Warning: Permanently added '13.120.95.1' (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/8429097-fedora-rawhide-s390x --chroot fedora-rawhide-s390x Version: 1.2 PID: 79365 Logging PID: 79366 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8429097, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '2677a1b87365ff5fa383c9b97ad13cde4ad50226', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.84-3', 'project_dirname': 'gcc-15-smoketest-3', 'project_name': 'gcc-15-smoketest-3', 'project_owner': 'dmalcolm', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/dmalcolm/gcc-15-smoketest-3/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'https://fedorapeople.org/~dmalcolm/gcc/gcc-15-mass-prebuild/$basearch', 'id': 'https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch', 'name': 'Additional repo https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch'}], 'sandbox': 'dmalcolm/gcc-15-smoketest-3--dmalcolm', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'dmalcolm', 'tags': [], 'task_id': '8429097-fedora-rawhide-s390x', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython'... Running: git checkout 2677a1b87365ff5fa383c9b97ad13cde4ad50226 -- cmd: ['git', 'checkout', '2677a1b87365ff5fa383c9b97ad13cde4ad50226', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython rc: 0 stdout: stderr: Note: switching to '2677a1b87365ff5fa383c9b97ad13cde4ad50226'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 2677a1b automatic import of python-biopython Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/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-1.84.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o biopython-1.84.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/dmalcolm/gcc-15-smoketest-3/python-biopython/biopython-1.84.tar.gz/md5/92e639d2f3627759f12f0d000131c24d/biopython-1.84.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 24.5M 100 24.5M 0 0 13.8M 0 0:00:01 0:00:01 --:--:-- 13.8M INFO: Reading stdout from command: md5sum biopython-1.84.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1735163894.596627 -r /var/lib/copr-rpmbuild/results/configs/child.cfg /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1735163894.596627 -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-ald2skco/python-biopython/python-biopython.spec) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Mock Version: 6.0 INFO: Mock Version: 6.0 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735163894.596627/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 container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-ddec333e-5bb6-4a96-83ae-af045add4a9d INFO: Checking that 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af image matches host's architecture INFO: Copy content of container 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735163894.596627/root INFO: mounting 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af with podman image mount INFO: image 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af as /var/lib/containers/storage/overlay/b9a3c3dc0226e3eb9238d4e612f4e94d9ad0bff832af1d98b7d9b65f4d4ec7db/merged INFO: umounting image 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af (/var/lib/containers/storage/overlay/b9a3c3dc0226e3eb9238d4e612f4e94d9ad0bff832af1d98b7d9b65f4d4ec7db/merged) with podman image umount INFO: Removing image mock-bootstrap-ddec333e-5bb6-4a96-83ae-af045add4a9d INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True 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-s390x-1735163894.596627/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-4.20.0-1.fc42.s390x rpm-sequoia-1.7.0-3.fc42.s390x dnf5-5.2.8.1-2.fc42.s390x dnf5-plugins-5.2.8.1-2.fc42.s390x Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 5.9 KiB/s | 3.8 KiB | 00m01s Copr repository 100% | 3.3 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 4.3 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 5.8 MiB/s | 6.9 MiB | 00m01s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash s390x 5.2.37-1.fc42 fedora 8.4 MiB bzip2 s390x 1.0.8-19.fc42 copr_base 84.4 KiB coreutils s390x 9.5-11.fc42 fedora 5.7 MiB cpio s390x 2.15-2.fc41 fedora 1.1 MiB diffutils s390x 3.10-8.fc42 copr_base 1.6 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils s390x 1:4.10.0-4.fc42 copr_base 1.9 MiB gawk s390x 5.3.0-4.fc41 fedora 1.8 MiB glibc-minimal-langpack s390x 2.40.9000-24.fc42 copr_base 0.0 B grep s390x 3.11-9.fc42 copr_base 1.0 MiB gzip s390x 1.13-2.fc42 copr_base 394.6 KiB info s390x 7.1.1-2.fc42 fedora 409.1 KiB patch s390x 2.7.6-25.fc42 copr_base 286.9 KiB redhat-rpm-config noarch 300-1.no_annobin.0.fc42 copr_base 186.6 KiB rpm-build s390x 4.20.0-1.fc42 fedora 200.4 KiB sed s390x 4.9-3.fc41 fedora 873.2 KiB shadow-utils s390x 2:4.17.0~rc1-2.fc42 fedora 4.0 MiB tar s390x 2:1.35-4.fc41 fedora 3.0 MiB unzip s390x 6.0-65.fc42 fedora 2.2 MiB util-linux s390x 2.40.2-8.fc42 fedora 3.7 MiB which s390x 2.21-42.fc41 fedora 83.9 KiB xz s390x 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism s390x 0.5.0-1.fc42 fedora 3.3 MiB alternatives s390x 1.31-1.fc42 fedora 60.6 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs s390x 4.0.2-1.fc42 copr_base 342.9 KiB authselect s390x 1.5.0-8.fc42 copr_base 151.8 KiB authselect-libs s390x 1.5.0-8.fc42 copr_base 817.4 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils s390x 2.43.50-9.fc42 copr_base 26.9 MiB build-reproducibility-srpm-macros noarch 0.5.0-1.fc42 fedora 735.0 B bzip2-libs s390x 1.0.8-19.fc42 copr_base 82.9 KiB ca-certificates noarch 2024.2.69_v8.0.401-4.fc42 fedora 2.6 MiB coreutils-common s390x 9.5-11.fc42 fedora 11.2 MiB cracklib s390x 2.9.11-6.fc42 copr_base 225.2 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl s390x 8.11.1-2.fc42 copr_base 475.8 KiB cyrus-sasl-lib s390x 2.1.28-27.fc41 fedora 2.4 MiB debugedit s390x 5.1-2.fc42 copr_base 193.2 KiB dwz s390x 0.15-8.fc42 copr_base 307.5 KiB ed s390x 1.20.2-2.fc41 fedora 150.6 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils s390x 0.192-7.fc42 copr_base 2.9 MiB elfutils-debuginfod-client s390x 0.192-7.fc42 copr_base 73.0 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 copr_base 1.8 KiB elfutils-libelf s390x 0.192-7.fc42 copr_base 1.2 MiB elfutils-libs s390x 0.192-7.fc42 copr_base 746.5 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.11 fedora 0.0 B fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file s390x 5.45-8.fc42 fedora 99.3 KiB file-libs s390x 5.45-8.fc42 fedora 9.9 MiB filesystem s390x 3.18-29.fc42 fedora 106.0 B filesystem-srpm-macros noarch 3.18-29.fc42 fedora 36.1 KiB fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal s390x 15.2-4.fc42 copr_base 14.7 MiB gdbm s390x 1:1.23-7.fc41 fedora 483.9 KiB gdbm-libs s390x 1:1.23-7.fc41 fedora 133.4 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc s390x 2.40.9000-24.fc42 copr_base 4.9 MiB glibc-common s390x 2.40.9000-24.fc42 copr_base 1.1 MiB glibc-gconv-extra s390x 2.40.9000-24.fc42 copr_base 6.5 MiB gmp s390x 1:6.3.0-2.fc41 fedora 770.0 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB jansson s390x 2.14-1.fc42 copr_base 86.6 KiB json-c s390x 0.18-1.fc42 copr_base 79.5 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs s390x 1.6.3-4.fc42 copr_base 48.6 KiB krb5-libs s390x 1.21.3-3.fc42 copr_base 2.4 MiB libacl s390x 2.3.2-2.fc42 copr_base 34.1 KiB libarchive s390x 3.7.7-1.fc42 copr_base 1.0 MiB libattr s390x 2.5.2-4.fc41 fedora 28.3 KiB libblkid s390x 2.40.2-8.fc42 fedora 286.4 KiB libbrotli s390x 1.1.0-5.fc42 copr_base 903.7 KiB libcap s390x 2.71-1.fc42 copr_base 201.3 KiB libcap-ng s390x 0.8.5-3.fc42 copr_base 58.3 KiB libcom_err s390x 1.47.1-6.fc42 fedora 67.0 KiB libcurl s390x 8.11.1-2.fc42 copr_base 857.0 KiB libeconf s390x 0.7.5-1.fc42 copr_base 62.5 KiB libevent s390x 2.1.12-14.fc42 copr_base 898.3 KiB libfdisk s390x 2.40.2-8.fc42 fedora 394.8 KiB libffi s390x 3.4.6-3.fc42 fedora 65.9 KiB libgcc s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 166.7 KiB libgomp s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 529.0 KiB libidn2 s390x 2.3.7-2.fc42 copr_base 323.5 KiB libmount s390x 2.40.2-8.fc42 fedora 375.8 KiB libnghttp2 s390x 1.64.0-1.fc42 fedora 177.9 KiB libpkgconf s390x 2.3.0-1.fc42 copr_base 79.8 KiB libpsl s390x 0.21.5-4.fc42 copr_base 71.1 KiB libpwquality s390x 1.4.5-11.fc42 copr_base 396.1 KiB libselinux s390x 3.8-0.rc3.1.fc42 fedora 203.4 KiB libsemanage s390x 3.8-0.rc3.1.fc42 fedora 305.1 KiB libsepol s390x 3.8-0.rc3.1.fc42 fedora 840.1 KiB libsmartcols s390x 2.40.2-8.fc42 fedora 192.2 KiB libssh s390x 0.11.1-1.fc42 copr_base 571.6 KiB libssh-config noarch 0.11.1-1.fc42 copr_base 277.0 B libstdc++ s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 3.1 MiB libtasn1 s390x 4.19.0-9.fc42 copr_base 181.5 KiB libtirpc s390x 1.3.6-1.fc42 fedora 212.5 KiB libtool-ltdl s390x 2.5.4-1.fc42 copr_base 67.9 KiB libunistring s390x 1.1-8.fc42 copr_base 1.8 MiB libuuid s390x 2.40.2-8.fc42 fedora 41.2 KiB libverto s390x 0.3.2-9.fc41 fedora 29.3 KiB libxcrypt s390x 4.4.36-12.fc42 fedora 269.1 KiB libxml2 s390x 2.12.9-1.fc42 fedora 1.8 MiB libzstd s390x 1.5.6-2.fc41 fedora 875.7 KiB lua-libs s390x 5.4.7-1.fc42 fedora 328.8 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs s390x 1.10.0-1.fc42 copr_base 195.3 KiB mpfr s390x 4.2.1-5.fc42 copr_base 693.2 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs s390x 6.5-2.20240629.fc41 fedora 1.1 MiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap s390x 2.6.8-6.fc42 copr_base 654.5 KiB openssl-libs s390x 1:3.2.2-8.fc42 copr_base 6.0 MiB p11-kit s390x 0.25.5-4.fc42 copr_base 2.4 MiB p11-kit-trust s390x 0.25.5-4.fc42 copr_base 456.4 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam s390x 1.7.0-3.fc42 copr_base 1.5 MiB pam-libs s390x 1.7.0-3.fc42 copr_base 118.1 KiB pcre2 s390x 10.44-1.fc42.1 copr_base 668.2 KiB pcre2-syntax noarch 10.44-1.fc42.1 copr_base 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf s390x 2.3.0-1.fc42 copr_base 86.9 KiB pkgconf-m4 noarch 2.3.0-1.fc42 copr_base 14.4 KiB pkgconf-pkg-config s390x 2.3.0-1.fc42 copr_base 988.0 B popt s390x 1.19-7.fc42 copr_base 138.7 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.1-4.fc42 fedora 456.0 B readline s390x 8.2-11.fc42 fedora 556.8 KiB rpm s390x 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs s390x 4.20.0-1.fc42 fedora 218.4 KiB rpm-libs s390x 4.20.0-1.fc42 fedora 813.6 KiB rpm-sequoia s390x 1.7.0-3.fc42 fedora 3.2 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs s390x 3.47.2-1.fc42 fedora 1.6 MiB systemd-libs s390x 257.1-1.fc42 fedora 2.2 MiB util-linux-core s390x 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs s390x 0.8.2-4.fc42 fedora 68.0 KiB xz-libs s390x 1:5.6.3-2.fc42 fedora 226.1 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip s390x 3.0-42.fc42 fedora 723.1 KiB zlib-ng-compat s390x 2.2.2-1.fc42 fedora 109.4 KiB zstd s390x 1.5.6-2.fc41 fedora 1.8 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 183 MiB extra will be used (install 183 MiB, remove 0 B). [1/1] tar-2:1.35-4.fc41.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] rpm-build-0:4.20.0-1.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] unzip-0:6.0-65.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] cpio-0:2.15-2.fc41.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] which-0:2.21-42.fc41.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. 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Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.5.0-1.fc42.s390x alternatives-1.31-1.fc42.s390x ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc42.s390x authselect-1.5.0-8.fc42.s390x authselect-libs-1.5.0-8.fc42.s390x basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.s390x binutils-2.43.50-9.fc42.s390x build-reproducibility-srpm-macros-0.5.0-1.fc42.noarch bzip2-1.0.8-19.fc42.s390x bzip2-libs-1.0.8-19.fc42.s390x ca-certificates-2024.2.69_v8.0.401-4.fc42.noarch coreutils-9.5-11.fc42.s390x coreutils-common-9.5-11.fc42.s390x cpio-2.15-2.fc41.s390x cracklib-2.9.11-6.fc42.s390x crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.11.1-2.fc42.s390x cyrus-sasl-lib-2.1.28-27.fc41.s390x debugedit-5.1-2.fc42.s390x diffutils-3.10-8.fc42.s390x dwz-0.15-8.fc42.s390x ed-1.20.2-2.fc41.s390x efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.s390x elfutils-debuginfod-client-0.192-7.fc42.s390x elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.s390x elfutils-libs-0.192-7.fc42.s390x fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.11.noarch fedora-release-common-42-0.11.noarch fedora-release-identity-basic-42-0.11.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-8.fc42.s390x file-libs-5.45-8.fc42.s390x filesystem-3.18-29.fc42.s390x filesystem-srpm-macros-3.18-29.fc42.noarch findutils-4.10.0-4.fc42.s390x fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.s390x gdb-minimal-15.2-4.fc42.s390x gdbm-1.23-7.fc41.s390x gdbm-libs-1.23-7.fc41.s390x ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-24.fc42.s390x glibc-common-2.40.9000-24.fc42.s390x glibc-gconv-extra-2.40.9000-24.fc42.s390x glibc-minimal-langpack-2.40.9000-24.fc42.s390x gmp-6.3.0-2.fc41.s390x gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc42.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc42.s390x gzip-1.13-2.fc42.s390x info-7.1.1-2.fc42.s390x jansson-2.14-1.fc42.s390x json-c-0.18-1.fc42.s390x kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc42.s390x krb5-libs-1.21.3-3.fc42.s390x libacl-2.3.2-2.fc42.s390x libarchive-3.7.7-1.fc42.s390x libattr-2.5.2-4.fc41.s390x libblkid-2.40.2-8.fc42.s390x libbrotli-1.1.0-5.fc42.s390x libcap-2.71-1.fc42.s390x libcap-ng-0.8.5-3.fc42.s390x libcom_err-1.47.1-6.fc42.s390x libcurl-8.11.1-2.fc42.s390x libeconf-0.7.5-1.fc42.s390x libevent-2.1.12-14.fc42.s390x libfdisk-2.40.2-8.fc42.s390x libffi-3.4.6-3.fc42.s390x libgcc-15.0.0-0.2.fc42.s390x libgomp-15.0.0-0.2.fc42.s390x libidn2-2.3.7-2.fc42.s390x libmount-2.40.2-8.fc42.s390x libnghttp2-1.64.0-1.fc42.s390x libpkgconf-2.3.0-1.fc42.s390x libpsl-0.21.5-4.fc42.s390x libpwquality-1.4.5-11.fc42.s390x libselinux-3.8-0.rc3.1.fc42.s390x libsemanage-3.8-0.rc3.1.fc42.s390x libsepol-3.8-0.rc3.1.fc42.s390x libsmartcols-2.40.2-8.fc42.s390x libssh-0.11.1-1.fc42.s390x libssh-config-0.11.1-1.fc42.noarch libstdc++-15.0.0-0.2.fc42.s390x libtasn1-4.19.0-9.fc42.s390x libtirpc-1.3.6-1.fc42.s390x libtool-ltdl-2.5.4-1.fc42.s390x libunistring-1.1-8.fc42.s390x libuuid-2.40.2-8.fc42.s390x libverto-0.3.2-9.fc41.s390x libxcrypt-4.4.36-12.fc42.s390x libxml2-2.12.9-1.fc42.s390x libzstd-1.5.6-2.fc41.s390x lua-libs-5.4.7-1.fc42.s390x lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc42.s390x mpfr-4.2.1-5.fc42.s390x ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.s390x ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.s390x openssl-libs-3.2.2-8.fc42.s390x p11-kit-0.25.5-4.fc42.s390x p11-kit-trust-0.25.5-4.fc42.s390x package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.s390x pam-libs-1.7.0-3.fc42.s390x patch-2.7.6-25.fc42.s390x pcre2-10.44-1.fc42.1.s390x pcre2-syntax-10.44-1.fc42.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.s390x pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.s390x popt-1.19-7.fc42.s390x publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.3-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.1-4.fc42.noarch readline-8.2-11.fc42.s390x redhat-rpm-config-300-1.no_annobin.0.fc42.noarch rpm-4.20.0-1.fc42.s390x rpm-build-4.20.0-1.fc42.s390x rpm-build-libs-4.20.0-1.fc42.s390x rpm-libs-4.20.0-1.fc42.s390x rpm-sequoia-1.7.0-3.fc42.s390x rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.s390x setup-2.15.0-5.fc41.noarch shadow-utils-4.17.0~rc1-2.fc42.s390x sqlite-libs-3.47.2-1.fc42.s390x systemd-libs-257.1-1.fc42.s390x tar-1.35-4.fc41.s390x unzip-6.0-65.fc42.s390x util-linux-2.40.2-8.fc42.s390x util-linux-core-2.40.2-8.fc42.s390x which-2.21-42.fc41.s390x xxhash-libs-0.8.2-4.fc42.s390x xz-5.6.3-2.fc42.s390x xz-libs-5.6.3-2.fc42.s390x zig-srpm-macros-1-3.fc41.noarch zip-3.0-42.fc42.s390x zlib-ng-compat-2.2.2-1.fc42.s390x zstd-1.5.6-2.fc41.s390x Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1735163894.596627/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-ald2skco/python-biopython/python-biopython.spec) Config(child) 0 minutes 20 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-1.84-3.fc42.src.rpm) Config(fedora-rawhide-s390x) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735163894.596627/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735163894.596627/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-s390x-1735163894.596627/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-4.20.0-1.fc42.s390x rpm-sequoia-1.7.0-3.fc42.s390x dnf5-5.2.8.1-2.fc42.s390x dnf5-plugins-5.2.8.1-2.fc42.s390x Finish: chroot init Start: build phase for python-biopython-1.84-3.fc42.src.rpm Start: build setup for python-biopython-1.84-3.fc42.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.src.rpm Updating and loading repositories: fedora 100% | 11.8 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 4.8 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 4.9 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 79.2 MiB pyproject-rpm-macros noarch 1.16.3-1.fc42 fedora 113.7 KiB python3-devel s390x 3.13.1-2.fc42 fedora 1.8 MiB python3-reportlab noarch 4.2.5-1.fc42 fedora 10.9 MiB Installing dependencies: annobin-docs noarch 12.80-1.fc42 fedora 98.6 KiB annobin-plugin-gcc s390x 12.80-1.fc42 fedora 988.6 KiB cpp s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 26.6 MiB dejavu-sans-fonts noarch 2.37-24.fc41 fedora 5.5 MiB expat s390x 2.6.4-1.fc42 copr_base 299.3 KiB fonts-filesystem noarch 1:2.0.5-17.fc41 fedora 0.0 B freetype s390x 2.13.3-1.fc42 copr_base 907.6 KiB fribidi s390x 1.0.16-1.fc42 copr_base 191.4 KiB gcc-plugin-annobin s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 51.3 KiB glib2 s390x 2.83.0-3.fc42 copr_base 14.9 MiB glibc-devel s390x 2.40.9000-24.fc42 copr_base 2.6 MiB gnutls s390x 3.8.8-1.fc42 copr_base 3.1 MiB graphite2 s390x 1.3.14-16.fc41 fedora 207.4 KiB harfbuzz s390x 10.1.0-2.fc42 copr_base 2.7 MiB jbigkit-libs s390x 2.1-30.fc42 copr_base 114.5 KiB kernel-headers s390x 6.13.0-0.rc4.36.fc42 fedora 6.5 MiB lcms2 s390x 2.16-4.fc42 copr_base 443.9 KiB libXau s390x 1.0.12-1.fc42 fedora 67.6 KiB libasan s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 1.6 MiB libatomic s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 26.0 KiB libb2 s390x 0.98.1-12.fc42 copr_base 40.6 KiB libimagequant s390x 4.0.3-5.fc41 fedora 835.9 KiB libjpeg-turbo s390x 3.0.4-1.fc42 copr_base 756.5 KiB liblerc s390x 4.0.0-7.fc42 copr_base 261.7 KiB libmpc s390x 1.3.1-6.fc42 copr_base 157.8 KiB libpng s390x 2:1.6.44-1.fc42 copr_base 248.3 KiB libraqm s390x 0.10.1-1.fc42 copr_base 31.2 KiB libtiff s390x 4.7.0-2.fc42 copr_base 648.0 KiB libubsan s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 480.5 KiB libwebp s390x 1.5.0-1.fc42 fedora 633.3 KiB libxcb s390x 1.17.0-3.fc42 fedora 1.2 MiB libxcrypt-devel s390x 4.4.36-12.fc42 fedora 30.5 KiB make s390x 1:4.4.1-9.fc42 copr_base 1.8 MiB mpdecimal s390x 2.5.1-16.fc42 copr_base 215.7 KiB nettle s390x 3.10-3.fc42 copr_base 825.2 KiB openjpeg s390x 2.5.3-2.fc42 fedora 479.1 KiB python-pip-wheel noarch 24.3.1-1.fc42 fedora 1.2 MiB python-rpm-macros noarch 3.13-3.fc41 fedora 22.1 KiB python3 s390x 3.13.1-2.fc42 fedora 22.4 KiB python3-chardet noarch 5.2.0-14.fc41 fedora 2.1 MiB python3-libs s390x 3.13.1-2.fc42 fedora 40.0 MiB python3-olefile noarch 0.47-5.fc41 fedora 340.4 KiB python3-packaging noarch 24.2-2.fc42 fedora 555.7 KiB python3-pillow s390x 11.0.0-1.fc42 fedora 4.0 MiB python3-rpm-generators noarch 14-11.fc41 fedora 81.7 KiB python3-rpm-macros noarch 3.13-3.fc41 fedora 6.4 KiB tzdata noarch 2024b-1.fc42 fedora 1.6 MiB Transaction Summary: Installing: 51 packages Total size of inbound packages is 71 MiB. Need to download 14 MiB. After this operation, 217 MiB extra will be used (install 217 MiB, remove 0 B). [1/1] pyproject-rpm-macros-0:1.16.3-1.f 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] python3-devel-0:3.13.1-2.fc42.s39 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] gcc-0:15.0.0-0.2.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/5] python-rpm-macros-0:3.13-3.fc41.n 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [3/6] python3-rpm-macros-0:3.13-3.fc41. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [4/7] python3-0:3.13.1-2.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [5/8] python3-libs-0:3.13.1-2.fc42.s390 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [ 6/10] python3-chardet-0:5.2.0-14.fc41 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded 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00m00s >>> Already downloaded [18/35] expat-0:2.6.4-1.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [19/36] libb2-0:0.98.1-12.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [20/37] mpdecimal-0:2.5.1-16.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [21/47] gcc-plugin-annobin-0:15.0.0-0.2 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [22/48] python3-rpm-generators-0:14-11. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [23/49] python3-packaging-0:24.2-2.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [24/50] annobin-plugin-gcc-0:12.80-1.fc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [25/51] annobin-docs-0:12.80-1.fc42.noa 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [26/51] python3-pillow-0:11.0.0-1.fc42. 100% | 1.2 MiB/s | 1.0 MiB | 00m01s [27/51] dejavu-sans-fonts-0:2.37-24.fc4 100% | 1.5 MiB/s | 1.3 MiB | 00m01s [28/51] fonts-filesystem-1:2.0.5-17.fc4 100% | 81.6 KiB/s | 8.5 KiB | 00m00s [29/51] libimagequant-0:4.0.3-5.fc41.s3 100% | 3.0 MiB/s | 337.5 KiB | 00m00s [30/51] python3-reportlab-0:4.2.5-1.fc4 100% | 3.3 MiB/s | 3.3 MiB | 00m01s [31/51] libxcb-0:1.17.0-3.fc42.s390x 100% | 2.3 MiB/s | 250.4 KiB | 00m00s [32/51] freetype-0:2.13.3-1.fc42.s390x 100% | 13.9 MiB/s | 426.3 KiB | 00m00s [33/51] python3-olefile-0:0.47-5.fc41.n 100% | 684.1 KiB/s | 74.6 KiB | 00m00s [34/51] libjpeg-turbo-0:3.0.4-1.fc42.s3 100% | 19.8 MiB/s | 243.5 KiB | 00m00s [35/51] libraqm-0:0.10.1-1.fc42.s390x 100% | 3.6 MiB/s | 22.1 KiB | 00m00s [36/51] libtiff-0:4.7.0-2.fc42.s390x 100% | 24.8 MiB/s | 229.0 KiB | 00m00s [37/51] libXau-0:1.0.12-1.fc42.s390x 100% | 285.9 KiB/s | 32.0 KiB | 00m00s [38/51] libwebp-0:1.5.0-1.fc42.s390x 100% | 2.2 MiB/s | 250.9 KiB | 00m00s [39/51] jbigkit-libs-0:2.1-30.fc42.s390 100% | 17.5 MiB/s | 53.7 KiB | 00m00s [40/51] liblerc-0:4.0.0-7.fc42.s390x 100% | 27.2 MiB/s | 111.6 KiB | 00m00s [41/51] openjpeg-0:2.5.3-2.fc42.s390x 100% | 1.8 MiB/s | 209.5 KiB | 00m00s [42/51] fribidi-0:1.0.16-1.fc42.s390x 100% | 13.2 MiB/s | 54.1 KiB | 00m00s [43/51] harfbuzz-0:10.1.0-2.fc42.s390x 100% | 132.7 MiB/s | 1.1 MiB | 00m00s [44/51] glib2-0:2.83.0-3.fc42.s390x 100% | 129.7 MiB/s | 3.0 MiB | 00m00s [45/51] gnutls-0:3.8.8-1.fc42.s390x 100% | 49.1 MiB/s | 1.0 MiB | 00m00s [46/51] libpng-2:1.6.44-1.fc42.s390x 100% | 12.3 MiB/s | 125.6 KiB | 00m00s [47/51] graphite2-0:1.3.14-16.fc41.s390 100% | 897.1 KiB/s | 100.5 KiB | 00m00s [48/51] lcms2-0:2.16-4.fc42.s390x 100% | 517.8 KiB/s | 180.7 KiB | 00m00s [49/51] nettle-0:3.10-3.fc42.s390x 100% | 1.7 MiB/s | 445.9 KiB | 00m00s -------------------------------------------------------------------------------- [51/51] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/53] Verify package files 100% | 228.0 B/s | 51.0 B | 00m00s [ 2/53] Prepare transaction 100% | 894.0 B/s | 51.0 B | 00m00s [ 3/53] Installing python-rpm-macros-0: 100% | 0.0 B/s | 22.8 KiB | 00m00s [ 4/53] Installing python3-rpm-macros-0 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Installing freetype-0:2.13.3-1. 100% | 222.0 MiB/s | 909.3 KiB | 00m00s [18/53] Installing fribidi-0:1.0.16-1.f 100% | 189.4 MiB/s | 193.9 KiB | 00m00s [19/53] Installing libraqm-0:0.10.1-1.f 100% | 0.0 B/s | 32.3 KiB | 00m00s [20/53] Installing liblerc-0:4.0.0-7.fc 100% | 257.0 MiB/s | 263.2 KiB | 00m00s [21/53] Installing jbigkit-libs-0:2.1-3 100% | 113.7 MiB/s | 116.4 KiB | 00m00s [22/53] Installing libtiff-0:4.7.0-2.fc 100% | 211.7 MiB/s | 650.3 KiB | 00m00s [23/53] Installing mpdecimal-0:2.5.1-16 100% | 211.8 MiB/s | 216.8 KiB | 00m00s [24/53] Installing libb2-0:0.98.1-12.fc 100% | 0.0 B/s | 41.7 KiB | 00m00s [25/53] Installing expat-0:2.6.4-1.fc42 100% | 294.3 MiB/s | 301.4 KiB | 00m00s [26/53] Installing openjpeg-0:2.5.3-2.f 100% | 234.9 MiB/s | 481.1 KiB | 00m00s [27/53] Installing lcms2-0:2.16-4.fc42. 100% | 217.5 MiB/s | 445.5 KiB | 00m00s [28/53] Installing make-1:4.4.1-9.fc42. 100% | 264.8 MiB/s | 1.9 MiB | 00m00s [29/53] Installing libubsan-0:15.0.0-0. 100% | 235.0 MiB/s | 481.4 KiB | 00m00s [30/53] Installing libatomic-0:15.0.0-0 100% | 0.0 B/s | 26.9 KiB | 00m00s [31/53] Installing libasan-0:15.0.0-0.2 100% | 198.9 MiB/s | 1.6 MiB | 00m00s [32/53] Installing kernel-headers-0:6.1 100% | 194.9 MiB/s | 6.6 MiB | 00m00s [33/53] Installing libxcrypt-devel-0:4. 100% | 16.0 MiB/s | 32.9 KiB | 00m00s [34/53] Installing glibc-devel-0:2.40.9 100% | 188.7 MiB/s | 2.6 MiB | 00m00s [35/53] Installing gcc-0:15.0.0-0.2.fc4 100% | 326.1 MiB/s | 79.2 MiB | 00m00s [36/53] Installing libXau-0:1.0.12-1.fc 100% | 67.5 MiB/s | 69.1 KiB | 00m00s [37/53] Installing libxcb-0:1.17.0-3.fc 100% | 207.6 MiB/s | 1.2 MiB | 00m00s [38/53] Installing libimagequant-0:4.0. 100% | 272.6 MiB/s | 837.5 KiB | 00m00s [39/53] Installing fonts-filesystem-1:2 100% | 0.0 B/s | 788.0 B | 00m00s [40/53] Installing dejavu-sans-fonts-0: 100% | 250.4 MiB/s | 5.5 MiB | 00m00s [41/53] Installing tzdata-0:2024b-1.fc4 100% | 57.1 MiB/s | 1.9 MiB | 00m00s [42/53] Installing python-pip-wheel-0:2 100% | 155.5 MiB/s | 1.2 MiB | 00m00s [43/53] Installing python3-libs-0:3.13. 100% | 290.7 MiB/s | 40.4 MiB | 00m00s [44/53] Installing python3-0:3.13.1-2.f 100% | 23.6 MiB/s | 24.2 KiB | 00m00s [45/53] Installing python3-chardet-0:5. 100% | 262.0 MiB/s | 2.1 MiB | 00m00s [46/53] Installing python3-olefile-0:0. 100% | 167.8 MiB/s | 343.6 KiB | 00m00s [47/53] Installing python3-pillow-0:11. 100% | 256.4 MiB/s | 4.1 MiB | 00m00s [48/53] Installing python3-packaging-0: 100% | 184.9 MiB/s | 568.0 KiB | 00m00s [49/53] Installing python3-rpm-generato 100% | 81.0 MiB/s | 82.9 KiB | 00m00s [50/53] Installing python3-devel-0:3.13 100% | 165.0 MiB/s | 1.8 MiB | 00m00s [51/53] Installing python3-reportlab-0: 100% | 291.1 MiB/s | 11.1 MiB | 00m00s [52/53] Installing gcc-plugin-annobin-0 100% | 5.2 MiB/s | 52.9 KiB | 00m00s [53/53] Installing annobin-plugin-gcc-0 100% | 8.9 MiB/s | 990.2 KiB | 00m00s Warning: skipped OpenPGP checks for 25 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch Complete! Finish: build setup for python-biopython-1.84-3.fc42.src.rpm Start: rpmbuild python-biopython-1.84-3.fc42.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.HNbuaa + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + test -d /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/rm -rf /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.84-build + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.1Ivhyl + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd /builddir/build/BUILD/python-biopython-1.84-build + rm -rf biopython-1.84 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.84.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd biopython-1.84 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-biopython-1.84-replace_deprecated_function.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.XwO3bU + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement not satisfied: setuptools >= 40.8 Exiting dependency generation pass: build backend + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 5.6 KiB/s | 3.8 KiB | 00m01s Copr repository 100% | 4.6 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 4.4 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.s390x" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.s390x" is already installed. Package "python3-packaging-24.2-2.fc42.noarch" is already installed. Package "python3-reportlab-4.2.5-1.fc42.noarch" is already installed. Package Arch Version Repository Size Installing: python3-pip noarch 24.3.1-1.fc42 fedora 11.3 MiB python3-setuptools noarch 74.1.3-4.fc42 fedora 8.4 MiB Transaction Summary: Installing: 2 packages Total size of inbound packages is 5 MiB. Need to download 0 B. After this operation, 20 MiB extra will be used (install 20 MiB, remove 0 B). [1/1] python3-pip-0:24.3.1-1.fc42.noarc 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] python3-setuptools-0:74.1.3-4.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [1/4] Verify package files 100% | 142.0 B/s | 2.0 B | 00m00s [2/4] Prepare transaction 100% | 71.0 B/s | 2.0 B | 00m00s [3/4] Installing python3-setuptools-0:7 100% | 186.1 MiB/s | 8.6 MiB | 00m00s [4/4] Installing python3-pip-0:24.3.1-1 100% | 159.1 MiB/s | 11.6 MiB | 00m00s Complete! Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.TtyYNt + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) 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 'Doc/_build' 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' 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 'Doc/_build' 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/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement not satisfied: numpy + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: Additional repo https_fedorapeople_org 100% | 4.6 KiB/s | 1.5 KiB | 00m00s fedora 100% | 10.8 KiB/s | 3.8 KiB | 00m00s Copr repository 100% | 12.7 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.s390x" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.s390x" is already installed. Package "python3-packaging-24.2-2.fc42.noarch" is already installed. Package "python3-pip-24.3.1-1.fc42.noarch" is already installed. Package "python3-reportlab-4.2.5-1.fc42.noarch" is already installed. Package "python3-setuptools-74.1.3-4.fc42.noarch" is already installed. Package Arch Version Repository Size Installing: python3-numpy s390x 1:2.2.1-1.fc42 fedora 36.0 MiB Installing dependencies: flexiblas s390x 3.4.4-3.fc42 copr_base 48.5 KiB flexiblas-netlib s390x 3.4.4-3.fc42 copr_base 12.3 MiB flexiblas-openblas-openmp s390x 3.4.4-3.fc42 copr_base 38.0 KiB libgfortran s390x 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 2.4 MiB openblas s390x 0.3.28-2.fc42 copr_base 106.6 KiB openblas-openmp s390x 0.3.28-2.fc42 copr_base 15.2 MiB python3-numpy-f2py s390x 1:2.2.1-1.fc42 fedora 2.0 MiB Transaction Summary: Installing: 8 packages Total size of inbound packages is 16 MiB. Need to download 0 B. After this operation, 68 MiB extra will be used (install 68 MiB, remove 0 B). [1/1] python3-numpy-1:2.2.1-1.fc42.s390 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [1/1] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/2] python3-numpy-f2py-1:2.2.1-1.fc42 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [2/2] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/3] flexiblas-netlib-0:3.4.4-3.fc42.s 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [3/3] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/4] flexiblas-0:3.4.4-3.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [4/4] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/5] flexiblas-openblas-openmp-0:3.4.4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [5/5] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/6] openblas-openmp-0:0.3.28-2.fc42.s 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [6/6] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/7] libgfortran-0:15.0.0-0.2.fc42.s39 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [7/7] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/8] openblas-0:0.3.28-2.fc42.s390x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [8/8] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/10] Verify package files 100% | 153.0 B/s | 8.0 B | 00m00s [ 2/10] Prepare transaction 100% | 222.0 B/s | 8.0 B | 00m00s [ 3/10] Installing libgfortran-0:15.0.0 100% | 299.8 MiB/s | 2.4 MiB | 00m00s [ 4/10] Installing openblas-0:0.3.28-2. 100% | 0.0 B/s | 108.3 KiB | 00m00s [ 5/10] Installing openblas-openmp-0:0. 100% | 316.0 MiB/s | 15.2 MiB | 00m00s [ 6/10] Installing flexiblas-0:3.4.4-3. 100% | 0.0 B/s | 49.7 KiB | 00m00s [ 7/10] Installing flexiblas-openblas-o 100% | 0.0 B/s | 38.9 KiB | 00m00s [ 8/10] Installing flexiblas-netlib-0:3 100% | 307.2 MiB/s | 12.3 MiB | 00m00s [ 9/10] Installing python3-numpy-f2py-1 100% | 137.8 MiB/s | 2.1 MiB | 00m00s [10/10] Installing python3-numpy-1:2.2. 100% | 286.0 MiB/s | 36.3 MiB | 00m00s Warning: skipped OpenPGP checks for 6 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch Complete! Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.ZuRaoi + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) 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 'Doc/_build' 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' 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 'Doc/_build' 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/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 2.2.1) + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires Updating and loading repositories: fedora 100% | 6.9 KiB/s | 3.8 KiB | 00m01s Additional repo https_fedorapeople_org 100% | 4.4 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 12.1 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.s390x" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.s390x" is already installed. Package "python3-numpy-1:2.2.1-1.fc42.s390x" is already installed. Package "python3-packaging-24.2-2.fc42.noarch" is already installed. Package "python3-pip-24.3.1-1.fc42.noarch" is already installed. Package "python3-reportlab-4.2.5-1.fc42.noarch" is already installed. Package "python3-setuptools-74.1.3-4.fc42.noarch" is already installed. Nothing to do. Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.NNUozC + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + cd biopython-1.84 + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(packaging)' + echo 'python3dist(pip) >= 19' + '[' -f pyproject.toml ']' + '[' -f setup.py ']' + echo 'python3dist(setuptools) >= 40.8' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + RPM_TOXENV=py313 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires -x tests Handling setuptools >= 40.8 from default build backend Requirement satisfied: setuptools >= 40.8 (installed: setuptools 74.1.3) 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 'Doc/_build' 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' 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 'Doc/_build' 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/python-biopython-1.84-build/biopython-1.84/biopython-1.84.dist-info' Handling numpy from hook generated metadata: Requires-Dist (biopython) Requirement satisfied: numpy (installed: numpy 2.2.1) + cat /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-buildrequires + rm -rfv biopython-1.84.dist-info/ removed 'biopython-1.84.dist-info/top_level.txt' removed 'biopython-1.84.dist-info/METADATA' removed 'biopython-1.84.dist-info/LICENSE' removed 'biopython-1.84.dist-info/LICENSE.rst' removed directory 'biopython-1.84.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.iN1NH7 + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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 -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-1.84 + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + LT_SYS_LIBRARY_PATH=/usr/lib64: + CC=gcc + CXX=g++ + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir Processing /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info writing /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/dependency_links.txt writing requirements to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Doc/_build' 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/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-fj2mcxr0/biopython-1.84.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-s390x-cpython-313 creating build/lib.linux-s390x-cpython-313/Bio copying Bio/File.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/LogisticRegression.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/MarkovModel.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/MaxEntropy.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/NaiveBayes.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/Seq.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/SeqFeature.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/SeqRecord.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/__init__.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/_utils.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/bgzf.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/kNN.py -> build/lib.linux-s390x-cpython-313/Bio copying Bio/pairwise2.py -> build/lib.linux-s390x-cpython-313/Bio creating build/lib.linux-s390x-cpython-313/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-s390x-cpython-313/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Affy creating build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-s390x-cpython-313/Bio/Align creating build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Align/Applications creating build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices creating build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/AlignIO creating build/lib.linux-s390x-cpython-313/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Alphabet creating build/lib.linux-s390x-cpython-313/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Application creating build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/_parser.py -> build/lib.linux-s390x-cpython-313/Bio/Blast copying Bio/Blast/_writers.py -> build/lib.linux-s390x-cpython-313/Bio/Blast creating build/lib.linux-s390x-cpython-313/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/CAPS creating build/lib.linux-s390x-cpython-313/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Cluster creating build/lib.linux-s390x-cpython-313/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-s390x-cpython-313/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-s390x-cpython-313/Bio/codonalign creating build/lib.linux-s390x-cpython-313/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Compass creating build/lib.linux-s390x-cpython-313/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-s390x-cpython-313/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-s390x-cpython-313/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-s390x-cpython-313/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Data creating build/lib.linux-s390x-cpython-313/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-s390x-cpython-313/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-s390x-cpython-313/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-s390x-cpython-313/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Emboss creating build/lib.linux-s390x-cpython-313/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-s390x-cpython-313/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Entrez creating build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-s390x-cpython-313/Bio/ExPASy creating build/lib.linux-s390x-cpython-313/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-s390x-cpython-313/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-s390x-cpython-313/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-s390x-cpython-313/Bio/GenBank creating build/lib.linux-s390x-cpython-313/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-s390x-cpython-313/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Geo creating build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics creating build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram creating build/lib.linux-s390x-cpython-313/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-s390x-cpython-313/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-s390x-cpython-313/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-s390x-cpython-313/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-s390x-cpython-313/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/HMM creating build/lib.linux-s390x-cpython-313/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG creating build/lib.linux-s390x-cpython-313/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/Compound creating build/lib.linux-s390x-cpython-313/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/Enzyme creating build/lib.linux-s390x-cpython-313/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/Gene creating build/lib.linux-s390x-cpython-313/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/Map creating build/lib.linux-s390x-cpython-313/Bio/PDB creating build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf creating build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML creating build/lib.linux-s390x-cpython-313/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Medline creating build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-s390x-cpython-313/Bio/motifs creating build/lib.linux-s390x-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-s390x-cpython-313/Bio/motifs/applications creating build/lib.linux-s390x-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-s390x-cpython-313/Bio/motifs/jaspar creating build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Nexus creating build/lib.linux-s390x-cpython-313/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-s390x-cpython-313/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-s390x-cpython-313/Bio/NMR creating build/lib.linux-s390x-cpython-313/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Pathway creating build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PDBMLParser.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/alphafold_db.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/binary_cif.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-s390x-cpython-313/Bio/PDB creating build/lib.linux-s390x-cpython-313/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-s390x-cpython-313/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-s390x-cpython-313/Bio/phenotype creating build/lib.linux-s390x-cpython-313/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen creating build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop creating build/lib.linux-s390x-cpython-313/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-s390x-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-s390x-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-s390x-cpython-313/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Restriction creating build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SCOP creating build/lib.linux-s390x-cpython-313/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HHsuiteIO creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO creating build/lib.linux-s390x-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-s390x-cpython-313/Bio/SearchIO/InterproscanIO creating build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/GfaIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-s390x-cpython-313/Bio/SeqIO creating build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-s390x-cpython-313/Bio/SeqUtils creating build/lib.linux-s390x-cpython-313/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing creating build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications creating build/lib.linux-s390x-cpython-313/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SVDSuperimposer creating build/lib.linux-s390x-cpython-313/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-s390x-cpython-313/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/SwissProt creating build/lib.linux-s390x-cpython-313/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/TogoWS creating build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo creating build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications creating build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML creating build/lib.linux-s390x-cpython-313/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/UniGene creating build/lib.linux-s390x-cpython-313/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-s390x-cpython-313/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-s390x-cpython-313/Bio/UniProt creating build/lib.linux-s390x-cpython-313/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-s390x-cpython-313/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-s390x-cpython-313/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-s390x-cpython-313/BioSQL copying BioSQL/Loader.py -> build/lib.linux-s390x-cpython-313/BioSQL copying BioSQL/__init__.py -> build/lib.linux-s390x-cpython-313/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 'Doc/_build' 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/python3.13/site-packages/setuptools/command/build_py.py:218: _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/python3.13/site-packages/setuptools/command/build_py.py:218: _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/python3.13/site-packages/setuptools/command/build_py.py:218: _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-s390x-cpython-313/Bio copying Bio/py.typed -> build/lib.linux-s390x-cpython-313/Bio copying Bio/Align/_aligncore.c -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/_codonaligner.c -> build/lib.linux-s390x-cpython-313/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-s390x-cpython-313/Bio/Align creating build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-s390x-cpython-313/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-s390x-cpython-313/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-s390x-cpython-313/Bio/Cluster creating build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs creating build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-s390x-cpython-313/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-s390x-cpython-313/Bio/Nexus copying Bio/PDB/bcifhelpermodule.c -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/ccealignmodule.c -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-s390x-cpython-313/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-s390x-cpython-313/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-s390x-cpython-313/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-s390x-cpython-313 creating build/temp.linux-s390x-cpython-313/Bio creating build/temp.linux-s390x-cpython-313/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Align/_codonaligner.c -o build/temp.linux-s390x-cpython-313/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/Align/_codonaligner.cpython-313-s390x-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-s390x-cpython-313/Bio/Align/_pairwisealigner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/Align/_pairwisealigner.cpython-313-s390x-linux-gnu.so building 'Bio.Align._aligncore' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Align/_aligncore.c -o build/temp.linux-s390x-cpython-313/Bio/Align/_aligncore.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/Align/_aligncore.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/Align/_aligncore.cpython-313-s390x-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/cpairwise2module.c -o build/temp.linux-s390x-cpython-313/Bio/cpairwise2module.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/cpairwise2.cpython-313-s390x-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-s390x-cpython-313/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Nexus/cnexus.c -o build/temp.linux-s390x-cpython-313/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/Nexus/cnexus.cpython-313-s390x-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-s390x-cpython-313/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/motifs/_pwm.c -o build/temp.linux-s390x-cpython-313/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/motifs/_pwm.cpython-313-s390x-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-s390x-cpython-313/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Cluster/cluster.c -o build/temp.linux-s390x-cpython-313/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/Cluster/clustermodule.c -o build/temp.linux-s390x-cpython-313/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/Cluster/cluster.o build/temp.linux-s390x-cpython-313/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/Cluster/_cluster.cpython-313-s390x-linux-gnu.so building 'Bio.PDB.ccealign' extension creating build/temp.linux-s390x-cpython-313/Bio/PDB gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-s390x-cpython-313/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/PDB/ccealign.cpython-313-s390x-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/PDB/kdtrees.c -o build/temp.linux-s390x-cpython-313/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/PDB/kdtrees.cpython-313-s390x-linux-gnu.so building 'Bio.PDB._bcif_helper' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/PDB/bcifhelpermodule.c -o build/temp.linux-s390x-cpython-313/Bio/PDB/bcifhelpermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/PDB/bcifhelpermodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/PDB/_bcif_helper.cpython-313-s390x-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-s390x-cpython-313/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fexceptions -fexceptions -O3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.13 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-s390x-cpython-313/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-313/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-s390x-linux-gnu.so installing to build/bdist.linux-s390x/wheel running install running install_lib creating build/bdist.linux-s390x creating build/bdist.linux-s390x/wheel creating build/bdist.linux-s390x/wheel/Bio copying build/lib.linux-s390x-cpython-313/Bio/File.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/LogisticRegression.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/MarkovModel.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/MaxEntropy.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/NaiveBayes.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/Seq.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/SeqFeature.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/SeqRecord.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/__init__.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/_utils.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/bgzf.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/kNN.py -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/pairwise2.py -> build/bdist.linux-s390x/wheel/./Bio creating build/bdist.linux-s390x/wheel/Bio/Affy copying build/lib.linux-s390x-cpython-313/Bio/Affy/CelFile.py -> build/bdist.linux-s390x/wheel/./Bio/Affy copying build/lib.linux-s390x-cpython-313/Bio/Affy/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Affy creating build/bdist.linux-s390x/wheel/Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/AlignInfo.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/a2m.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/analysis.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/bed.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/bigbed.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/bigmaf.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/bigpsl.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/chain.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/clustal.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/emboss.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/exonerate.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/fasta.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/hhr.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/interfaces.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/maf.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/mauve.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/msf.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/nexus.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/phylip.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/psl.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/sam.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/stockholm.py -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/tabular.py -> build/bdist.linux-s390x/wheel/./Bio/Align creating build/bdist.linux-s390x/wheel/Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Prank.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications copying build/lib.linux-s390x-cpython-313/Bio/Align/Applications/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Align/Applications creating build/bdist.linux-s390x/wheel/Bio/Align/substitution_matrices copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices creating build/bdist.linux-s390x/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/NUC.4.4 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-s390x/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-313/Bio/Align/_aligncore.c -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/_codonaligner.c -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/_pairwisealigner.c -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/_codonaligner.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/_pairwisealigner.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/Align copying build/lib.linux-s390x-cpython-313/Bio/Align/_aligncore.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/Align creating build/bdist.linux-s390x/wheel/Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/FastaIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/Interfaces.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/MafIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/MauveIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/MsfIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/NexusIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO copying build/lib.linux-s390x-cpython-313/Bio/AlignIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/AlignIO creating build/bdist.linux-s390x/wheel/Bio/Alphabet copying build/lib.linux-s390x-cpython-313/Bio/Alphabet/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Alphabet creating build/bdist.linux-s390x/wheel/Bio/Application copying build/lib.linux-s390x-cpython-313/Bio/Application/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Application creating build/bdist.linux-s390x/wheel/Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/Applications.py -> build/bdist.linux-s390x/wheel/./Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/NCBIWWW.py -> build/bdist.linux-s390x/wheel/./Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/NCBIXML.py -> build/bdist.linux-s390x/wheel/./Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/_parser.py -> build/bdist.linux-s390x/wheel/./Bio/Blast copying build/lib.linux-s390x-cpython-313/Bio/Blast/_writers.py -> build/bdist.linux-s390x/wheel/./Bio/Blast creating build/bdist.linux-s390x/wheel/Bio/CAPS copying build/lib.linux-s390x-cpython-313/Bio/CAPS/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/CAPS creating build/bdist.linux-s390x/wheel/Bio/Cluster copying build/lib.linux-s390x-cpython-313/Bio/Cluster/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Cluster copying build/lib.linux-s390x-cpython-313/Bio/Cluster/cluster.c -> build/bdist.linux-s390x/wheel/./Bio/Cluster copying build/lib.linux-s390x-cpython-313/Bio/Cluster/cluster.h -> build/bdist.linux-s390x/wheel/./Bio/Cluster copying build/lib.linux-s390x-cpython-313/Bio/Cluster/clustermodule.c -> build/bdist.linux-s390x/wheel/./Bio/Cluster copying build/lib.linux-s390x-cpython-313/Bio/Cluster/_cluster.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/Cluster creating build/bdist.linux-s390x/wheel/Bio/codonalign copying build/lib.linux-s390x-cpython-313/Bio/codonalign/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/codonalign copying build/lib.linux-s390x-cpython-313/Bio/codonalign/codonalignment.py -> build/bdist.linux-s390x/wheel/./Bio/codonalign copying build/lib.linux-s390x-cpython-313/Bio/codonalign/codonseq.py -> build/bdist.linux-s390x/wheel/./Bio/codonalign creating build/bdist.linux-s390x/wheel/Bio/Compass copying build/lib.linux-s390x-cpython-313/Bio/Compass/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Compass creating build/bdist.linux-s390x/wheel/Bio/Data copying build/lib.linux-s390x-cpython-313/Bio/Data/CodonTable.py -> build/bdist.linux-s390x/wheel/./Bio/Data copying build/lib.linux-s390x-cpython-313/Bio/Data/IUPACData.py -> build/bdist.linux-s390x/wheel/./Bio/Data copying build/lib.linux-s390x-cpython-313/Bio/Data/PDBData.py -> build/bdist.linux-s390x/wheel/./Bio/Data copying build/lib.linux-s390x-cpython-313/Bio/Data/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Data creating build/bdist.linux-s390x/wheel/Bio/Emboss copying build/lib.linux-s390x-cpython-313/Bio/Emboss/Applications.py -> build/bdist.linux-s390x/wheel/./Bio/Emboss copying build/lib.linux-s390x-cpython-313/Bio/Emboss/Primer3.py -> build/bdist.linux-s390x/wheel/./Bio/Emboss copying build/lib.linux-s390x-cpython-313/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-s390x/wheel/./Bio/Emboss copying build/lib.linux-s390x-cpython-313/Bio/Emboss/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Emboss creating build/bdist.linux-s390x/wheel/Bio/Entrez copying build/lib.linux-s390x-cpython-313/Bio/Entrez/Parser.py -> build/bdist.linux-s390x/wheel/./Bio/Entrez copying build/lib.linux-s390x-cpython-313/Bio/Entrez/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Entrez creating build/bdist.linux-s390x/wheel/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/EMBL_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/GenBank_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/HomoloGene.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-common1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-display1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-format1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-link1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Project.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NSE.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/NSE.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/OMSSA.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PDB_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PIR_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PRF_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/SP_General.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/SP_General.mod.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/archivearticle.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/archivecustom-classes.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/archivecustom-models.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/archivecustom-modules.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/articlemeta.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/backmatter.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/chars.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/common.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/default-classes.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/default-mixes.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/display.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eInfo_020511.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eLink_090910.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eLink_101123.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eSearch_020511.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eSpell.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/eSummary_041029.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/egquery.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/einfo.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/elink.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/epost.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/esearch.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/esummary-v1.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/esummary_gene.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/format.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/htmltable.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamsa.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamsb.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamsc.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamsn.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamso.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isoamsr.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isobox.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isocyr1.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isocyr2.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isogrk1.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isogrk2.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isogrk3.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isolat1.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-s390x/wheel/./Bio/Entrez/DTDs creating build/bdist.linux-s390x/wheel/Bio/Entrez/XSDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/XSDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/XSDs copying build/lib.linux-s390x-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/bdist.linux-s390x/wheel/./Bio/Entrez/XSDs creating build/bdist.linux-s390x/wheel/Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/Enzyme.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/Prodoc.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/Prosite.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy copying build/lib.linux-s390x-cpython-313/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-s390x/wheel/./Bio/ExPASy creating build/bdist.linux-s390x/wheel/Bio/GenBank copying build/lib.linux-s390x-cpython-313/Bio/GenBank/Record.py -> build/bdist.linux-s390x/wheel/./Bio/GenBank copying build/lib.linux-s390x-cpython-313/Bio/GenBank/Scanner.py -> build/bdist.linux-s390x/wheel/./Bio/GenBank copying build/lib.linux-s390x-cpython-313/Bio/GenBank/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/GenBank copying build/lib.linux-s390x-cpython-313/Bio/GenBank/utils.py -> build/bdist.linux-s390x/wheel/./Bio/GenBank creating build/bdist.linux-s390x/wheel/Bio/Geo copying build/lib.linux-s390x-cpython-313/Bio/Geo/Record.py -> build/bdist.linux-s390x/wheel/./Bio/Geo copying build/lib.linux-s390x-cpython-313/Bio/Geo/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Geo creating build/bdist.linux-s390x/wheel/Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/Comparative.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/Distribution.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/KGML_vis.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics copying build/lib.linux-s390x-cpython-313/Bio/Graphics/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics creating build/bdist.linux-s390x/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-313/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Graphics/GenomeDiagram creating build/bdist.linux-s390x/wheel/Bio/HMM copying build/lib.linux-s390x-cpython-313/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-s390x/wheel/./Bio/HMM copying build/lib.linux-s390x-cpython-313/Bio/HMM/MarkovModel.py -> build/bdist.linux-s390x/wheel/./Bio/HMM copying build/lib.linux-s390x-cpython-313/Bio/HMM/Trainer.py -> build/bdist.linux-s390x/wheel/./Bio/HMM copying build/lib.linux-s390x-cpython-313/Bio/HMM/Utilities.py -> build/bdist.linux-s390x/wheel/./Bio/HMM copying build/lib.linux-s390x-cpython-313/Bio/HMM/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/HMM creating build/bdist.linux-s390x/wheel/Bio/KEGG copying build/lib.linux-s390x-cpython-313/Bio/KEGG/REST.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG copying build/lib.linux-s390x-cpython-313/Bio/KEGG/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG creating build/bdist.linux-s390x/wheel/Bio/KEGG/Compound copying build/lib.linux-s390x-cpython-313/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/Compound creating build/bdist.linux-s390x/wheel/Bio/KEGG/Enzyme copying build/lib.linux-s390x-cpython-313/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/Enzyme creating build/bdist.linux-s390x/wheel/Bio/KEGG/Gene copying build/lib.linux-s390x-cpython-313/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/Gene creating build/bdist.linux-s390x/wheel/Bio/KEGG/Map copying build/lib.linux-s390x-cpython-313/Bio/KEGG/Map/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/Map creating build/bdist.linux-s390x/wheel/Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-313/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/KEGG/KGML creating build/bdist.linux-s390x/wheel/Bio/PDB creating build/bdist.linux-s390x/wheel/Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-s390x/wheel/./Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-313/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-s390x/wheel/./Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-313/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Atom.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Chain.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/DSSP.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Dice.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Entity.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/FragmentMapper.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/HSExposure.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/MMCIFParser.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Model.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/NACCESS.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/NeighborSearch.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PDBExceptions.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PDBIO.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PDBList.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PDBMLParser.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PDBParser.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PICIO.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/PSEA.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Polypeptide.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Residue.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/ResidueDepth.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/SASA.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/SCADIO.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Selection.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Structure.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/StructureAlignment.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/StructureBuilder.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/Superimposer.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/alphafold_db.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/binary_cif.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/cealign.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/ic_data.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/ic_rebuild.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/internal_coords.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/mmcifio.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/qcprot.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/vectors.py -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/bcifhelpermodule.c -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/ccealignmodule.c -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/kdtrees.c -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/ccealign.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/kdtrees.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/PDB copying build/lib.linux-s390x-cpython-313/Bio/PDB/_bcif_helper.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/PDB creating build/bdist.linux-s390x/wheel/Bio/Medline copying build/lib.linux-s390x-cpython-313/Bio/Medline/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Medline creating build/bdist.linux-s390x/wheel/Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/alignace.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/clusterbuster.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/mast.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/matrix.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/meme.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/minimal.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/pfm.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/thresholds.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/transfac.py -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/xms.py -> build/bdist.linux-s390x/wheel/./Bio/motifs creating build/bdist.linux-s390x/wheel/Bio/motifs/applications copying build/lib.linux-s390x-cpython-313/Bio/motifs/applications/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/motifs/applications copying build/lib.linux-s390x-cpython-313/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-s390x/wheel/./Bio/motifs/applications creating build/bdist.linux-s390x/wheel/Bio/motifs/jaspar copying build/lib.linux-s390x-cpython-313/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/motifs/jaspar copying build/lib.linux-s390x-cpython-313/Bio/motifs/jaspar/db.py -> build/bdist.linux-s390x/wheel/./Bio/motifs/jaspar copying build/lib.linux-s390x-cpython-313/Bio/motifs/_pwm.c -> build/bdist.linux-s390x/wheel/./Bio/motifs copying build/lib.linux-s390x-cpython-313/Bio/motifs/_pwm.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/motifs creating build/bdist.linux-s390x/wheel/Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/Nexus.py -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/Nodes.py -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/StandardData.py -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/Trees.py -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/cnexus.c -> build/bdist.linux-s390x/wheel/./Bio/Nexus copying build/lib.linux-s390x-cpython-313/Bio/Nexus/cnexus.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/Nexus creating build/bdist.linux-s390x/wheel/Bio/NMR copying build/lib.linux-s390x-cpython-313/Bio/NMR/NOEtools.py -> build/bdist.linux-s390x/wheel/./Bio/NMR copying build/lib.linux-s390x-cpython-313/Bio/NMR/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/NMR copying build/lib.linux-s390x-cpython-313/Bio/NMR/xpktools.py -> build/bdist.linux-s390x/wheel/./Bio/NMR creating build/bdist.linux-s390x/wheel/Bio/Pathway copying build/lib.linux-s390x-cpython-313/Bio/Pathway/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Pathway creating build/bdist.linux-s390x/wheel/Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-s390x/wheel/./Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-s390x/wheel/./Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-313/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Pathway/Rep creating build/bdist.linux-s390x/wheel/Bio/phenotype copying build/lib.linux-s390x-cpython-313/Bio/phenotype/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/phenotype copying build/lib.linux-s390x-cpython-313/Bio/phenotype/phen_micro.py -> build/bdist.linux-s390x/wheel/./Bio/phenotype copying build/lib.linux-s390x-cpython-313/Bio/phenotype/pm_fitting.py -> build/bdist.linux-s390x/wheel/./Bio/phenotype creating build/bdist.linux-s390x/wheel/Bio/PopGen copying build/lib.linux-s390x-cpython-313/Bio/PopGen/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen creating build/bdist.linux-s390x/wheel/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-313/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/PopGen/GenePop creating build/bdist.linux-s390x/wheel/Bio/Restriction copying build/lib.linux-s390x-cpython-313/Bio/Restriction/PrintFormat.py -> build/bdist.linux-s390x/wheel/./Bio/Restriction copying build/lib.linux-s390x-cpython-313/Bio/Restriction/Restriction.py -> build/bdist.linux-s390x/wheel/./Bio/Restriction copying build/lib.linux-s390x-cpython-313/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-s390x/wheel/./Bio/Restriction copying build/lib.linux-s390x-cpython-313/Bio/Restriction/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Restriction creating build/bdist.linux-s390x/wheel/Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Cla.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Des.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Dom.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Hie.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Raf.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/Residues.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP copying build/lib.linux-s390x-cpython-313/Bio/SCOP/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SCOP creating build/bdist.linux-s390x/wheel/Bio/SearchIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlatIO.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/FastaIO.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_index.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_utils.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO creating build/bdist.linux-s390x/wheel/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model/_base.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model/hit.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/_model/query.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/_model creating build/bdist.linux-s390x/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/BlastIO creating build/bdist.linux-s390x/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HHsuiteIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HHsuiteIO creating build/bdist.linux-s390x/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/HmmerIO creating build/bdist.linux-s390x/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/ExonerateIO creating build/bdist.linux-s390x/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/InterproscanIO copying build/lib.linux-s390x-cpython-313/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-s390x/wheel/./Bio/SearchIO/InterproscanIO creating build/bdist.linux-s390x/wheel/Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/AbiIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/AceIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/FastaIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/GckIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/GfaIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/IgIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/Interfaces.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/NibIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/PdbIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/PhdIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/PirIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/QualityIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/SffIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/SwissIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/TabIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/_index.py -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-s390x/wheel/./Bio/SeqIO copying build/lib.linux-s390x-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio/SeqIO creating build/bdist.linux-s390x/wheel/Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils copying build/lib.linux-s390x-cpython-313/Bio/SeqUtils/lcc.py -> build/bdist.linux-s390x/wheel/./Bio/SeqUtils creating build/bdist.linux-s390x/wheel/Bio/Sequencing copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Ace.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Phd.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing creating build/bdist.linux-s390x/wheel/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-313/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-s390x/wheel/./Bio/Sequencing/Applications creating build/bdist.linux-s390x/wheel/Bio/SVDSuperimposer copying build/lib.linux-s390x-cpython-313/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SVDSuperimposer creating build/bdist.linux-s390x/wheel/Bio/SwissProt copying build/lib.linux-s390x-cpython-313/Bio/SwissProt/KeyWList.py -> build/bdist.linux-s390x/wheel/./Bio/SwissProt copying build/lib.linux-s390x-cpython-313/Bio/SwissProt/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/SwissProt creating build/bdist.linux-s390x/wheel/Bio/TogoWS copying build/lib.linux-s390x-cpython-313/Bio/TogoWS/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/TogoWS creating build/bdist.linux-s390x/wheel/Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/BaseTree.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/CDAO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/CDAOIO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Consensus.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/NeXML.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Newick.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/NewickIO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/NexusIO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PhyloXML.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/_io.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo copying build/lib.linux-s390x-cpython-313/Bio/Phylo/_utils.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo creating build/bdist.linux-s390x/wheel/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-313/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/Applications creating build/bdist.linux-s390x/wheel/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-313/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-s390x/wheel/./Bio/Phylo/PAML creating build/bdist.linux-s390x/wheel/Bio/UniGene copying build/lib.linux-s390x-cpython-313/Bio/UniGene/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/UniGene creating build/bdist.linux-s390x/wheel/Bio/UniProt copying build/lib.linux-s390x-cpython-313/Bio/UniProt/GOA.py -> build/bdist.linux-s390x/wheel/./Bio/UniProt copying build/lib.linux-s390x-cpython-313/Bio/UniProt/__init__.py -> build/bdist.linux-s390x/wheel/./Bio/UniProt copying build/lib.linux-s390x-cpython-313/Bio/cpairwise2module.c -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/py.typed -> build/bdist.linux-s390x/wheel/./Bio copying build/lib.linux-s390x-cpython-313/Bio/cpairwise2.cpython-313-s390x-linux-gnu.so -> build/bdist.linux-s390x/wheel/./Bio creating build/bdist.linux-s390x/wheel/BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/BioSeq.py -> build/bdist.linux-s390x/wheel/./BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/BioSeqDatabase.py -> build/bdist.linux-s390x/wheel/./BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/DBUtils.py -> build/bdist.linux-s390x/wheel/./BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/Loader.py -> build/bdist.linux-s390x/wheel/./BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/__init__.py -> build/bdist.linux-s390x/wheel/./BioSQL copying build/lib.linux-s390x-cpython-313/BioSQL/py.typed -> build/bdist.linux-s390x/wheel/./BioSQL running install_egg_info Copying biopython.egg-info to build/bdist.linux-s390x/wheel/./biopython-1.84-py3.13.egg-info running install_scripts creating build/bdist.linux-s390x/wheel/biopython-1.84.dist-info/WHEEL creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-wheel-xl7zgxaj/.tmp-8_6bsk46/biopython-1.84-cp313-cp313-linux_s390x.whl' and adding 'build/bdist.linux-s390x/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-313-s390x-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/_aligncore.c' adding 'Bio/Align/_aligncore.cpython-313-s390x-linux-gnu.so' adding 'Bio/Align/_codonaligner.c' adding 'Bio/Align/_codonaligner.cpython-313-s390x-linux-gnu.so' adding 'Bio/Align/_pairwisealigner.c' adding 'Bio/Align/_pairwisealigner.cpython-313-s390x-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/__init__.py' adding 'Bio/Blast/_parser.py' adding 'Bio/Blast/_writers.py' adding 'Bio/CAPS/__init__.py' adding 'Bio/Cluster/__init__.py' adding 'Bio/Cluster/_cluster.cpython-313-s390x-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 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'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/GfaIO.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-313-s390x-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-313-s390x-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-1.84.dist-info/LICENSE' adding 'biopython-1.84.dist-info/LICENSE.rst' adding 'biopython-1.84.dist-info/METADATA' adding 'biopython-1.84.dist-info/WHEEL' adding 'biopython-1.84.dist-info/top_level.txt' adding 'biopython-1.84.dist-info/RECORD' removing build/bdist.linux-s390x/wheel Building wheel for biopython (pyproject.toml): finished with status 'done' Created wheel for biopython: filename=biopython-1.84-cp313-cp313-linux_s390x.whl size=3210379 sha256=00bfcb4cf59870eac9f95427d1e0cc87a97b060da1cab23ee5aaac716b135b12 Stored in directory: /builddir/.cache/pip/wheels/fa/1c/1f/5139d73471cb8006e195b0c98d34603006f6d66d4eae28da02 Successfully built biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.GiXe0Z + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + '[' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT ++ dirname /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT + mkdir -p /builddir/build/BUILD/python-biopython-1.84-build + mkdir /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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 -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-1.84 ++ ls /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_s390x.whl ++ xargs basename --multiple ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=biopython==1.84 + '[' -z biopython==1.84 ']' + TMPDIR=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --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/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir biopython==1.84 Using pip 24.3.1 from /usr/lib/python3.13/site-packages/pip (python 3.13) Looking in links: /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir Processing ./pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_s390x.whl Installing collected packages: biopython Successfully installed biopython-1.84 + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin ']' + rm -f /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages '!=' /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages ']' + '[' -d /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages ']' + site_dirs+=("/usr/lib64/python3.13/site-packages") + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT$site_dir/*.dist-info + echo '%ghost /usr/lib64/python3.13/site-packages/biopython-1.84.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --record /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD --output /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-record + rm -fv /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD removed '/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/RECORD' + rm -fv /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED removed '/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/biopython-1.84.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_FILES_ESCAPE=4.19 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-modules --buildroot /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT --sitelib /usr/lib/python3.13/site-packages --sitearch /usr/lib64/python3.13/site-packages --python-version 3.13 --pyproject-record /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.s390x-pyproject-record --prefix /usr Bio BioSQL + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.84-3.fc42 --unique-debug-suffix -1.84-3.fc42.s390x --unique-debug-src-base python-biopython-1.84-3.fc42.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84 find-debuginfo: starting Extracting debug info from 11 files DWARF-compressing 11 files sepdebugcrcfix: Updated 11 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-1.84-3.fc42.s390x find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT 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/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/BioSQL/__pycache__/Loader.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/BioSQL/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents Scanned 159 directories and 1362 files, processed 438 inodes, 438 modified (220 replaced + 218 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/python-biopython-1.84-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.H0acUa + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS ~/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests ~/build/BUILD/python-biopython-1.84-build/biopython-1.84 + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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 -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-1.84 + pushd Tests ++ 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_Blast_parser.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_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_PDBList.py test_PDB_PDBMLParser.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_alphafold_db.py test_PDB_binary_cif.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_igraph.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_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_Gfa.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.py test_UniProt_GOA.py test_UniProt_Parser.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 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Ace.py test_Ace ... ok test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser) Test to check that contig parser parses each contig into a contig. ... ok test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.037 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Affy.py test_Affy ... ok testAffy3 (test_Affy.AffyTest.testAffy3) ... ok testAffy4 (test_Affy.AffyTest.testAffy4) ... ok testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO.py test_AlignIO ... ok test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files) Check that parsing an empty file returns an empty list. ... ok test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate) Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files) Check that writers can cope with no alignments. ... ok test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments) Check that writers reject records that are not alignments. ... ok test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok ---------------------------------------------------------------------- Ran 1 test in 2.465 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_ClustalIO.py test_AlignIO_ClustalIO ... ok test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header) Make sure we can parse the Biopython header. ... ok test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok test_empty (test_AlignIO_ClustalIO.TestClustalIO.test_empty) Checking empty file. ... ok test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO.test_kalign_header) Make sure we can parse the Kalign header. ... ok test_one (test_AlignIO_ClustalIO.TestClustalIO.test_one) ... ok test_three (test_AlignIO_ClustalIO.TestClustalIO.test_three) ... ok test_two (test_AlignIO_ClustalIO.TestClustalIO.test_two) ... ok test_write_read (test_AlignIO_ClustalIO.TestClustalIO.test_write_read) Checking write/read. ... ok test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO.test_write_read_single) Testing write/read when there is only one sequence. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_PhylipIO.py test_AlignIO_PhylipIO ... ok test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.044 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignIO_convert.py test_AlignIO_convert ... ok Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type) Converting Clustal to NEXUS with a molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type) Converting Clustal to NEXUS without a molecule type. ... ok test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.147 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_AlignInfo.py test_AlignInfo ... ok Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux 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 0.068 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_Alignment.py test_Align_Alignment ... ok test_mapall (test_Align_Alignment.TestAlign_mapall.test_mapall) ... ok test_nucleotide_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_nucleotide_nucleotide_str) ... ok test_protein_nucleotide_many_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_many_str) ... ok test_protein_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_str) ... ok test_aligned (test_Align_Alignment.TestAlign_out_of_order.test_aligned) ... ok test_array (test_Align_Alignment.TestAlign_out_of_order.test_array) ... ok test_indices (test_Align_Alignment.TestAlign_out_of_order.test_indices) ... ok test_row (test_Align_Alignment.TestAlign_out_of_order.test_row) ... ok test_row_col (test_Align_Alignment.TestAlign_out_of_order.test_row_col) ... ok test_row_iterable (test_Align_Alignment.TestAlign_out_of_order.test_row_iterable) ... ok test_row_slice (test_Align_Alignment.TestAlign_out_of_order.test_row_slice) ... ok test_rows_col (test_Align_Alignment.TestAlign_out_of_order.test_rows_col) ... ok test_rows_cols (test_Align_Alignment.TestAlign_out_of_order.test_rows_cols) ... ok test_str (test_Align_Alignment.TestAlign_out_of_order.test_str) ... ok test_substitutions (test_Align_Alignment.TestAlign_out_of_order.test_substitutions) ... ok test_empty_alignment (test_Align_Alignment.TestAlignment.test_empty_alignment) ... ok test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok test_a2m (test_Align_Alignment.TestAlignment_pairwise_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_pairwise_format.test_bed) ... ok test_clustal (test_Align_Alignment.TestAlignment_pairwise_format.test_clustal) ... ok test_exonerate (test_Align_Alignment.TestAlignment_pairwise_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_pairwise_format.test_fasta) ... ok test_maf (test_Align_Alignment.TestAlignment_pairwise_format.test_maf) ... ok test_phylip (test_Align_Alignment.TestAlignment_pairwise_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_pairwise_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_pairwise_format.test_sam) ... ok test_add (test_Align_Alignment.TestMultipleAlignment.test_add) ... ok test_comparison (test_Align_Alignment.TestMultipleAlignment.test_comparison) ... ok test_indexing_slicing (test_Align_Alignment.TestMultipleAlignment.test_indexing_slicing) ... ok test_sort (test_Align_Alignment.TestMultipleAlignment.test_sort) ... ok test_substitutions (test_Align_Alignment.TestMultipleAlignment.test_substitutions) ... ok test_target_query_properties (test_Align_Alignment.TestMultipleAlignment.test_target_query_properties) ... ok test_add (test_Align_Alignment.TestPairwiseAlignment.test_add) ... ok test_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... ok test_reverse_complement (test_Align_Alignment.TestPairwiseAlignment.test_reverse_complement) ... ok test_sort (test_Align_Alignment.TestPairwiseAlignment.test_sort) ... ok test_substitutions (test_Align_Alignment.TestPairwiseAlignment.test_substitutions) ... ok test_target_query_properties (test_Align_Alignment.TestPairwiseAlignment.test_target_query_properties) ... ok ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux Ran 1 test in 0.280 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_a2m.py test_Align_a2m ... ok test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bed.py test_Align_bed ... ok test_reading (test_Align_bed.TestAlign_bed12.test_reading) Test parsing alignments in file formats BED3 through BED12. ... ok test_writing (test_Align_bed.TestAlign_bed12.test_writing) Test writing the alignments in bed12.bed as BED3 through BED12. ... ok test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.bed. ... ok test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.bed. ... ok test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.bed. ... ok test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.bed. ... ok test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.bed. ... ok test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.bed. ... ok test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.bed. ... ok test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.bed. ... ok test_reading (test_Align_bed.TestAlign_dna_rna.test_reading) Test parsing dna_rna.bed. ... ok test_writing (test_Align_bed.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.bed. ... ok test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.bed. ... ok test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.bed. ... ok test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.bed. ... ok test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.bed. ... ok test_reading (test_Align_bed.TestAlign_searching.test_reading) Test reading bigbedtest.bed. ... ok test_writing (test_Align_bed.TestAlign_searching.test_writing) Test writing bigbedtest.bed. ... ok test_format (test_Align_bed.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.140 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigmaf.py test_Align_bigmaf ... ok test_reading (test_Align_bigmaf.TestAlign_bundle_without_target.test_reading) Test parsing bundle_without_target.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_bundle_without_target.test_writing) Test writing bundle_without_target.bb. ... ok test_declaration (test_Align_bigmaf.TestAlign_declaration.test_declaration) ... ok test_search_chromosome (test_Align_bigmaf.TestAlign_searching.test_search_chromosome) ... ok test_search_position (test_Align_bigmaf.TestAlign_searching.test_search_position) ... ok test_search_region (test_Align_bigmaf.TestAlign_searching.test_search_region) ... ok test_reading (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_reading) Test parsing file ucsc_mm9_chr10.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_mm9_chr10.test_writing) Test writing file ucsc_mm9_chr10.bb. ... ok test_reading (test_Align_bigmaf.TestAlign_ucsc_test.test_reading) Test reading ucsc_test.bb. ... ok test_writing (test_Align_bigmaf.TestAlign_ucsc_test.test_writing) Test writing ucsc_test.bb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.461 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_bigpsl.py test_Align_bigpsl ... ok test_reading (test_Align_bigpsl.TestAlign_bigpsl.test_reading) Test parsing bigPsl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_bigpsl.test_writing) Test writing bigPsl.bb. ... ok test_declaration (test_Align_bigpsl.TestAlign_declaration.test_declaration) ... ok test_reading_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl.bb. ... ok test_reading_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl.bb. ... ok test_reading_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl.bb. ... ok test_reading_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl.bb. ... ok test_writing_psl_34_001 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_001) Test writing psl_34_001.psl.bb. ... ok test_writing_psl_34_003 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_003) Test writing psl_34_003.psl.bb. ... ok test_writing_psl_34_004 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_004) Test writing psl_34_004.psl.bb. ... ok test_writing_psl_34_005 (test_Align_bigpsl.TestAlign_dna.test_writing_psl_34_005) Test writing psl_34_005.psl.bb. ... ok test_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl.bb. ... ok test_writing (test_Align_bigpsl.TestAlign_dna_rna.test_writing) Test writing dna_rna.psl.bb. ... ok test_reading_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl.bb. ... ok test_reading_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl.bb. ... ok test_writing_psl_35_001 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing psl_35_001.psl.bb. ... ok test_writing_psl_35_002 (test_Align_bigpsl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing psl_35_002.psl.bb. ... ok test_search_chromosome (test_Align_bigpsl.TestAlign_searching.test_search_chromosome) ... ok test_search_position (test_Align_bigpsl.TestAlign_searching.test_search_position) ... ok test_search_region (test_Align_bigpsl.TestAlign_searching.test_search_region) ... ok test_three_iterators (test_Align_bigpsl.TestAlign_searching.test_three_iterators) Create three iterators and use them concurrently. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.388 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_chain.py test_Align_chain ... ok test_reading_chain_34_002 (test_Align_chain.TestAlign_dna.test_reading_chain_34_002) Test parsing psl_34_002.chain. ... ok test_reading_psl_34_001 (test_Align_chain.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.chain. ... ok test_reading_psl_34_003 (test_Align_chain.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.chain. ... ok test_reading_psl_34_004 (test_Align_chain.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.chain. ... ok test_reading_psl_34_005 (test_Align_chain.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.chain. ... ok test_writing_chain_34_001 (test_Align_chain.TestAlign_dna.test_writing_chain_34_001) Test writing the alignments in psl_34_001.chain. ... ok test_writing_psl_34_002 (test_Align_chain.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.chain. ... ok test_writing_psl_34_003 (test_Align_chain.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.chain. ... ok test_writing_psl_34_004 (test_Align_chain.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.chain. ... ok test_writing_psl_34_005 (test_Align_chain.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.chain. ... ok test_reading (test_Align_chain.TestAlign_dna_rna.test_reading) Test parsing dna_rna.chain. ... ok test_writing (test_Align_chain.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.chain. ... ok test_format (test_Align_chain.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.146 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_clustal.py test_Align_clustal ... ok test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign) Make sure we can parse the Kalign header. ... ok test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_codonalign.py test_Align_codonalign ... ok test_aligner (test_Align_codonalign.TestBasic.test_aligner) ... ok test_alignments (test_Align_codonalign.TestBasic.test_alignments) ... ok test1 (test_Align_codonalign.TestBuildAndIO.test1) ... ok test2 (test_Align_codonalign.TestBuildAndIO.test2) ... ok test3 (test_Align_codonalign.TestBuildAndIO.test3) ... ok test4 (test_Align_codonalign.TestBuildAndIO.test4) ... ok test5 (test_Align_codonalign.TestBuildAndIO.test5) ... ok test_mk (test_Align_codonalign.Test_MK.test_mk) ... ok test_build1 (test_Align_codonalign.Test_build.test_build1) ... ok test_build2 (test_Align_codonalign.Test_build.test_build2) ... ok test_build3 (test_Align_codonalign.Test_build.test_build3) ... ok test_dn_ds (test_Align_codonalign.Test_dn_ds.test_dn_ds) ... ok ---------------------------------------------------------------------- Ran 1 test in 4.373 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_emboss.py test_Align_emboss ... ok test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2) Test parsing a local alignment. ... ok test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_exonerate.py test_Align_exonerate ... ok test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar) Test parsing exn_22_m_affine_local_cigar.exn. ... ok test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar) Test parsing exn_22_m_affine_local_vulgar.exn. ... ok test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar) Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar) Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar) Test parsing exn_22_m_coding2coding_cigar.exn. ... ok test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar) Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar) Test parsing exn_22_m_cigar_fshifts.exn). ... ok test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar) Test parsing exn_22_o_vulgar_fshifts.exn. ... ok test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar) Test parsing exn_22_m_coding2genome_cigar.exn. ... ok test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar) Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar) Test parsing exn_22_m_dna2protein_cigar.exn. ... ok test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar) Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar) Test parsing exn_22_m_est2genome_cigar.exn. ... ok test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar) Test parsing exn_22_m_est2genome_vulgar.exn. ... ok test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar) Test parsing exn_22_o_vulgar_cigar.exn. ... ok test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar) Test parsing exn_22_o_vulgar.exn. ... ok test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar) Test parsing exn_22_q_multiple_cigar.exn. ... ok test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar) Test parsing exn_22_q_multiple_vulgar.exn. ... ok test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar) Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar) Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar) Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar) Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar) Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar) Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar) Test parsing exn_22_m_protein2genome_cigar.exn. ... ok test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar) Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar) Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar) Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar) Test parsing exn_22_m_ungapped_cigar.exn. ... ok test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar) Test parsing exn_22_m_ungapped_vulgar.exn. ... ok test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar) Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar) Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.118 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_fasta.py test_Align_fasta ... ok 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 0.062 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_hhr.py test_Align_hhr ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_7rbx_A_hhsearch_trunc.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_allx.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_allx.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhpred_9590198.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhpred_9590198.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.test_reading) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.290 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_maf.py test_Align_maf ... ok test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453) Test parsing bug2453.maf. ... ok test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target) Test parsing bundle_without_target.maf. ... ok test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch) Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature) Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10) Test parsing MAF file ucsc_mm9_chr10.maf. ... ok test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad) Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test) Test parsing ucsc_test.maf. ... ok test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453) Test reading and writing bug2453.maf. ... ok test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target) Test reading and writing bundle_without_target.maf. ... ok test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10) Test reading and writing ucsc_mm9_chr10.maf. ... ok test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test) Test reading and writing ucsc_test.maf. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.716 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_mauve.py test_Align_mauve ... ok test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok test_parse (test_Align_mauve.TestSeparateFiles.test_parse) ... ok test_write_read (test_Align_mauve.TestSeparateFiles.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_msf.py test_Align_msf ... ok test_empty (test_Align_msf.TestMSF.test_empty) Checking empty file. ... ok test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.049 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_nexus.py test_Align_nexus ... ok test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_phylip.py test_Align_phylip ... ok test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok test_interlaced (test_Align_phylip.TestPhylipReading.test_interlaced) ... ok test_interlaced2 (test_Align_phylip.TestPhylipReading.test_interlaced2) ... ok test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok test_sequential (test_Align_phylip.TestPhylipReading.test_sequential) ... ok test_sequential2 (test_Align_phylip.TestPhylipReading.test_sequential2) ... ok test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_psl.py test_Align_psl ... ok test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002) Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.psl. ... ok test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.psl. ... ok test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.psl. ... ok test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.psl. ... ok test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.psl. ... ok test_reading (test_Align_psl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl. ... ok test_writing (test_Align_psl.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.psl. ... ok test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl. ... ok test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.psl. ... ok test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.psl. ... ok test_format (test_Align_psl.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.341 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_sam.py test_Align_sam ... ok test_4D8I6M (test_Align_sam.TestAlign_clipping.test_4D8I6M) Test alignment starting with deletion followed by insertion. ... ok test_4I8D6M (test_Align_sam.TestAlign_clipping.test_4I8D6M) Test alignment starting with insertion followed by deletion. ... ok test_4S6M (test_Align_sam.TestAlign_clipping.test_4S6M) Test alignment starting with soft clip at non-zero position. ... ok test_4S8D6M (test_Align_sam.TestAlign_clipping.test_4S8D6M) Test alignment starting with soft clip followed by deletion. ... ok test_4S8I6M (test_Align_sam.TestAlign_clipping.test_4S8I6M) Test alignment starting with soft clip followed by insertion. ... ok test_6M (test_Align_sam.TestAlign_clipping.test_6M) Test alignment starting at non-zero position. ... ok test_8D6M_ex1 (test_Align_sam.TestAlign_clipping.test_8D6M_ex1) Test alignment starting with deletion. ... ok test_8D6M_ex2 (test_Align_sam.TestAlign_clipping.test_8D6M_ex2) Test alignment starting with deletion at non-zero position. ... ok test_8I6M_ex1 (test_Align_sam.TestAlign_clipping.test_8I6M_ex1) Test alignment starting with insertion. ... ok test_8I6M_ex2 (test_Align_sam.TestAlign_clipping.test_8I6M_ex2) Test alignment starting with insertion at non-zero position. ... ok test_8S6M (test_Align_sam.TestAlign_clipping.test_8S6M) Test alignment starting with soft clip. ... ok test_reading_psl_34_001 (test_Align_sam.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.sam. ... ok test_reading_psl_34_003 (test_Align_sam.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.sam. ... ok test_reading_psl_34_004 (test_Align_sam.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.sam. ... ok test_reading_psl_34_005 (test_Align_sam.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.sam. ... ok test_writing_psl_34_001 (test_Align_sam.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.sam. ... ok test_writing_psl_34_003 (test_Align_sam.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.sam. ... ok test_writing_psl_34_004 (test_Align_sam.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.sam. ... ok test_writing_psl_34_005 (test_Align_sam.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.sam. ... ok test_reading (test_Align_sam.TestAlign_dna_rna.test_reading) Test parsing dna_rna.sam. ... ok test_reading_psl_comparison (test_Align_sam.TestAlign_dna_rna.test_reading_psl_comparison) Test parsing dna_rna.sam and comparing to dna_rna.psl. ... ok test_writing (test_Align_sam.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.sam. ... ok test_ex1 (test_Align_sam.TestAlign_sambam.test_ex1) ... ok test_ex1_header (test_Align_sam.TestAlign_sambam.test_ex1_header) ... ok test_sam1 (test_Align_sam.TestAlign_sambam.test_sam1) ... ok test_sam2 (test_Align_sam.TestAlign_sambam.test_sam2) ... ok test_format (test_Align_sam.TestAlign_strand.test_format) Test alignment with the target on the opposite strand. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.338 seconds Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages:/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib/python3.13/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/python3 run_tests.py --offline --verbose -v test_Align_stockholm.py test_Align_stockholm ... FAIL 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. ... ERROR test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ... ERROR test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ... ERROR test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ... ERROR test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ... ERROR test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ... ERROR test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ... ERROR test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ... ERROR test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ... ERROR test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ... ERROR test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ... ERROR test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ... ERROR test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ... ERROR test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ... ERROR test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ... ERROR test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ... ERROR test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ... ERROR test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ... ERROR test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ... ERROR test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ... ERROR ====================================================================== ERROR: 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. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6696, in test_io_nonstandard_annotations alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6556, in test_reading_alignments_cath1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6564, in test_reading_alignments_cath2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6606, in test_reading_alignments_cath3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 26, in test_reading_example alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 5902, in test_reading_writing_alignments_globins45 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 5931, in test_reading_writing_alignments_pfam1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6037, in test_reading_writing_alignments_pfam2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6097, in test_reading_writing_alignments_pfam3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6115, in test_reading_writing_alignments_pfam4 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6131, in test_reading_writing_alignments_pfam5 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6147, in test_reading_writing_alignments_pfam6 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6163, in test_reading_writing_alignments_pfam7 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6179, in test_reading_writing_alignments_pfam8 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6195, in test_reading_writing_alignments_pfam9 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6238, in test_reading_writing_alignments_rfam1 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6366, in test_reading_writing_alignments_rfam2 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6382, in test_reading_writing_alignments_rfam3 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6476, in test_reading_writing_alignments_rfam4 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ====================================================================== ERROR: test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests/test_Align_stockholm.py", line 6492, in test_reading_writing_alignments_rfam5 alignment = next(alignments) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/interfaces.py", line 76, in __next__ alignment = self._read_next_alignment(stream) File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 348, in _read_next_alignment AlignmentIterator._store_per_column_annotations( ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ alignment, gc, columns, skipped_columns ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ) ^ File "/builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/stockholm.py", line 250, in _store_per_column_annotations if skipped_columns: ^^^^^^^^^^^^^^^ ValueError: The truth value of an empty array is ambiguous. Use `array.size > 0` to check that an array is not empty. ---------------------------------------------------------------------- Ran 1 test in 0.109 seconds FAILED (failures = 1) Skipping any tests requiring internet access Python version: 3.13.1 (main, Dec 9 2024, 00:00:00) [GCC 14.2.1 20241104 (Red Hat 14.2.1-6)] Operating system: posix linux error: Bad exit status from /var/tmp/rpm-tmp.H0acUa (%check) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.H0acUa (%check) Finish: rpmbuild python-biopython-1.84-3.fc42.src.rpm Finish: build phase for python-biopython-1.84-3.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1735163894.596627/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names ERROR: Exception(/var/lib/copr-rpmbuild/results/python-biopython-1.84-3.fc42.src.rpm) Config(fedora-rawhide-s390x) 1 minutes 9 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_failure=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot ERROR: Command failed: # /usr/bin/systemd-nspawn -q -M 29ade04f7c16414f815558683b71f441 -D /var/lib/mock/fedora-rawhide-s390x-1735163894.596627/root -a -u mockbuild --capability=cap_ipc_lock --rlimit=RLIMIT_NOFILE=10240 --capability=cap_ipc_lock --bind=/tmp/mock-resolv.jss3mbub:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/fuse --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin '--setenv=PROMPT_COMMAND=printf "\033]0;\007"' '--setenv=PS1= \s-\v\$ ' --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c '/usr/bin/rpmbuild -ba --noprep --target s390x /builddir/build/originals/python-biopython.spec' Copr build error: Build failed