ok
test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag)
Test that we can handle non-ascii tags. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.253 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_FastaIO.py
test_SeqIO_FastaIO ... ok
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 0.061 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Gck.py
test_SeqIO_Gck ... ok
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 0.062 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... ok
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 0.119 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_NibIO.py
test_SeqIO_NibIO ... ok
test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok
test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok
test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok
test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.060 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader)
Read a single-chain CIF without a header by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse)
Parse a multi-chain structure by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read)
Read a single-chain structure by ATOM entries. ... ok
test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader)
Read a single-chain PDB without a header by ATOM entries. ... ok
test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion)
Read a PDB with residue insertion code. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read)
Read a single-chain structure by sequence entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.880 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_QualityIO.py
test_SeqIO_QualityIO ... ok
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 0.375 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_SeqXML.py
test_SeqIO_SeqXML ... ok
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 0.071 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_SnapGene.py
test_SeqIO_SnapGene ... ok
test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna)
Read a file with supernumerary DNA packet. ... ok
test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie)
Read a file with missing or invalid cookie packet. ... ok
test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna)
Read a file without a DNA packet. ... ok
test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet)
Read a file with incomplete packet. ... ok
test_read (test_SeqIO_SnapGene.TestSnapGene.test_read)
Read sample files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.067 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_TwoBitIO.py
test_SeqIO_TwoBitIO ... ok
test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok
test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok
test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok
test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok
test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok
test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok
test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok
test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok
test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok
test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok
test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok
test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok
test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok
test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok
test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok
test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok
test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok
test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok
test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok
test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok
test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok
test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok
test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok
test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok
test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok
test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok
test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok
test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok
test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok
test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok
test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok
test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok
test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok
test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok
test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok
test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok
test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.766 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_Xdna.py
test_SeqIO_Xdna ... ok
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 0.064 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_features.py
test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line
  warnings.warn(
ok
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 0.475 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails)
Reject alphabet argument in Bio.SeqIO.index(). ... ok
test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db)
Reject alphabet argument in Bio.SeqIO.index_db(). ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index)
Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db)
Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict)
Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok
test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok
test_key_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_key_checks_with_pathobj) ... ok
test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok
test_raw_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_raw_checks_with_pathobj) ... ok
test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok
test_simple_checks_with_pathobj (test_SeqIO_index.IndexDictTests.test_simple_checks_with_pathobj) ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db)
Check index_db preserves order in multiple indexed files. ... ok
test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index)
Check index preserves order in indexed file. ... ok
test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db)
Check index_db preserves ordering indexed file. ... ok
test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict)
Check to_dict preserves order in indexed file. ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest.test_old)
Load existing index with no options (from parent directory). ... ok
test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread)
Setting check_same_thread to False doesn't raise an exception. ... ok
test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest.test_old_files)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest.test_old_format)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel)
Load existing index (with relative paths) with no options (from same directory). ... ok
test_pathobj (test_SeqIO_index.OldIndexTest.test_pathobj)
Load existing index from a pathlib.Path object. ... ok
----------------------------------------------------------------------
Ran 1 test in 13.225 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.056 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok
test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.108 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqRecord.py
test_SeqRecord ... ok
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 0.106 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok
test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation)
Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok
test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization)
Test Codon Adaptation Index (CAI) initialization from sequences. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok
test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction)
Tests gc_fraction function. ... ok
test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok
test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.076 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Seq_objs.py
test_Seq_objs ... ok
test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok
test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok
test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok
test_le (test_Seq_objs.ComparisonTests.test_le) ... ok
test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok
test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok
test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq)
Test if feature extraction works properly for unknown sequences. ... ok
test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok
test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok
test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok
test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok
test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok
test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok
test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok
test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok
test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok
test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend)
Check extending a MutableSeq object. ... ok
test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error)
Check MutableSeq __init__ raises the appropriate exceptions. ... ok
test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem)
Check setting sequence contents of a MutableSeq object. ... ok
test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error)
Check Seq __init__ raises the appropriate exceptions. ... ok
test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap)
Check count_overlap exception matches python string count method. ... ok
test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG)
Check our count_overlap method using GG with variable ends and starts. ... ok
test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN)
Check our count_overlap method using NN with variable ends and starts. ... ok
test_equality (test_Seq_objs.StringMethodTests.test_equality)
Test equality when mixing types. ... ok
test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq)
Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok
test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed)
Check MutableSeq objects can be joined. ... ok
test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file)
Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok
test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq)
Checks if Seq join correctly concatenates sequence with the spacer. ... ok
test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError)
Checks that a TypeError is thrown for all non-iterable types. ... ok
test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file)
Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok
test_search (test_Seq_objs.StringMethodTests.test_search)
Check the search method of Seq objects. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok
test_str_count (test_Seq_objs.StringMethodTests.test_str_count)
Check matches the python string count method. ... ok
test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG)
Check our count_overlap method using GG. ... ok
test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN)
Check our count_overlap method using NN. ... ok
test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode)
Check matches the python string encode method. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests.test_str_find)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok
test_str_index (test_Seq_objs.StringMethodTests.test_str_index)
Check matches the python string index method. ... ok
test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower)
Check matches the python string islower method. ... ok
test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper)
Check matches the python string isupper method. ... ok
test_str_length (test_Seq_objs.StringMethodTests.test_str_length)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower)
Check matches the python string lower method. ... ok
test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip)
Check matches the python string lstrip method. ... ok
test_str_removeprefix (test_Seq_objs.StringMethodTests.test_str_removeprefix)
Check matches the python string removeprefix method. ... ok
test_str_removesuffix (test_Seq_objs.StringMethodTests.test_str_removesuffix)
Check matches the python string removesuffix method. ... ok
test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace)
Check matches the python string replace method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind)
Check matches the python string rfind method. ... ok
test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex)
Check matches the python string rindex method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit)
Check matches the python string rsplit method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests.test_str_split)
Check matches the python string split method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable)
Check creating a MutableSeq object. ... ok
test_toseq (test_Seq_objs.StringMethodTests.test_toseq)
Check creating a Seq object. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.186 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SffIO.py
test_SffIO ... ok
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 0.076 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_SwissProt.py
test_SwissProt ... ok
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 0.160 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_TreeConstruction.py
test_TreeConstruction ... ok
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 0.371 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_UniGene.py
test_UniGene ... ok
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 0.023 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_UniProt_GOA.py
test_UniProt_GOA ... ok
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 0.017 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_P60904 (test_Uniprot.TestUniprot.test_P60904)
Parsing SwissProt file P60904.txt. ... ok
test_P84001 (test_Uniprot.TestUniprot.test_P84001)
Parse mass spec structured comment with unknown loc. ... ok
test_Q13639 (test_Uniprot.TestUniprot.test_Q13639)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_sp016 (test_Uniprot.TestUniprot.test_sp016)
Parsing SwissProt file sp016. ... ok
test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed)
Checks if parser supports new XML Element (submittedName). ... ok
test_uni001 (test_Uniprot.TestUniprot.test_uni001)
Parsing Uniprot file uni001. ... ok
test_uni003 (test_Uniprot.TestUniprot.test_uni003)
Parsing Uniprot file uni003. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.182 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_XXmotif_tool.py
test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.058 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_align.py
test_align ... ok
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 0.123 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_align_substitution_matrices.py
test_align_substitution_matrices ... ok
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 0.317 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_bgzf.py
test_bgzf ... ok
test_BgzfBlocks_TypeError (test_bgzf.BgzfTests.test_BgzfBlocks_TypeError)
Check get expected TypeError from BgzfBlocks. ... ok
test_append_mode (test_bgzf.BgzfTests.test_append_mode) ... ok
test_bam_ex1 (test_bgzf.BgzfTests.test_bam_ex1)
Reproduce BGZF compression for BAM file. ... ok
test_double_flush (test_bgzf.BgzfTests.test_double_flush) ... ok
test_example_cor6 (test_bgzf.BgzfTests.test_example_cor6)
Reproduce BGZF compression for cor6_6.gb GenBank file. ... ok
test_example_fastq (test_bgzf.BgzfTests.test_example_fastq)
Reproduce BGZF compression for a FASTQ file. ... ok
test_example_gb (test_bgzf.BgzfTests.test_example_gb)
Reproduce BGZF compression for NC_000932 GenBank file. ... ok
test_example_wnts_xml (test_bgzf.BgzfTests.test_example_wnts_xml)
Reproduce BGZF compression for wnts.xml BLAST file. ... ok
test_iter_bam_ex1 (test_bgzf.BgzfTests.test_iter_bam_ex1)
Check iteration over SamBam/ex1.bam. ... ok
test_iter_example_cor6 (test_bgzf.BgzfTests.test_iter_example_cor6)
Check iteration over GenBank/cor6_6.gb.bgz. ... ok
test_iter_example_fastq (test_bgzf.BgzfTests.test_iter_example_fastq)
Check iteration over Quality/example.fastq.bgz. ... ok
test_iter_example_gb (test_bgzf.BgzfTests.test_iter_example_gb)
Check iteration over GenBank/NC_000932.gb.bgz. ... ok
test_iter_wnts_xml (test_bgzf.BgzfTests.test_iter_wnts_xml)
Check iteration over Blast/wnts.xml.bgz. ... ok
test_many_blocks_in_single_read (test_bgzf.BgzfTests.test_many_blocks_in_single_read) ... ok
test_random_bam_ex1 (test_bgzf.BgzfTests.test_random_bam_ex1)
Check random access to SamBam/ex1.bam. ... ok
test_random_bam_ex1_header (test_bgzf.BgzfTests.test_random_bam_ex1_header)
Check random access to SamBam/ex1_header.bam. ... ok
test_random_bam_ex1_refresh (test_bgzf.BgzfTests.test_random_bam_ex1_refresh)
Check random access to SamBam/ex1_refresh.bam. ... ok
test_random_example_cor6 (test_bgzf.BgzfTests.test_random_example_cor6)
Check random access to GenBank/cor6_6.gb.bgz. ... ok
test_random_example_dos_fastq (test_bgzf.BgzfTests.test_random_example_dos_fastq)
Check random access to Quality/example_dos.fastq.bgz (DOS newlines). ... ok
test_random_example_fastq (test_bgzf.BgzfTests.test_random_example_fastq)
Check random access to Quality/example.fastq.bgz (Unix newlines). ... ok
test_random_wnts_xml (test_bgzf.BgzfTests.test_random_wnts_xml)
Check random access to Blast/wnts.xml.bgz. ... ok
test_reader_with_binary_fileobj (test_bgzf.BgzfTests.test_reader_with_binary_fileobj)
A BgzfReader must accept a binary mode file object. ... ok
test_reader_with_non_binary_fileobj (test_bgzf.BgzfTests.test_reader_with_non_binary_fileobj)
A BgzfReader must raise ValueError on a non-binary file object. ... ok
test_text_example_fastq (test_bgzf.BgzfTests.test_text_example_fastq)
Check text mode access to Quality/example.fastq.bgz. ... ok
test_text_wnts_xml (test_bgzf.BgzfTests.test_text_wnts_xml)
Check text mode access to Blast/wnts.xml.bgz. ... ok
test_write_tell (test_bgzf.BgzfTests.test_write_tell)
Check offset works during BGZF writing. ... ok
test_writer_with_binary_fileobj (test_bgzf.BgzfTests.test_writer_with_binary_fileobj)
A BgzfWriter must accept a binary mode file object. ... ok
test_writer_with_non_binary_fileobj (test_bgzf.BgzfTests.test_writer_with_non_binary_fileobj)
A BgzfWriter must raise ValueError on a non-binary file object. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.941 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_cellosaurus.py
test_cellosaurus ... ok
test__str__ (test_cellosaurus.TestCellosaurus.test__str__)
Test string function. ... ok
test_parse (test_cellosaurus.TestCellosaurus.test_parse)
Test parsing function. ... ok
test_read (test_cellosaurus.TestCellosaurus.test_read)
Test read function. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_codonalign.py
test_codonalign ... ok
test_TypeError (test_codonalign.TestAddition.test_TypeError)
Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok
test_ValueError (test_codonalign.TestAddition.test_ValueError)
Check that ValueError is thrown for Alignments of different lengths. ... ok
test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment)
Check addition of CodonAlignment and CodonAlignment. ... ok
test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment)
Check addition of CodonAlignment and MultipleSeqAlignment. ... ok
test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok
test_align (test_codonalign.TestCodonAlignment.test_align) ... ok
test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok
test_mk (test_codonalign.Test_MK.test_mk) ... ok
test_build (test_codonalign.Test_build.test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok
test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok
----------------------------------------------------------------------
Ran 1 test in 3.861 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_geo.py
test_geo ... ok
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 0.051 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_kNN.py
test_kNN ... ok
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 0.010 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_mmtf.py
test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)

----------------------------------------------------------------------
Ran 1 test in 0.050 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_mmtf_online.py
test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)

----------------------------------------------------------------------
Ran 1 test in 0.047 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs.py
test_motifs ... ok
test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok
test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok
test_simple (test_motifs.MotifTestPWM.test_simple)
Test if Bio.motifs PWM scoring works. ... ok
test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_alignace_parsing (test_motifs.TestAlignAce.test_alignace_parsing)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_format (test_motifs.TestBasic.test_format) ... ok
test_relative_entropy (test_motifs.TestBasic.test_relative_entropy) ... ok
test_reverse_complement (test_motifs.TestBasic.test_reverse_complement)
Test if motifs can be reverse-complemented. ... ok
test_clusterbuster_parsing_and_output (test_motifs.TestClusterBuster.test_clusterbuster_parsing_and_output)
Test if Bio.motifs can parse and output Cluster-Buster PFM files. ... ok
test_pfm_four_columns_parsing (test_motifs.TestJASPAR.test_pfm_four_columns_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok
test_pfm_four_rows_parsing (test_motifs.TestJASPAR.test_pfm_four_rows_parsing)
Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok
test_pfm_parsing (test_motifs.TestJASPAR.test_pfm_parsing)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_sites_parsing (test_motifs.TestJASPAR.test_sites_parsing)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1)
Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok
test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2)
Parse motifs/mast.adh.de.oops.html.xml file. ... ok
test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3)
Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok
test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1)
Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok
test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2)
Parsing motifs/meme.adh.classic.oops.xml file. ... ok
test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3)
Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok
test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna)
Test if Bio.motifs can parse MEME output files using RNA. ... ok
test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser)
Parse motifs/minimal_test.meme file. ... ok
test_TFoutput (test_motifs.TestTransfac.test_TFoutput)
Ensure that we can write proper TransFac output files. ... ok
test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser)
Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok
test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser)
Parse motifs/transfac.dat file. ... ok
test_xms_parsing (test_motifs.TestXMS.test_xms_parsing)
Test if Bio.motifs can parse and output xms PFM files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.263 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.036 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2.py
test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
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 0.073 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise2_no_C.py
test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(
ok
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 0.074 seconds
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise_aligner.py
test_pairwise_aligner ... ok
test_str_seq_seqrecord (test_pairwise_aligner.TestAlignerInput.test_str_seq_seqrecord)
Test aligning sequences provided as str, Seq, or SeqRecord objects. ... ok
test_three_letter_amino_acids_global (test_pairwise_aligner.TestAlignerInput.test_three_letter_amino_acids_global)
Test aligning sequences provided as lists of three-letter amino acids. ... ok
test_three_letter_amino_acids_local (test_pairwise_aligner.TestAlignerInput.test_three_letter_amino_acids_local) ... ok
test_pickle_aligner_match_mismatch (test_pairwise_aligner.TestAlignerPickling.test_pickle_aligner_match_mismatch) ... ok
test_pickle_aligner_substitution_matrix (test_pairwise_aligner.TestAlignerPickling.test_pickle_aligner_substitution_matrix) ... ok
test_aligner_nonexisting_property (test_pairwise_aligner.TestAlignerProperties.test_aligner_nonexisting_property) ... ok
test_aligner_property_epsilon (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_epsilon) ... ok
test_aligner_property_gapscores (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_gapscores) ... ok
test_aligner_property_match_mismatch (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_match_mismatch) ... ok
test_aligner_property_mode (test_pairwise_aligner.TestAlignerProperties.test_aligner_property_mode) ... ok
test_alignment_end_gap (test_pairwise_aligner.TestAlignmentFormat.test_alignment_end_gap) ... ok
test_alignment_simple (test_pairwise_aligner.TestAlignmentFormat.test_alignment_simple) ... ok
test_alignment_wildcard (test_pairwise_aligner.TestAlignmentFormat.test_alignment_wildcard) ... ok
test_aligner_array_errors (test_pairwise_aligner.TestArgumentErrors.test_aligner_array_errors) ... ok
test_aligner_string_errors (test_pairwise_aligner.TestArgumentErrors.test_aligner_string_errors) ... ok
test_confusing_arguments (test_pairwise_aligner.TestKeywordArgumentsConstructor.test_confusing_arguments) ... ok
test_align_overflow_error (test_pairwise_aligner.TestOverflowError.test_align_overflow_error) ... ok
test_extend_penalty1 (test_pairwise_aligner.TestPairwiseExtendPenalty.test_extend_penalty1) ... ok
test_extend_penalty2 (test_pairwise_aligner.TestPairwiseExtendPenalty.test_extend_penalty2) ... ok
test_align_affine1_score (test_pairwise_aligner.TestPairwiseGlobal.test_align_affine1_score) ... ok
test_needlemanwunsch_simple1 (test_pairwise_aligner.TestPairwiseGlobal.test_needlemanwunsch_simple1) ... ok
test_gotoh_local (test_pairwise_aligner.TestPairwiseLocal.test_gotoh_local) ... ok
test_smithwaterman (test_pairwise_aligner.TestPairwiseLocal.test_smithwaterman) ... ok
test_match_dictionary1 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary1) ... ok
test_match_dictionary2 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary2) ... ok
test_match_dictionary3 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary3) ... ok
test_match_dictionary4 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary4) ... ok
test_match_dictionary5 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary5) ... ok
test_match_dictionary6 (test_pairwise_aligner.TestPairwiseMatchDictionary.test_match_dictionary6) ... ok
test_align_one_char1 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char1) ... ok
test_align_one_char2 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char2) ... ok
test_align_one_char3 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char3) ... ok
test_align_one_char_score3 (test_pairwise_aligner.TestPairwiseOneCharacter.test_align_one_char_score3) ... ok
test_match_score_open_penalty1 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty1) ... ok
test_match_score_open_penalty2 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty2) ... ok
test_match_score_open_penalty3 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty3) ... ok
test_match_score_open_penalty4 (test_pairwise_aligner.TestPairwiseOpenPenalty.test_match_score_open_penalty4) ... ok
test_penalize_end_gaps (test_pairwise_aligner.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) ... ok
test_penalize_extend_when_opening (test_pairwise_aligner.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) ... ok
test_separate_gap_penalties1 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) ... ok
test_separate_gap_penalties2 (test_pairwise_aligner.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) ... ok
test_separate_gap_penalties_with_extension (test_pairwise_aligner.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) ... ok
test_broken_gap_function (test_pairwise_aligner.TestPerSiteGapPenalties.test_broken_gap_function) ... ok
test_gap_here_only_1 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_1) ... ok
test_gap_here_only_2 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_2) ... ok
test_gap_here_only_3 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_3) ... ok
test_gap_here_only_local_1 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_1) ... ok
test_gap_here_only_local_2 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_2) ... ok
test_gap_here_only_local_3 (test_pairwise_aligner.TestPerSiteGapPenalties.test_gap_here_only_local_3) ... ok
test_blastn (test_pairwise_aligner.TestPredefinedScoringSchemes.test_blastn) ... ok
test_blastp (test_pairwise_aligner.TestPredefinedScoringSchemes.test_blastp) ... ok
test_megablast (test_pairwise_aligner.TestPredefinedScoringSchemes.test_megablast) ... ok
test_align_affine1_score (test_pairwise_aligner.TestUnicodeStrings.test_align_affine1_score) ... ok
test_gotoh_local (test_pairwise_aligner.TestUnicodeStrings.test_gotoh_local) ... ok
test_needlemanwunsch_simple1 (test_pairwise_aligner.TestUnicodeStrings.test_needlemanwunsch_simple1) ... ok
test_smithwaterman (test_pairwise_aligner.TestUnicodeStrings.test_smithwaterman) ... ok
test_needlemanwunsch_simple1 (test_pairwise_aligner.TestUnknownCharacter.test_needlemanwunsch_simple1) ... ok
test_needlemanwunsch_simple2 (test_pairwise_aligner.TestUnknownCharacter.test_needlemanwunsch_simple2) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.260 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_pairwise_alignment_map.py
test_pairwise_alignment_map ... ok
test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok
test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok
test_chimp (test_pairwise_alignment_map.TestLiftOver.test_chimp) ... ok
test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok
test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok
test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok
test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok
test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok
test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok
test1 (test_pairwise_alignment_map.TestZeroGaps.test1) ... ok
test2 (test_pairwise_alignment_map.TestZeroGaps.test2) ... ok
test3 (test_pairwise_alignment_map.TestZeroGaps.test3) ... ok
test4 (test_pairwise_alignment_map.TestZeroGaps.test4) ... ok
test5 (test_pairwise_alignment_map.TestZeroGaps.test5) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.170 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_phenotype.py
test_phenotype ... ok
test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator)
Test basic functionalities of CsvIterator file parser. ... ok
test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator)
Test basic functionalities of JsonIterator file parser. ... ok
test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord)
Test basic functionalities of PlateRecord objects. ... ok
test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors)
Test bad arguments with PlateRecord objects. ... ok
test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord)
Test basic functionalities of WellRecord objects. ... ok
test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args)
Test error handling of the fit method. ... ok
test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO)
Test basic functionalities of phenotype IO methods. ... ok
test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors)
Test bad arguments to phenotype IO methods. ... ok
----------------------------------------------------------------------
Ran 1 test in 5.752 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_phenotype_fit.py
test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality.
----------------------------------------------------------------------
Ran 1 test in 0.007 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_phyml_tool.py
test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc)
Parsing an excerpt of prosite.doc. ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100)
Reading Prodoc record PDOC00100. ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113)
Reading Prodoc record PDOC00113. ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144)
Reading Prodoc record PDOC00144. ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149)
Reading Prodoc record PDOC00149. ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340)
Reading Prodoc record PDOC00340. ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424)
Reading Prodoc record PDOC00424. ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472)
Reading Prodoc record PDOC00472. ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640)
Reading Prodoc record PDOC00640. ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787)
Reading Prodoc record PDOC00787. ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933)
Reading Prodoc record PDOC00933. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_prosite.py
test_prosite ... ok
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
----------------------------------------------------------------------
Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
Ran 1 test in 0.063 seconds

+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.057 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_samtools_tool.py
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_seq.py
test_seq ... ok
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 0.061 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py`
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ PATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+ PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/lib/python3.12/site-packages
+ PYTHONDONTWRITEBYTECODE=1
+ PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/biopython-1.83/.pyproject-builddir'
+ PYTEST_XDIST_AUTO_NUM_WORKERS=4
+ /usr/bin/python3 run_tests.py --offline --verbose -v test_translate.py
test_translate ... ok
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 0.034 seconds

Skipping any tests requiring internet access
Python version: 3.12.3 (main, Apr 10 2024, 00:00:00) [GCC 14.0.1 20240328 (Red Hat 14.0.1-0)]
Operating system: posix linux
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: python3-biopython-1.83-5.fc41.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.PhkdzX
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/share/doc/python3-biopython
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/biopython-1.83/Doc /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/share/doc/python3-biopython
+ cp -pr /builddir/build/BUILD/biopython-1.83/Scripts /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64/usr/share/doc/python3-biopython
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: python-biopython = 1.83-5.fc41 python3-biopython = 1.83-5.fc41 python3-biopython(aarch-64) = 1.83-5.fc41 python3.12-biopython = 1.83-5.fc41 python3.12dist(biopython) = 1.83 python3dist(biopython) = 1.83
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) python(abi) = 3.12 python3.12dist(numpy) rtld(GNU_HASH)
Processing files: python-biopython-debugsource-1.83-5.fc41.aarch64
Provides: python-biopython-debugsource = 1.83-5.fc41 python-biopython-debugsource(aarch-64) = 1.83-5.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python3-biopython-debuginfo-1.83-5.fc41.aarch64
Provides: debuginfo(build-id) = 17bb2811cd8c575da08675fca068eea0b089c732 debuginfo(build-id) = 1bec7abeb12428381d99924e7432b50a0acbcc6d debuginfo(build-id) = 3c40ae0bc1a07ae85dc07472189e8195ca44f82e debuginfo(build-id) = 6fb957ea33127712a112753e8801fbc471f16288 debuginfo(build-id) = 8651cf203b31890285b1e090a765a6b359a6d3a3 debuginfo(build-id) = 91304fc6e78f6b9f546405a153168861ba41e41e debuginfo(build-id) = a3e156b245c3dbaa2428b0ee1c24eeb5a8e55d38 debuginfo(build-id) = d9fc6ca8054afffd5e3eae1a12b9e84a3898cd16 debuginfo(build-id) = f0e865c752d774c762b58ac3f322e043287e86bd python-biopython-debuginfo = 1.83-5.fc41 python3-biopython-debuginfo = 1.83-5.fc41 python3-biopython-debuginfo(aarch-64) = 1.83-5.fc41 python3.12-biopython-debuginfo = 1.83-5.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: python-biopython-debugsource(aarch-64) = 1.83-5.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64
Wrote: /builddir/build/SRPMS/python-biopython-1.83-5.fc41.src.rpm
Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.83-5.fc41.aarch64.rpm
Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.83-5.fc41.aarch64.rpm
Wrote: /builddir/build/RPMS/python3-biopython-1.83-5.fc41.aarch64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qlipH1
+ umask 022
+ cd /builddir/build/BUILD
+ cd biopython-1.83
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.83-5.fc41.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.df64L1
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/biopython-1.83-SPECPARTS
+ rm -rf biopython-1.83 biopython-1.83.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild python-biopython-1.83-5.fc41.src.rpm
Finish: build phase for python-biopython-1.83-5.fc41.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1713009811.077841/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.83-5.fc41.src.rpm) Config(child) 3 minutes 18 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-debuginfo",
            "epoch": null,
            "version": "1.83",
            "release": "5.fc41",
            "arch": "aarch64"
        },
        {
            "name": "python3-biopython",
            "epoch": null,
            "version": "1.83",
            "release": "5.fc41",
            "arch": "aarch64"
        },
        {
            "name": "python-biopython",
            "epoch": null,
            "version": "1.83",
            "release": "5.fc41",
            "arch": "src"
        },
        {
            "name": "python-biopython-debugsource",
            "epoch": null,
            "version": "1.83",
            "release": "5.fc41",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished