Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c15b' (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/8477059-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.2 PID: 23867 Logging PID: 23868 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8477059, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '9dc52f1ad269a6315fca29619fdb9fd25539de7a', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3.failed/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.84-3', 'project_dirname': 'gcc-15-smoketest-3.failed', 'project_name': 'gcc-15-smoketest-3.failed', 'project_owner': 'dmalcolm', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/dmalcolm/gcc-15-smoketest-3.failed/fedora-rawhide-x86_64/', '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.failed--dmalcolm', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'dmalcolm', 'tags': [], 'task_id': '8477059-fedora-rawhide-x86_64', '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.failed/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3.failed/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython'... Running: git checkout 9dc52f1ad269a6315fca29619fdb9fd25539de7a -- cmd: ['git', 'checkout', '9dc52f1ad269a6315fca29619fdb9fd25539de7a', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython rc: 0 stdout: stderr: Note: switching to '9dc52f1ad269a6315fca29619fdb9fd25539de7a'. 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 9dc52f1 automatic import of python-biopython Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/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.failed/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 64.9M 0 --:--:-- --:--:-- --:--:-- 65.0M INFO: Reading stdout from command: md5sum biopython-1.84.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736228517.796432 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-hy31fd5e/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hy31fd5e/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1736228517.796432 -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-hy31fd5e/python-biopython/python-biopython.spec) Config(fedora-rawhide-x86_64) 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-x86_64-bootstrap-1736228517.796432/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-bbe16892-d4f4-4658-8965-8d8e4a7d032c INFO: Checking that 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 image matches host's architecture INFO: Copy content of container 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736228517.796432/root INFO: mounting 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 with podman image mount INFO: image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 as /var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged INFO: umounting image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 (/var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged) with podman image umount INFO: Removing image mock-bootstrap-bbe16892-d4f4-4658-8965-8d8e4a7d032c 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-x86_64-1736228517.796432/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.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 788.8 KiB/s | 27.6 KiB | 00m00s Copr repository 100% | 33.3 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 24.2 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 3.6 MiB/s | 315.9 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-11.fc42 copr_base 5.5 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-26.fc42 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1.1-2.fc42 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 300-1.no_annobin.0.fc42 copr_base 186.6 KiB rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.17.0-2.fc42 fedora 4.0 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-65.fc42 fedora 398.2 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.5.0-1.fc42 fedora 2.4 MiB alternatives x86_64 1.31-1.fc42 fedora 64.8 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-8.fc42 fedora 157.5 KiB authselect-libs x86_64 1.5.0-8.fc42 fedora 822.2 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.50-9.fc42 fedora 25.8 MiB build-reproducibility-srpm-macros noarch 0.5.0-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-4.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-11.fc42 copr_base 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl x86_64 8.11.1-2.fc42 fedora 452.0 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-2.fc42 fedora 200.3 KiB dwz x86_64 0.15-8.fc42 fedora 299.2 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils x86_64 0.192-7.fc42 fedora 2.6 MiB elfutils-debuginfod-client x86_64 0.192-7.fc42 fedora 81.4 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 fedora 1.8 KiB elfutils-libelf x86_64 0.192-7.fc42 fedora 1.2 MiB elfutils-libs x86_64 0.192-7.fc42 fedora 662.9 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 x86_64 5.45-8.fc42 fedora 103.7 KiB file-libs x86_64 5.45-8.fc42 fedora 9.9 MiB filesystem x86_64 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 x86_64 15.2-4.fc42 fedora 12.7 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-26.fc42 fedora 6.7 MiB glibc-common x86_64 2.40.9000-26.fc42 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-26.fc42 fedora 8.0 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 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 x86_64 2.14-1.fc42 fedora 93.1 KiB json-c x86_64 0.18-1.fc42 fedora 83.3 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-3.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.7-1.fc42 fedora 932.3 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.71-1.fc42 fedora 210.8 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB libcurl x86_64 8.11.1-2.fc42 fedora 817.3 KiB libeconf x86_64 0.7.5-1.fc42 fedora 66.7 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 266.9 KiB libgomp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 529.3 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.8-0.rc3.1.fc42 fedora 191.6 KiB libsemanage x86_64 3.8-0.rc3.1.fc42 fedora 305.3 KiB libsepol x86_64 3.8-0.rc3.1.fc42 fedora 812.3 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 2.7 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-1.rc3.fc42 fedora 197.6 KiB libtool-ltdl x86_64 2.5.4-1.fc42 copr_base 68.1 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.37-4.fc42 fedora 269.6 KiB libxml2 x86_64 2.12.9-1.fc42 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-6.fc42 fedora 647.4 KiB openssl-libs x86_64 1:3.2.2-10.fc42 fedora 7.7 MiB p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.7.0-3.fc42 fedora 1.8 MiB pam-libs x86_64 1.7.0-3.fc42 fedora 139.4 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 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 x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB rpm-sequoia x86_64 1.7.0-3.fc42 fedora 2.3 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-9.fc42 fedora 720.7 KiB sqlite-libs x86_64 3.47.2-1.fc42 fedora 1.4 MiB systemd-libs x86_64 257.1-1.fc42 fedora 2.2 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.3-1.fc42 fedora 88.5 KiB xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-42.fc42 fedora 695.9 KiB zlib-ng-compat x86_64 2.2.2-1.fc42 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 155 packages Total size of inbound packages is 51 MiB. Need to download 0 B. After this operation, 178 MiB extra will be used (install 178 MiB, remove 0 B). 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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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MiB/s | 818.4 KiB | 00m00s [125/157] Installing elfutils-debuginfo 100% | 40.9 MiB/s | 83.8 KiB | 00m00s [126/157] Installing elfutils-0:0.192-7 100% | 240.4 MiB/s | 2.6 MiB | 00m00s [127/157] Installing binutils-0:2.43.50 100% | 280.5 MiB/s | 25.8 MiB | 00m00s [128/157] Installing gdb-minimal-0:15.2 100% | 303.0 MiB/s | 12.7 MiB | 00m00s [129/157] Installing debugedit-0:5.1-2. 100% | 99.1 MiB/s | 203.0 KiB | 00m00s [130/157] Installing curl-0:8.11.1-2.fc 100% | 24.7 MiB/s | 454.5 KiB | 00m00s [131/157] Installing rpm-0:4.20.0-1.fc4 100% | 89.5 MiB/s | 2.5 MiB | 00m00s [132/157] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [133/157] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [134/157] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [135/157] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [136/157] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [137/157] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [138/157] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [139/157] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [140/157] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [141/157] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [142/157] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [143/157] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [144/157] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [145/157] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [146/157] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [147/157] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [148/157] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [149/157] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [150/157] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [151/157] Installing redhat-rpm-config- 100% | 62.9 MiB/s | 193.2 KiB | 00m00s [152/157] Installing rpm-build-0:4.20.0 100% | 49.5 MiB/s | 202.9 KiB | 00m00s [153/157] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [154/157] Installing util-linux-0:2.40. 100% | 90.6 MiB/s | 3.7 MiB | 00m00s [155/157] Installing authselect-0:1.5.0 100% | 39.5 MiB/s | 161.9 KiB | 00m00s [156/157] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [157/157] Installing info-0:7.1.1-2.fc4 100% | 125.2 KiB/s | 362.2 KiB | 00m03s Warning: skipped OpenPGP checks for 7 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch Complete! 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.x86_64 alternatives-1.31-1.fc42.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-8.fc42.x86_64 authselect-libs-1.5.0-8.fc42.x86_64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.43.50-9.fc42.x86_64 build-reproducibility-srpm-macros-0.5.0-1.fc42.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-4.fc42.noarch coreutils-9.5-11.fc42.x86_64 coreutils-common-9.5-11.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.11.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-2.fc42.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-8.fc42.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.x86_64 elfutils-debuginfod-client-0.192-7.fc42.x86_64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.x86_64 elfutils-libs-0.192-7.fc42.x86_64 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.x86_64 file-libs-5.45-8.fc42.x86_64 filesystem-3.18-29.fc42.x86_64 filesystem-srpm-macros-3.18-29.fc42.noarch findutils-4.10.0-4.fc41.x86_64 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.x86_64 gdb-minimal-15.2-4.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-26.fc42.x86_64 glibc-common-2.40.9000-26.fc42.x86_64 glibc-gconv-extra-2.40.9000-26.fc42.x86_64 glibc-minimal-langpack-2.40.9000-26.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 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.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1.1-2.fc42.x86_64 jansson-2.14-1.fc42.x86_64 json-c-0.18-1.fc42.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-3.fc42.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.7-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.71-1.fc42.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc42.x86_64 libcurl-8.11.1-2.fc42.x86_64 libeconf-0.7.5-1.fc42.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-15.0.0-0.2.fc42.x86_64 libgomp-15.0.0-0.2.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.64.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.8-0.rc3.1.fc42.x86_64 libsemanage-3.8-0.rc3.1.fc42.x86_64 libsepol-3.8-0.rc3.1.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-15.0.0-0.2.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-1.rc3.fc42.x86_64 libtool-ltdl-2.5.4-1.fc42.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.37-4.fc42.x86_64 libxml2-2.12.9-1.fc42.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.7-1.fc42.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.x86_64 openssl-libs-3.2.2-10.fc42.x86_64 p11-kit-0.25.5-4.fc42.x86_64 p11-kit-trust-0.25.5-4.fc42.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.x86_64 pam-libs-1.7.0-3.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 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.x86_64 redhat-rpm-config-300-1.no_annobin.0.fc42.noarch rpm-4.20.0-1.fc42.x86_64 rpm-build-4.20.0-1.fc42.x86_64 rpm-build-libs-4.20.0-1.fc42.x86_64 rpm-libs-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-9.fc42.noarch shadow-utils-4.17.0-2.fc42.x86_64 sqlite-libs-3.47.2-1.fc42.x86_64 systemd-libs-257.1-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-65.fc42.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.3-1.fc42.x86_64 xz-5.6.3-2.fc42.x86_64 xz-libs-5.6.3-2.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-42.fc42.x86_64 zlib-ng-compat-2.2.2-1.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 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-x86_64-1736228517.796432/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-hy31fd5e/python-biopython/python-biopython.spec) Config(child) 0 minutes 17 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-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736228517.796432/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1736228517.796432/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-x86_64-1736228517.796432/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.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-2.fc42.x86_64 dnf5-plugins-5.2.8.1-2.fc42.x86_64 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Wrote: /builddir/build/SRPMS/python-biopython-1.84-3.fc42.src.rpm Updating and loading repositories: fedora 100% | 812.0 KiB/s | 27.6 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 23.1 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 37.3 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 109.9 MiB pyproject-rpm-macros noarch 1.16.3-1.fc42 fedora 113.7 KiB python3-devel x86_64 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 x86_64 12.80-1.fc42 fedora 992.8 KiB cpp x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 37.5 MiB dejavu-sans-fonts noarch 2.37-24.fc41 fedora 5.5 MiB expat x86_64 2.6.4-1.fc42 fedora 285.5 KiB fonts-filesystem noarch 1:2.0.5-17.fc41 fedora 0.0 B freetype x86_64 2.13.3-1.fc42 fedora 850.5 KiB fribidi x86_64 1.0.16-1.fc42 fedora 194.5 KiB gcc-plugin-annobin x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 59.6 KiB glib2 x86_64 2.83.0-3.fc42 fedora 14.6 MiB glibc-devel x86_64 2.40.9000-26.fc42 fedora 2.3 MiB gnutls x86_64 3.8.8-1.fc42 fedora 3.2 MiB graphite2 x86_64 1.3.14-16.fc41 fedora 192.0 KiB harfbuzz x86_64 10.1.0-2.fc42 fedora 2.7 MiB jbigkit-libs x86_64 2.1-30.fc41 fedora 117.6 KiB kernel-headers x86_64 6.13.0-0.rc5.42.fc42 fedora 6.5 MiB lcms2 x86_64 2.16-4.fc41 fedora 424.9 KiB libXau x86_64 1.0.12-1.fc42 fedora 75.8 KiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libimagequant x86_64 4.0.3-5.fc41 fedora 666.7 KiB libjpeg-turbo x86_64 3.1.0-1.fc42 fedora 787.0 KiB liblerc x86_64 4.0.0-7.fc41 fedora 607.5 KiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libpng x86_64 2:1.6.44-1.fc42 fedora 245.8 KiB libraqm x86_64 0.10.1-1.fc42 fedora 32.7 KiB libtiff x86_64 4.7.0-2.fc42 fedora 620.0 KiB libwebp x86_64 1.5.0-1.fc42 fedora 814.4 KiB libxcb x86_64 1.17.0-3.fc42 fedora 1.2 MiB libxcrypt-devel x86_64 4.4.37-4.fc42 fedora 30.5 KiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB nettle x86_64 3.10-3.fc41 fedora 793.0 KiB openjpeg x86_64 2.5.3-2.fc42 fedora 451.4 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 x86_64 3.13.1-2.fc42 fedora 30.6 KiB python3-chardet noarch 5.2.0-14.fc41 fedora 2.1 MiB python3-libs x86_64 3.13.1-2.fc42 fedora 39.8 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 x86_64 11.0.0-1.fc42 fedora 3.9 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: 48 packages Total size of inbound packages is 80 MiB. Need to download 6 MiB. After this operation, 256 MiB extra will be used (install 256 MiB, remove 0 B). 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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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.YZ76Mz + 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.DgVglu + 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.SuVtvS + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + 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.x86_64-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.x86_64-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: Copr repository 100% | 47.8 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 29.4 KiB/s | 1.5 KiB | 00m00s fedora 100% | 1.0 MiB/s | 27.6 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.x86_64" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.x86_64" 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 3 MiB. After this operation, 20 MiB extra will be used (install 20 MiB, remove 0 B). [1/2] python3-setuptools-0:74.1.3-4.fc4 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [2/2] python3-pip-0:24.3.1-1.fc42.noarc 100% | 11.4 MiB/s | 2.7 MiB | 00m00s -------------------------------------------------------------------------------- [2/2] Total 100% | 10.0 MiB/s | 2.7 MiB | 00m00s Running transaction [1/4] Verify package files 100% | 125.0 B/s | 2.0 B | 00m00s [2/4] Prepare transaction 100% | 64.0 B/s | 2.0 B | 00m00s [3/4] Installing python3-setuptools-0:7 100% | 111.2 MiB/s | 8.6 MiB | 00m00s [4/4] Installing python3-pip-0:24.3.1-1 100% | 99.3 MiB/s | 11.6 MiB | 00m00s Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.TnZNss + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + 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.x86_64-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.x86_64-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% | 28.8 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 51.0 KiB/s | 1.5 KiB | 00m00s fedora 100% | 1.0 MiB/s | 27.6 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.x86_64" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.x86_64" 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 x86_64 1:2.2.1-1.fc42 fedora 40.8 MiB Installing dependencies: flexiblas x86_64 3.4.4-3.fc41 fedora 48.5 KiB flexiblas-netlib x86_64 3.4.4-3.fc41 fedora 10.7 MiB flexiblas-openblas-openmp x86_64 3.4.4-3.fc41 fedora 43.3 KiB libgfortran x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 3.3 MiB libquadmath x86_64 15.0.0-0.2.fc42 https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 319.5 KiB openblas x86_64 0.3.28-2.fc42 fedora 106.6 KiB openblas-openmp x86_64 0.3.28-2.fc42 fedora 39.3 MiB python3-numpy-f2py x86_64 1:2.2.1-1.fc42 fedora 2.0 MiB Transaction Summary: Installing: 9 packages Total size of inbound packages is 18 MiB. Need to download 0 B. After this operation, 97 MiB extra will be used (install 97 MiB, remove 0 B). [1/1] python3-numpy-1:2.2.1-1.fc42.x86_ 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] flexiblas-netlib-0:3.4.4-3.fc41.x 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] python3-numpy-f2py-1:2.2.1-1.fc42 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.fc41.x86_64 100% | 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.x 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.x86 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.x86_64 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [8/8] Total 100% | 0.0 B/s | 0.0 B | 00m00s [1/9] libquadmath-0:15.0.0-0.2.fc42.x86 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [9/9] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction [ 1/11] Verify package files 100% | 160.0 B/s | 9.0 B | 00m00s [ 2/11] Prepare transaction 100% | 225.0 B/s | 9.0 B | 00m00s [ 3/11] Installing libgfortran-0:15.0.0 100% | 273.1 MiB/s | 3.3 MiB | 00m00s [ 4/11] Installing libquadmath-0:15.0.0 100% | 156.6 MiB/s | 320.7 KiB | 00m00s [ 5/11] Installing openblas-0:0.3.28-2. 100% | 105.8 MiB/s | 108.3 KiB | 00m00s [ 6/11] Installing openblas-openmp-0:0. 100% | 451.6 MiB/s | 39.3 MiB | 00m00s [ 7/11] Installing flexiblas-0:3.4.4-3. 100% | 48.5 MiB/s | 49.7 KiB | 00m00s [ 8/11] Installing flexiblas-openblas-o 100% | 43.1 MiB/s | 44.1 KiB | 00m00s [ 9/11] Installing flexiblas-netlib-0:3 100% | 323.2 MiB/s | 10.7 MiB | 00m00s [10/11] Installing python3-numpy-f2py-1 100% | 82.7 MiB/s | 2.1 MiB | 00m00s [11/11] Installing python3-numpy-1:2.2. 100% | 181.8 MiB/s | 41.1 MiB | 00m00s Warning: skipped OpenPGP checks for 2 packages from repository: https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.lj8ARx + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + 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.x86_64-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.x86_64-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% | 1.0 MiB/s | 27.6 KiB | 00m00s Copr repository 100% | 47.8 KiB/s | 1.5 KiB | 00m00s Additional repo https_fedorapeople_org 100% | 29.4 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "gcc-15.0.0-0.2.fc42.x86_64" is already installed. Package "pyproject-rpm-macros-1.16.3-1.fc42.noarch" is already installed. Package "python3-devel-3.13.1-2.fc42.x86_64" is already installed. Package "python3-numpy-1:2.2.1-1.fc42.x86_64" 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: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1721347200 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.rnqL8x + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + 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.x86_64-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.x86_64-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.w1JU2T + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + VALAFLAGS=-g + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + 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-0zfwhb19/biopython.egg-info writing /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-0zfwhb19/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-0zfwhb19/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-0zfwhb19/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-0zfwhb19/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-0zfwhb19/biopython.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-0zfwhb19/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-0zfwhb19/biopython.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-modern-metadata-0zfwhb19/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-x86_64-cpython-313 creating build/lib.linux-x86_64-cpython-313/Bio copying Bio/File.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-313/Bio creating build/lib.linux-x86_64-cpython-313/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-313/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Affy creating build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/analysis.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/chain.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-313/Bio/Align creating build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/Applications creating build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices creating build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/AlignIO creating build/lib.linux-x86_64-cpython-313/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Alphabet creating build/lib.linux-x86_64-cpython-313/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Application creating build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/_parser.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast copying Bio/Blast/_writers.py -> build/lib.linux-x86_64-cpython-313/Bio/Blast creating build/lib.linux-x86_64-cpython-313/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/CAPS creating build/lib.linux-x86_64-cpython-313/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Cluster creating build/lib.linux-x86_64-cpython-313/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-313/Bio/codonalign creating build/lib.linux-x86_64-cpython-313/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Compass creating build/lib.linux-x86_64-cpython-313/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-313/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-313/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-313/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Data creating build/lib.linux-x86_64-cpython-313/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Emboss creating build/lib.linux-x86_64-cpython-313/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-313/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Entrez creating build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-313/Bio/ExPASy creating build/lib.linux-x86_64-cpython-313/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-313/Bio/GenBank creating build/lib.linux-x86_64-cpython-313/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-313/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Geo creating build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics creating build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram creating build/lib.linux-x86_64-cpython-313/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/HMM creating build/lib.linux-x86_64-cpython-313/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map creating build/lib.linux-x86_64-cpython-313/Bio/PDB creating build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf creating build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML creating build/lib.linux-x86_64-cpython-313/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Medline creating build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs creating build/lib.linux-x86_64-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/applications creating build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar creating build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Nexus creating build/lib.linux-x86_64-cpython-313/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-313/Bio/NMR creating build/lib.linux-x86_64-cpython-313/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway creating build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PDBMLParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/alphafold_db.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/binary_cif.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-313/Bio/PDB creating build/lib.linux-x86_64-cpython-313/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-313/Bio/phenotype creating build/lib.linux-x86_64-cpython-313/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen creating build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop creating build/lib.linux-x86_64-cpython-313/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Restriction creating build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SCOP creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO creating build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO creating build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/GfaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO creating build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-313/Bio/SeqUtils creating build/lib.linux-x86_64-cpython-313/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing creating build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications creating build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer creating build/lib.linux-x86_64-cpython-313/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-313/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/SwissProt creating build/lib.linux-x86_64-cpython-313/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/TogoWS creating build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo creating build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications creating build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML creating build/lib.linux-x86_64-cpython-313/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/UniGene creating build/lib.linux-x86_64-cpython-313/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-313/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-313/Bio/UniProt creating build/lib.linux-x86_64-cpython-313/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-313/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-313/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-313/BioSQL copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-313/BioSQL copying BioSQL/__init__.py -> build/lib.linux-x86_64-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-x86_64-cpython-313/Bio copying Bio/py.typed -> build/lib.linux-x86_64-cpython-313/Bio copying Bio/Align/_aligncore.c -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/_codonaligner.c -> build/lib.linux-x86_64-cpython-313/Bio/Align copying Bio/Align/_pairwisealigner.c -> build/lib.linux-x86_64-cpython-313/Bio/Align creating build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-313/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-313/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-313/Bio/Cluster creating build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs creating build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-313/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-313/Bio/Nexus copying Bio/PDB/bcifhelpermodule.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-313/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-313/Bio/SeqIO copying BioSQL/py.typed -> build/lib.linux-x86_64-cpython-313/BioSQL running build_ext building 'Bio.Align._codonaligner' extension creating build/temp.linux-x86_64-cpython-313 creating build/temp.linux-x86_64-cpython-313/Bio creating build/temp.linux-x86_64-cpython-313/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_codonaligner.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_codonaligner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/Align/_codonaligner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so building 'Bio.Align._pairwisealigner' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_pairwisealigner.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-x86_64-linux-gnu.so building 'Bio.Align._aligncore' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Align/_aligncore.c -o build/temp.linux-x86_64-cpython-313/Bio/Align/_aligncore.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/Align/_aligncore.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.cpython-313-x86_64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-313/Bio/cpairwise2module.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-x86_64-cpython-313/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-313/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.cpython-313-x86_64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-x86_64-cpython-313/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-313/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.cpython-313-x86_64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-x86_64-cpython-313/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-313/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/Cluster/_cluster.cpython-313-x86_64-linux-gnu.so building 'Bio.PDB.ccealign' extension creating build/temp.linux-x86_64-cpython-313/Bio/PDB gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealign.cpython-313-x86_64-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.cpython-313-x86_64-linux-gnu.so building 'Bio.PDB._bcif_helper' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/PDB/bcifhelpermodule.c -o build/temp.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-x86_64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-x86_64-cpython-313/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/usr/include/python3.13 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-x86_64-linux-gnu.so installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/Bio copying build/lib.linux-x86_64-cpython-313/Bio/File.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/LogisticRegression.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/MarkovModel.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/MaxEntropy.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/NaiveBayes.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/Seq.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/SeqFeature.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/SeqRecord.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/bgzf.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/kNN.py -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/pairwise2.py -> build/bdist.linux-x86_64/wheel/./Bio creating build/bdist.linux-x86_64/wheel/Bio/Affy copying build/lib.linux-x86_64-cpython-313/Bio/Affy/CelFile.py -> build/bdist.linux-x86_64/wheel/./Bio/Affy copying build/lib.linux-x86_64-cpython-313/Bio/Affy/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Affy creating build/bdist.linux-x86_64/wheel/Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/AlignInfo.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/a2m.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/analysis.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/bed.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigbed.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigmaf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/bigpsl.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/chain.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/clustal.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/emboss.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/exonerate.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/fasta.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/hhr.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/maf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/mauve.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/msf.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/nexus.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/phylip.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/psl.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/sam.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/stockholm.py -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/tabular.py -> build/bdist.linux-x86_64/wheel/./Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_ClustalOmega.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Clustalw.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Dialign.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_MSAProbs.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Mafft.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Muscle.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Prank.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_Probcons.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/_TCoffee.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Align/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/Applications creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices creating build/bdist.linux-x86_64/wheel/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER22 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER6 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BENNER74 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLASTN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLASTP -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM45 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM50 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM62 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM80 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/BLOSUM90 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/DAYHOFF -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/FENG -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/GENETIC -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/GONNET1992 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/HOXD70 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/JOHNSON -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/JONES -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/LEVIN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MCLACHLAN -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MDM78 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/MEGABLAST -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/NUC.4.4 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM250 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM30 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/PAM70 -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/RAO -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/RISLER -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/SCHNEIDER -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/STR -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/substitution_matrices/data/TRANS -> build/bdist.linux-x86_64/wheel/./Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.c -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.c -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.c -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/_pairwisealigner.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align copying build/lib.linux-x86_64-cpython-313/Bio/Align/_aligncore.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Align creating build/bdist.linux-x86_64/wheel/Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/ClustalIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/EmbossIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MafIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MauveIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/MsfIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/NexusIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/PhylipIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/StockholmIO.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO copying build/lib.linux-x86_64-cpython-313/Bio/AlignIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/AlignIO creating build/bdist.linux-x86_64/wheel/Bio/Alphabet copying build/lib.linux-x86_64-cpython-313/Bio/Alphabet/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Alphabet creating build/bdist.linux-x86_64/wheel/Bio/Application copying build/lib.linux-x86_64-cpython-313/Bio/Application/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Application creating build/bdist.linux-x86_64/wheel/Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/Applications.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/NCBIWWW.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/NCBIXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/_parser.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast copying build/lib.linux-x86_64-cpython-313/Bio/Blast/_writers.py -> build/bdist.linux-x86_64/wheel/./Bio/Blast creating build/bdist.linux-x86_64/wheel/Bio/CAPS copying build/lib.linux-x86_64-cpython-313/Bio/CAPS/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/CAPS creating build/bdist.linux-x86_64/wheel/Bio/Cluster copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Cluster copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/cluster.c -> build/bdist.linux-x86_64/wheel/./Bio/Cluster copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/cluster.h -> build/bdist.linux-x86_64/wheel/./Bio/Cluster copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/clustermodule.c -> build/bdist.linux-x86_64/wheel/./Bio/Cluster copying build/lib.linux-x86_64-cpython-313/Bio/Cluster/_cluster.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Cluster creating build/bdist.linux-x86_64/wheel/Bio/codonalign copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/codonalignment.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign copying build/lib.linux-x86_64-cpython-313/Bio/codonalign/codonseq.py -> build/bdist.linux-x86_64/wheel/./Bio/codonalign creating build/bdist.linux-x86_64/wheel/Bio/Compass copying build/lib.linux-x86_64-cpython-313/Bio/Compass/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Compass creating build/bdist.linux-x86_64/wheel/Bio/Data copying build/lib.linux-x86_64-cpython-313/Bio/Data/CodonTable.py -> build/bdist.linux-x86_64/wheel/./Bio/Data copying build/lib.linux-x86_64-cpython-313/Bio/Data/IUPACData.py -> build/bdist.linux-x86_64/wheel/./Bio/Data copying build/lib.linux-x86_64-cpython-313/Bio/Data/PDBData.py -> build/bdist.linux-x86_64/wheel/./Bio/Data copying build/lib.linux-x86_64-cpython-313/Bio/Data/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Data creating build/bdist.linux-x86_64/wheel/Bio/Emboss copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/Applications.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/Primer3.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/PrimerSearch.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss copying build/lib.linux-x86_64-cpython-313/Bio/Emboss/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Emboss creating build/bdist.linux-x86_64/wheel/Bio/Entrez copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/Parser.py -> build/bdist.linux-x86_64/wheel/./Bio/Entrez copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Entrez creating build/bdist.linux-x86_64/wheel/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/EMBL_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/GenBank_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/HomoloGene.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-common1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-display1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-format1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-link1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-list1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-math1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-para1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-references1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-section1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Features.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Access.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Project.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NCBI_all.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NSE.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/NSE.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/OMSSA.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PDB_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PIR_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PRF_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/SP_General.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/SP_General.mod.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/archivearticle.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/archivecustom-classes.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/archivecustom-models.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/archivecustom-modules.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/articlemeta.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/backmatter.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/chars.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/common.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/default-classes.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/default-mixes.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/display.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eInfo_020511.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eLink_090910.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eLink_101123.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/ePost_020511.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eSearch_020511.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eSpell.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/eSummary_041029.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/egquery.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/einfo.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/elink.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/elink_020122.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/epost.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/esearch.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/esummary-v1.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/esummary_clinvar.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/esummary_gene.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/format.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/htmltable.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamsa.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamsb.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamsc.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamsn.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamso.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isoamsr.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isobox.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isocyr1.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isocyr2.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isodia.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isogrk1.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isogrk2.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isogrk3.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isogrk4.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isolat1.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isolat2.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isomfrk.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isomopf.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isomscr.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isonum.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isopub.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/isotech.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/journalmeta.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/link.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/list.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/math.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathml2.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathml3-qname1.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathml3.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mathmlsetup.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mmlalias.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/mmlextra.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/modules.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/notat.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/para.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/phrase.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pmc-1.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_020114.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_080101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_090101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_100101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_100301.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_110101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_120101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_130101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_130501.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_140101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_150101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_180101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_180601.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/pubmed_190101.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/references.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/section.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/taxon.dtd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/xhtml-table-1.mod -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/DTDs/xmlspecchars.ent -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/DTDs creating build/bdist.linux-x86_64/wheel/Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/IPGReportSet.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-313/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd -> build/bdist.linux-x86_64/wheel/./Bio/Entrez/XSDs creating build/bdist.linux-x86_64/wheel/Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Enzyme.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Prodoc.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/Prosite.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/ScanProsite.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy copying build/lib.linux-x86_64-cpython-313/Bio/ExPASy/cellosaurus.py -> build/bdist.linux-x86_64/wheel/./Bio/ExPASy creating build/bdist.linux-x86_64/wheel/Bio/GenBank copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/Record.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/Scanner.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank copying build/lib.linux-x86_64-cpython-313/Bio/GenBank/utils.py -> build/bdist.linux-x86_64/wheel/./Bio/GenBank creating build/bdist.linux-x86_64/wheel/Bio/Geo copying build/lib.linux-x86_64-cpython-313/Bio/Geo/Record.py -> build/bdist.linux-x86_64/wheel/./Bio/Geo copying build/lib.linux-x86_64-cpython-313/Bio/Geo/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Geo creating build/bdist.linux-x86_64/wheel/Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/BasicChromosome.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/ColorSpiral.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/Comparative.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/DisplayRepresentation.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/Distribution.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/KGML_vis.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics creating build/bdist.linux-x86_64/wheel/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Colors.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Diagram.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Feature.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Graph.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/_Track.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-313/Bio/Graphics/GenomeDiagram/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Graphics/GenomeDiagram creating build/bdist.linux-x86_64/wheel/Bio/HMM copying build/lib.linux-x86_64-cpython-313/Bio/HMM/DynamicProgramming.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM copying build/lib.linux-x86_64-cpython-313/Bio/HMM/MarkovModel.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM copying build/lib.linux-x86_64-cpython-313/Bio/HMM/Trainer.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM copying build/lib.linux-x86_64-cpython-313/Bio/HMM/Utilities.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM copying build/lib.linux-x86_64-cpython-313/Bio/HMM/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/HMM creating build/bdist.linux-x86_64/wheel/Bio/KEGG copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/REST.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Compound/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Compound creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Enzyme copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Enzyme/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Enzyme creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Gene copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Gene/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Gene creating build/bdist.linux-x86_64/wheel/Bio/KEGG/Map copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/Map/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/Map creating build/bdist.linux-x86_64/wheel/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/KGML_parser.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/KGML_pathway.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-313/Bio/KEGG/KGML/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/KEGG/KGML creating build/bdist.linux-x86_64/wheel/Bio/PDB creating build/bdist.linux-x86_64/wheel/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/DefaultParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmtf/mmtfio.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-313/Bio/PDB/AbstractPropertyMap.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Atom.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Chain.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/DSSP.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Dice.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Entity.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/FragmentMapper.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/HSExposure.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/MMCIF2Dict.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/MMCIFParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Model.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/NACCESS.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/NeighborSearch.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBExceptions.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBList.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBMLParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PDBParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PICIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/PSEA.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Polypeptide.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Residue.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ResidueDepth.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/SASA.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/SCADIO.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Selection.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Structure.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/StructureAlignment.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/StructureBuilder.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/Superimposer.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/alphafold_db.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/binary_cif.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/cealign.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ic_data.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ic_rebuild.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/internal_coords.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/mmcifio.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/parse_pdb_header.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/qcprot.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/vectors.py -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/bcifhelpermodule.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealignmodule.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.c -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/ccealign.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/kdtrees.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB copying build/lib.linux-x86_64-cpython-313/Bio/PDB/_bcif_helper.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/PDB creating build/bdist.linux-x86_64/wheel/Bio/Medline copying build/lib.linux-x86_64-cpython-313/Bio/Medline/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Medline creating build/bdist.linux-x86_64/wheel/Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/alignace.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/clusterbuster.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/mast.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/matrix.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/meme.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/minimal.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/pfm.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/thresholds.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/transfac.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/xms.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-313/Bio/motifs/applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/applications copying build/lib.linux-x86_64-cpython-313/Bio/motifs/applications/_xxmotif.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/applications creating build/bdist.linux-x86_64/wheel/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-313/Bio/motifs/jaspar/db.py -> build/bdist.linux-x86_64/wheel/./Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.c -> build/bdist.linux-x86_64/wheel/./Bio/motifs copying build/lib.linux-x86_64-cpython-313/Bio/motifs/_pwm.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/motifs creating build/bdist.linux-x86_64/wheel/Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Nexus.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Nodes.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/StandardData.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/Trees.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.c -> build/bdist.linux-x86_64/wheel/./Bio/Nexus copying build/lib.linux-x86_64-cpython-313/Bio/Nexus/cnexus.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/Nexus creating build/bdist.linux-x86_64/wheel/Bio/NMR copying build/lib.linux-x86_64-cpython-313/Bio/NMR/NOEtools.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR copying build/lib.linux-x86_64-cpython-313/Bio/NMR/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR copying build/lib.linux-x86_64-cpython-313/Bio/NMR/xpktools.py -> build/bdist.linux-x86_64/wheel/./Bio/NMR creating build/bdist.linux-x86_64/wheel/Bio/Pathway copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway creating build/bdist.linux-x86_64/wheel/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/Graph.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/MultiGraph.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-313/Bio/Pathway/Rep/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Pathway/Rep creating build/bdist.linux-x86_64/wheel/Bio/phenotype copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/phen_micro.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype copying build/lib.linux-x86_64-cpython-313/Bio/phenotype/pm_fitting.py -> build/bdist.linux-x86_64/wheel/./Bio/phenotype creating build/bdist.linux-x86_64/wheel/Bio/PopGen copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen creating build/bdist.linux-x86_64/wheel/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/Controller.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/EasyController.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/FileParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/LargeFileParser.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-313/Bio/PopGen/GenePop/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/PopGen/GenePop creating build/bdist.linux-x86_64/wheel/Bio/Restriction copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/PrintFormat.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/Restriction.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/Restriction_Dictionary.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction copying build/lib.linux-x86_64-cpython-313/Bio/Restriction/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Restriction creating build/bdist.linux-x86_64/wheel/Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Cla.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Des.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Dom.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Hie.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Raf.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/Residues.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP copying build/lib.linux-x86_64-cpython-313/Bio/SCOP/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SCOP creating build/bdist.linux-x86_64/wheel/Bio/SearchIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlatIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_index.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/hit.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/hsp.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/_model/query.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/_model creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/blast_tab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/BlastIO/blast_xml.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/BlastIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HHsuiteIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/HmmerIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/_base.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/ExonerateIO creating build/bdist.linux-x86_64/wheel/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-313/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/bdist.linux-x86_64/wheel/./Bio/SearchIO/InterproscanIO creating build/bdist.linux-x86_64/wheel/Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/AbiIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/AceIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/FastaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/GckIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/GfaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/IgIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/InsdcIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/Interfaces.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/NibIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PdbIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PhdIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/PirIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/QualityIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SeqXmlIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SffIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SnapGeneIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/SwissIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/TabIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/TwoBitIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/UniprotIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/XdnaIO.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_index.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.c -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO copying build/lib.linux-x86_64-cpython-313/Bio/SeqIO/_twoBitIO.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio/SeqIO creating build/bdist.linux-x86_64/wheel/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/CheckSum.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/IsoelectricPoint.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/MeltingTemp.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/ProtParam.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/ProtParamData.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils copying build/lib.linux-x86_64-cpython-313/Bio/SeqUtils/lcc.py -> build/bdist.linux-x86_64/wheel/./Bio/SeqUtils creating build/bdist.linux-x86_64/wheel/Bio/Sequencing copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Ace.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Phd.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing creating build/bdist.linux-x86_64/wheel/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_Novoalign.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_bwa.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Sequencing/Applications/_samtools.py -> build/bdist.linux-x86_64/wheel/./Bio/Sequencing/Applications creating build/bdist.linux-x86_64/wheel/Bio/SVDSuperimposer copying build/lib.linux-x86_64-cpython-313/Bio/SVDSuperimposer/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SVDSuperimposer creating build/bdist.linux-x86_64/wheel/Bio/SwissProt copying build/lib.linux-x86_64-cpython-313/Bio/SwissProt/KeyWList.py -> build/bdist.linux-x86_64/wheel/./Bio/SwissProt copying build/lib.linux-x86_64-cpython-313/Bio/SwissProt/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/SwissProt creating build/bdist.linux-x86_64/wheel/Bio/TogoWS copying build/lib.linux-x86_64-cpython-313/Bio/TogoWS/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/TogoWS creating build/bdist.linux-x86_64/wheel/Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/BaseTree.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/CDAO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/CDAOIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Consensus.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NeXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NeXMLIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Newick.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NewickIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/NexusIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PhyloXML.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PhyloXMLIO.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/TreeConstruction.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_cdao_owl.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_io.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/_utils.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo creating build/bdist.linux-x86_64/wheel/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Fasttree.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Phyml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/_Raxml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/Applications/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/Applications creating build/bdist.linux-x86_64/wheel/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_paml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_baseml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_codeml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/_parse_yn00.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/baseml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/chi2.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/codeml.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-313/Bio/Phylo/PAML/yn00.py -> build/bdist.linux-x86_64/wheel/./Bio/Phylo/PAML creating build/bdist.linux-x86_64/wheel/Bio/UniGene copying build/lib.linux-x86_64-cpython-313/Bio/UniGene/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/UniGene creating build/bdist.linux-x86_64/wheel/Bio/UniProt copying build/lib.linux-x86_64-cpython-313/Bio/UniProt/GOA.py -> build/bdist.linux-x86_64/wheel/./Bio/UniProt copying build/lib.linux-x86_64-cpython-313/Bio/UniProt/__init__.py -> build/bdist.linux-x86_64/wheel/./Bio/UniProt copying build/lib.linux-x86_64-cpython-313/Bio/cpairwise2module.c -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/py.typed -> build/bdist.linux-x86_64/wheel/./Bio copying build/lib.linux-x86_64-cpython-313/Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./Bio creating build/bdist.linux-x86_64/wheel/BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/BioSeq.py -> build/bdist.linux-x86_64/wheel/./BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/BioSeqDatabase.py -> build/bdist.linux-x86_64/wheel/./BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/DBUtils.py -> build/bdist.linux-x86_64/wheel/./BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/Loader.py -> build/bdist.linux-x86_64/wheel/./BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/__init__.py -> build/bdist.linux-x86_64/wheel/./BioSQL copying build/lib.linux-x86_64-cpython-313/BioSQL/py.typed -> build/bdist.linux-x86_64/wheel/./BioSQL running install_egg_info Copying biopython.egg-info to build/bdist.linux-x86_64/wheel/./biopython-1.84-py3.13.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/biopython-1.84.dist-info/WHEEL creating '/builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/.pyproject-builddir/pip-wheel-uuckbhl6/.tmp-gviyvsk6/biopython-1.84-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'Bio/File.py' adding 'Bio/LogisticRegression.py' adding 'Bio/MarkovModel.py' adding 'Bio/MaxEntropy.py' adding 'Bio/NaiveBayes.py' adding 'Bio/Seq.py' adding 'Bio/SeqFeature.py' adding 'Bio/SeqRecord.py' adding 'Bio/__init__.py' adding 'Bio/_utils.py' adding 'Bio/bgzf.py' adding 'Bio/cpairwise2.cpython-313-x86_64-linux-gnu.so' adding 'Bio/cpairwise2module.c' adding 'Bio/kNN.py' adding 'Bio/pairwise2.py' adding 'Bio/py.typed' adding 'Bio/Affy/CelFile.py' adding 'Bio/Affy/__init__.py' adding 'Bio/Align/AlignInfo.py' adding 'Bio/Align/__init__.py' adding 'Bio/Align/_aligncore.c' adding 'Bio/Align/_aligncore.cpython-313-x86_64-linux-gnu.so' adding 'Bio/Align/_codonaligner.c' adding 'Bio/Align/_codonaligner.cpython-313-x86_64-linux-gnu.so' adding 'Bio/Align/_pairwisealigner.c' adding 'Bio/Align/_pairwisealigner.cpython-313-x86_64-linux-gnu.so' adding 'Bio/Align/a2m.py' adding 'Bio/Align/analysis.py' adding 'Bio/Align/bed.py' adding 'Bio/Align/bigbed.py' adding 'Bio/Align/bigmaf.py' adding 'Bio/Align/bigpsl.py' adding 'Bio/Align/chain.py' adding 'Bio/Align/clustal.py' adding 'Bio/Align/emboss.py' adding 'Bio/Align/exonerate.py' adding 'Bio/Align/fasta.py' adding 'Bio/Align/hhr.py' adding 'Bio/Align/interfaces.py' adding 'Bio/Align/maf.py' adding 'Bio/Align/mauve.py' adding 'Bio/Align/msf.py' adding 'Bio/Align/nexus.py' adding 'Bio/Align/phylip.py' adding 'Bio/Align/psl.py' adding 'Bio/Align/sam.py' adding 'Bio/Align/stockholm.py' adding 'Bio/Align/tabular.py' adding 'Bio/Align/Applications/_ClustalOmega.py' adding 'Bio/Align/Applications/_Clustalw.py' adding 'Bio/Align/Applications/_Dialign.py' adding 'Bio/Align/Applications/_MSAProbs.py' adding 'Bio/Align/Applications/_Mafft.py' adding 'Bio/Align/Applications/_Muscle.py' adding 'Bio/Align/Applications/_Prank.py' adding 'Bio/Align/Applications/_Probcons.py' adding 'Bio/Align/Applications/_TCoffee.py' adding 'Bio/Align/Applications/__init__.py' adding 'Bio/Align/substitution_matrices/__init__.py' adding 'Bio/Align/substitution_matrices/data/BENNER22' adding 'Bio/Align/substitution_matrices/data/BENNER6' adding 'Bio/Align/substitution_matrices/data/BENNER74' adding 'Bio/Align/substitution_matrices/data/BLASTN' adding 'Bio/Align/substitution_matrices/data/BLASTP' adding 'Bio/Align/substitution_matrices/data/BLOSUM45' adding 'Bio/Align/substitution_matrices/data/BLOSUM50' adding 'Bio/Align/substitution_matrices/data/BLOSUM62' adding 'Bio/Align/substitution_matrices/data/BLOSUM80' adding 'Bio/Align/substitution_matrices/data/BLOSUM90' adding 'Bio/Align/substitution_matrices/data/DAYHOFF' adding 'Bio/Align/substitution_matrices/data/FENG' adding 'Bio/Align/substitution_matrices/data/GENETIC' adding 'Bio/Align/substitution_matrices/data/GONNET1992' adding 'Bio/Align/substitution_matrices/data/HOXD70' adding 'Bio/Align/substitution_matrices/data/JOHNSON' adding 'Bio/Align/substitution_matrices/data/JONES' adding 'Bio/Align/substitution_matrices/data/LEVIN' adding 'Bio/Align/substitution_matrices/data/MCLACHLAN' adding 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adding 'Bio/PDB/ic_rebuild.py' adding 'Bio/PDB/internal_coords.py' adding 'Bio/PDB/kdtrees.c' adding 'Bio/PDB/kdtrees.cpython-313-x86_64-linux-gnu.so' adding 'Bio/PDB/mmcifio.py' adding 'Bio/PDB/parse_pdb_header.py' adding 'Bio/PDB/qcprot.py' adding 'Bio/PDB/vectors.py' adding 'Bio/PDB/mmtf/DefaultParser.py' adding 'Bio/PDB/mmtf/__init__.py' adding 'Bio/PDB/mmtf/mmtfio.py' adding 'Bio/Pathway/__init__.py' adding 'Bio/Pathway/Rep/Graph.py' adding 'Bio/Pathway/Rep/MultiGraph.py' adding 'Bio/Pathway/Rep/__init__.py' adding 'Bio/Phylo/BaseTree.py' adding 'Bio/Phylo/CDAO.py' adding 'Bio/Phylo/CDAOIO.py' adding 'Bio/Phylo/Consensus.py' adding 'Bio/Phylo/NeXML.py' adding 'Bio/Phylo/NeXMLIO.py' adding 'Bio/Phylo/Newick.py' adding 'Bio/Phylo/NewickIO.py' adding 'Bio/Phylo/NexusIO.py' adding 'Bio/Phylo/PhyloXML.py' adding 'Bio/Phylo/PhyloXMLIO.py' adding 'Bio/Phylo/TreeConstruction.py' adding 'Bio/Phylo/__init__.py' adding 'Bio/Phylo/_cdao_owl.py' adding 'Bio/Phylo/_io.py' adding 'Bio/Phylo/_utils.py' adding 'Bio/Phylo/Applications/_Fasttree.py' adding 'Bio/Phylo/Applications/_Phyml.py' adding 'Bio/Phylo/Applications/_Raxml.py' adding 'Bio/Phylo/Applications/__init__.py' adding 'Bio/Phylo/PAML/__init__.py' adding 'Bio/Phylo/PAML/_paml.py' adding 'Bio/Phylo/PAML/_parse_baseml.py' adding 'Bio/Phylo/PAML/_parse_codeml.py' adding 'Bio/Phylo/PAML/_parse_yn00.py' adding 'Bio/Phylo/PAML/baseml.py' adding 'Bio/Phylo/PAML/chi2.py' adding 'Bio/Phylo/PAML/codeml.py' adding 'Bio/Phylo/PAML/yn00.py' adding 'Bio/PopGen/__init__.py' adding 'Bio/PopGen/GenePop/Controller.py' adding 'Bio/PopGen/GenePop/EasyController.py' adding 'Bio/PopGen/GenePop/FileParser.py' adding 'Bio/PopGen/GenePop/LargeFileParser.py' adding 'Bio/PopGen/GenePop/__init__.py' adding 'Bio/Restriction/PrintFormat.py' adding 'Bio/Restriction/Restriction.py' adding 'Bio/Restriction/Restriction_Dictionary.py' adding 'Bio/Restriction/__init__.py' adding 'Bio/SCOP/Cla.py' adding 'Bio/SCOP/Des.py' adding 'Bio/SCOP/Dom.py' adding 'Bio/SCOP/Hie.py' adding 'Bio/SCOP/Raf.py' adding 'Bio/SCOP/Residues.py' adding 'Bio/SCOP/__init__.py' adding 'Bio/SVDSuperimposer/__init__.py' adding 'Bio/SearchIO/BlatIO.py' adding 'Bio/SearchIO/FastaIO.py' adding 'Bio/SearchIO/__init__.py' adding 'Bio/SearchIO/_index.py' adding 'Bio/SearchIO/_utils.py' adding 'Bio/SearchIO/BlastIO/__init__.py' adding 'Bio/SearchIO/BlastIO/blast_tab.py' adding 'Bio/SearchIO/BlastIO/blast_xml.py' adding 'Bio/SearchIO/ExonerateIO/__init__.py' adding 'Bio/SearchIO/ExonerateIO/_base.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_cigar.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_text.py' adding 'Bio/SearchIO/ExonerateIO/exonerate_vulgar.py' adding 'Bio/SearchIO/HHsuiteIO/__init__.py' adding 'Bio/SearchIO/HHsuiteIO/hhsuite2_text.py' adding 'Bio/SearchIO/HmmerIO/__init__.py' adding 'Bio/SearchIO/HmmerIO/_base.py' adding 'Bio/SearchIO/HmmerIO/hmmer2_text.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_domtab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_tab.py' adding 'Bio/SearchIO/HmmerIO/hmmer3_text.py' adding 'Bio/SearchIO/InterproscanIO/__init__.py' adding 'Bio/SearchIO/InterproscanIO/interproscan_xml.py' adding 'Bio/SearchIO/_model/__init__.py' adding 'Bio/SearchIO/_model/_base.py' adding 'Bio/SearchIO/_model/hit.py' adding 'Bio/SearchIO/_model/hsp.py' adding 'Bio/SearchIO/_model/query.py' adding 'Bio/SeqIO/AbiIO.py' adding 'Bio/SeqIO/AceIO.py' adding 'Bio/SeqIO/FastaIO.py' adding 'Bio/SeqIO/GckIO.py' adding 'Bio/SeqIO/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-x86_64-linux-gnu.so' adding 'Bio/SeqUtils/CheckSum.py' adding 'Bio/SeqUtils/IsoelectricPoint.py' adding 'Bio/SeqUtils/MeltingTemp.py' adding 'Bio/SeqUtils/ProtParam.py' adding 'Bio/SeqUtils/ProtParamData.py' adding 'Bio/SeqUtils/__init__.py' adding 'Bio/SeqUtils/lcc.py' adding 'Bio/Sequencing/Ace.py' adding 'Bio/Sequencing/Phd.py' adding 'Bio/Sequencing/__init__.py' adding 'Bio/Sequencing/Applications/_Novoalign.py' adding 'Bio/Sequencing/Applications/__init__.py' adding 'Bio/Sequencing/Applications/_bwa.py' adding 'Bio/Sequencing/Applications/_samtools.py' adding 'Bio/SwissProt/KeyWList.py' adding 'Bio/SwissProt/__init__.py' adding 'Bio/TogoWS/__init__.py' adding 'Bio/UniGene/__init__.py' adding 'Bio/UniProt/GOA.py' adding 'Bio/UniProt/__init__.py' adding 'Bio/codonalign/__init__.py' adding 'Bio/codonalign/codonalignment.py' adding 'Bio/codonalign/codonseq.py' adding 'Bio/motifs/__init__.py' adding 'Bio/motifs/_pwm.c' adding 'Bio/motifs/_pwm.cpython-313-x86_64-linux-gnu.so' adding 'Bio/motifs/alignace.py' adding 'Bio/motifs/clusterbuster.py' adding 'Bio/motifs/mast.py' adding 'Bio/motifs/matrix.py' adding 'Bio/motifs/meme.py' adding 'Bio/motifs/minimal.py' adding 'Bio/motifs/pfm.py' adding 'Bio/motifs/thresholds.py' adding 'Bio/motifs/transfac.py' adding 'Bio/motifs/xms.py' adding 'Bio/motifs/applications/__init__.py' adding 'Bio/motifs/applications/_xxmotif.py' adding 'Bio/motifs/jaspar/__init__.py' adding 'Bio/motifs/jaspar/db.py' adding 'Bio/phenotype/__init__.py' adding 'Bio/phenotype/phen_micro.py' adding 'Bio/phenotype/pm_fitting.py' adding 'BioSQL/BioSeq.py' adding 'BioSQL/BioSeqDatabase.py' adding 'BioSQL/DBUtils.py' adding 'BioSQL/Loader.py' adding 'BioSQL/__init__.py' adding 'BioSQL/py.typed' adding 'biopython-1.84.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-x86_64/wheel Building wheel for biopython (pyproject.toml): finished with status 'done' Created wheel for biopython: filename=biopython-1.84-cp313-cp313-linux_x86_64.whl size=3160080 sha256=7af5c791cab4857ea2cba0d8627ca458445e2a304892ce9587078bacb7e9b466 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.zIsSYy + 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 ++ xargs basename --multiple ++ ls /builddir/build/BUILD/python-biopython-1.84-build/biopython-1.84/pyproject-wheeldir/biopython-1.84-cp313-cp313-linux_x86_64.whl ++ 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_x86_64.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.x86_64-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.x86_64-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.x86_64-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.x86_64-pyproject-files --output-modules /builddir/build/BUILD/python-biopython-1.84-build/python-biopython-1.84-3.fc42.x86_64-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.x86_64-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.x86_64 --unique-debug-src-base python-biopython-1.84-3.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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.x86_64 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 /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Affy/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Affy/__pycache__/CelFile.cpython-313.pyc: replacing with normalized version /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/_ClustalOmega.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Affy/__pycache__/CelFile.cpython-313.opt-1.pyc: replacing with normalized version /builddir/build/BUILD/python-biopython-1.84-build/BUILDROOT/usr/lib64/python3.13/site-packages/Bio/Align/Applications/__pycache__/_Dialign.cpython-313.pyc: rewriting with normalized contents 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/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 /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 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.4P1oQR + umask 022 + cd /builddir/build/BUILD/python-biopython-1.84-build ~/build/BUILD/python-biopython-1.84-build/biopython-1.84/Tests ~/build/BUILD/python-biopython-1.84-build/biopython-1.84 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 ++ 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_++ grep -v test_Tutorial.py 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_Align_bigbed.py + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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 0.041 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 ---------------------------------------------------------------------- Ran 1 test in 0.015 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 2.205 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.043 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.064 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.043 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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 0.141 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.069 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 ---------------------------------------------------------------------- Ran 1 test in 0.304 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.143 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.487 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.389 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.152 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.066 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 3.319 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.078 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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 0.120 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.064 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.296 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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 0.768 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.081 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.052 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.082 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.097 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 ---------------------------------------------------------------------- Ran 1 test in 0.352 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=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 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_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 0.304 seconds + for test in `ls test_*.py | grep -v test_Align_bigbed.py | grep -v test_Tutorial.py` + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 0.110 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.4P1oQR (%check) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.4P1oQR (%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-x86_64-1736228517.796432/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-x86_64) 1 minutes 3 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 b89fb3f07269475289badb983e381af8 -D /var/lib/mock/fedora-rawhide-x86_64-1736228517.796432/root -a -u mockbuild --capability=cap_ipc_lock --rlimit=RLIMIT_NOFILE=10240 --capability=cap_ipc_lock --bind=/tmp/mock-resolv.p17_qn5g:/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 x86_64 /builddir/build/originals/python-biopython.spec' Copr build error: Build failed