Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c148' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5175150 --chroot fedora-rawhide-x86_64 --detached Version: 0.62 PID: 19888 Logging PID: 19889 Task: {'appstream': False, 'background': True, 'build_id': 5175150, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.80-1', 'project_dirname': 'gcc-13-test', 'project_name': 'gcc-13-test', 'project_owner': 'jakub', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/', 'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch', 'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}], 'sandbox': 'jakub/gcc-13-test--jakub', 'source_json': {}, 'source_type': None, 'submitter': 'jakub', 'tags': [], 'task_id': '5175150-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython'... Running: git checkout af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa cmd: ['git', 'checkout', 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython rc: 0 stdout: stderr: Note: switching to 'af214c487f0ec0f4dd938d0ce3cfbbe9dd7b74fa'. 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 af214c4 automatic import of python-biopython Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/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-1.80.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated INFO: Calling: curl -H Pragma: -o biopython-1.80.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/python-biopython/biopython-1.80.tar.gz/md5/0d1c25c9d67a29534220e03e39f69052/biopython-1.80.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 17.0M 100 17.0M 0 0 28.2M 0 --:--:-- --:--:-- --:--:-- 28.2M INFO: Reading stdout from command: md5sum biopython-1.80.tar.gz Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672135248.183296 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-pxkg7ivm/python-biopython/python-biopython.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672135248.183296/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 65 MB/s | 35 MB 00:00 Additional repo https_jakub_fedorapeople_org_fe 315 kB/s | 92 kB 00:00 fedora 21 MB/s | 65 MB 00:03 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: dnf noarch 4.14.0-1.fc38 fedora 480 k dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k Installing dependencies: alternatives x86_64 1.21-1.fc38 copr_base 39 k audit-libs x86_64 3.0.9-2.fc38 fedora 116 k basesystem noarch 11-14.fc37 fedora 7.0 k bash x86_64 5.2.9-3.fc38 copr_base 1.8 M bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-1.fc38 copr_base 346 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 copr_base 793 k dbus-libs x86_64 1:1.14.4-1.fc38 copr_base 156 k dnf-data noarch 4.14.0-1.fc38 fedora 43 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf x86_64 0.188-3.fc38 copr_base 196 k elfutils-libs x86_64 0.188-3.fc38 copr_base 257 k expat x86_64 2.5.0-1.fc38 copr_base 111 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-common noarch 38-0.6 fedora 21 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file-libs x86_64 5.42-4.fc38 copr_base 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M findutils x86_64 1:4.9.0-2.fc38 copr_base 483 k gawk x86_64 5.1.1-4.fc38 copr_base 1.0 M gdbm-libs x86_64 1:1.23-2.fc38 copr_base 56 k glib2 x86_64 2.74.1-2.fc38 copr_base 2.7 M glibc x86_64 2.36.9000-19.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-19.fc38 fedora 309 k glibc-minimal-langpack x86_64 2.36.9000-19.fc38 fedora 30 k gmp x86_64 1:6.2.1-3.fc38 copr_base 315 k gnupg2 x86_64 2.3.8-1.fc38 copr_base 2.5 M gnutls x86_64 3.7.8-9.fc38 copr_base 1.1 M gpgme x86_64 1.17.1-3.fc38 copr_base 210 k grep x86_64 3.8-1.fc38 copr_base 282 k ima-evm-utils x86_64 1.4-6.fc38 copr_base 63 k json-c x86_64 0.16-3.fc38 copr_base 42 k keyutils-libs x86_64 1.6.1-5.fc38 copr_base 32 k krb5-libs x86_64 1.20.1-3.fc38 copr_base 719 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-3.fc38 copr_base 397 k libassuan x86_64 2.5.5-5.fc38 copr_base 68 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libb2 x86_64 0.98.1-7.fc38 copr_base 25 k libblkid x86_64 2.38.1-3.fc38 fedora 106 k libbrotli x86_64 1.0.9-9.fc38 copr_base 316 k libcap x86_64 2.48-5.fc38 copr_base 67 k libcap-ng x86_64 0.8.3-4.fc38 copr_base 33 k libcom_err x86_64 1.46.5-3.fc38 copr_base 26 k libcomps x86_64 0.1.18-4.fc38 copr_base 77 k libcurl x86_64 7.87.0-1.fc38 copr_base 302 k libdnf x86_64 0.68.0-1.fc38 copr_base 659 k libevent x86_64 2.1.12-7.fc38 copr_base 259 k libffi x86_64 3.4.4-1.fc38 copr_base 38 k libfsverity x86_64 1.4-8.fc38 copr_base 20 k libgcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k libgcrypt x86_64 1.10.1-6.fc38 copr_base 512 k libgomp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 300 k libgpg-error x86_64 1.46-1.fc38 copr_base 222 k libidn2 x86_64 2.3.4-1.fc38 copr_base 154 k libksba x86_64 1.6.3-1.fc38 copr_base 158 k libmodulemd x86_64 2.14.0-4.fc38 copr_base 237 k libmount x86_64 2.38.1-3.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc38 copr_base 31 k libpsl x86_64 0.21.1-6.fc38 copr_base 65 k librepo x86_64 1.15.1-1.fc38 copr_base 97 k libreport-filesystem noarch 2.17.6-1.fc38 copr_base 14 k libselinux x86_64 3.4-6.fc38 copr_base 86 k libsemanage x86_64 3.4-6.fc38 copr_base 120 k libsepol x86_64 3.4-4.fc38 copr_base 321 k libsigsegv x86_64 2.14-3.fc38 copr_base 27 k libsmartcols x86_64 2.38.1-3.fc38 fedora 64 k libsolv x86_64 0.7.22-3.fc38 copr_base 406 k libssh x86_64 0.10.4-2.fc38 copr_base 210 k libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k libstdc++ x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 799 k libtasn1 x86_64 4.19.0-1.fc38 copr_base 76 k libtirpc x86_64 1.3.3-0.fc38 copr_base 94 k libunistring x86_64 1.0-2.fc38 copr_base 541 k libuuid x86_64 2.38.1-3.fc38 fedora 27 k libverto x86_64 0.3.2-4.fc38 copr_base 21 k libxcrypt x86_64 4.4.33-5.fc38 copr_base 120 k libxml2 x86_64 2.10.3-2.fc38 copr_base 704 k libyaml x86_64 0.2.5-8.fc38 copr_base 60 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 copr_base 133 k lz4-libs x86_64 1.9.3-5.fc38 copr_base 70 k mpdecimal x86_64 2.5.1-4.fc38 copr_base 102 k mpfr x86_64 4.1.1-2.fc38 copr_base 599 k ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k ncurses-libs x86_64 6.3-5.20221126.fc38 copr_base 329 k nettle x86_64 3.8-2.fc38 copr_base 414 k npth x86_64 1.6-10.fc38 copr_base 25 k openldap x86_64 2.6.3-1.fc38 copr_base 254 k openssl-libs x86_64 1:3.0.5-6.fc38 copr_base 2.1 M p11-kit x86_64 0.24.1-5.fc38 copr_base 360 k p11-kit-trust x86_64 0.24.1-5.fc38 copr_base 138 k pcre2 x86_64 10.40-1.fc38.1 copr_base 236 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k popt x86_64 1.19-1.fc38 copr_base 59 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.1-1.fc38 fedora 27 k python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k python3-dbus x86_64 1.3.2-1.fc38 copr_base 147 k python3-distro noarch 1.8.0-1.fc38 fedora 49 k python3-dnf noarch 4.14.0-1.fc38 fedora 607 k python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k python3-gpg x86_64 1.17.1-3.fc38 copr_base 282 k python3-hawkey x86_64 0.68.0-1.fc38 copr_base 110 k python3-libcomps x86_64 0.1.18-4.fc38 copr_base 48 k python3-libdnf x86_64 0.68.0-1.fc38 copr_base 820 k python3-libs x86_64 3.11.1-1.fc38 fedora 9.6 M python3-rpm x86_64 4.18.0-8.fc38 fedora 94 k python3-six noarch 1.16.0-8.fc37 fedora 42 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-8.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-8.fc38 fedora 94 k rpm-libs x86_64 4.18.0-8.fc38 fedora 309 k rpm-sequoia x86_64 1.2.0-1.fc38 fedora 829 k rpm-sign-libs x86_64 4.18.0-8.fc38 fedora 27 k sed x86_64 4.8-11.fc37 fedora 306 k setup noarch 2.14.3-1.fc38 fedora 152 k shadow-utils x86_64 2:4.13-3.fc38 fedora 1.3 M sqlite-libs x86_64 3.40.0-1.fc38 fedora 661 k systemd-libs x86_64 252.4-598.fc38 fedora 632 k tpm2-tss x86_64 4.0.0-0.1.rc2.fc38 fedora 710 k tzdata noarch 2022g-1.fc38 fedora 716 k xz-libs x86_64 5.2.9-1.fc38 fedora 93 k zchunk-libs x86_64 1.2.3-1.fc38 fedora 51 k zlib x86_64 1.2.13-1.fc38 fedora 94 k Transaction Summary ========================================================================================================================= Install 137 Packages Total download size: 57 M Installed size: 200 M Downloading Packages: (1/137): bzip2-libs-1.0.8-12.fc38.x86_64.rpm 411 kB/s | 42 kB 00:00 (2/137): alternatives-1.21-1.fc38.x86_64.rpm 348 kB/s | 39 kB 00:00 (3/137): bash-5.2.9-3.fc38.x86_64.rpm 12 MB/s | 1.8 MB 00:00 (4/137): coreutils-9.1-8.fc38.x86_64.rpm 22 MB/s | 1.1 MB 00:00 (5/137): coreutils-common-9.1-8.fc38.x86_64.rpm 32 MB/s | 2.0 MB 00:00 (6/137): curl-7.87.0-1.fc38.x86_64.rpm 14 MB/s | 346 kB 00:00 (7/137): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rp 26 MB/s | 793 kB 00:00 (8/137): dbus-libs-1.14.4-1.fc38.x86_64.rpm 15 MB/s | 156 kB 00:00 (9/137): elfutils-default-yama-scope-0.188-3.fc 1.7 MB/s | 16 kB 00:00 (10/137): elfutils-libelf-0.188-3.fc38.x86_64.r 19 MB/s | 196 kB 00:00 (11/137): elfutils-libs-0.188-3.fc38.x86_64.rpm 23 MB/s | 257 kB 00:00 (12/137): expat-2.5.0-1.fc38.x86_64.rpm 9.3 MB/s | 111 kB 00:00 (13/137): file-libs-5.42-4.fc38.x86_64.rpm 44 MB/s | 676 kB 00:00 (14/137): findutils-4.9.0-2.fc38.x86_64.rpm 29 MB/s | 483 kB 00:00 (15/137): gawk-5.1.1-4.fc38.x86_64.rpm 18 MB/s | 1.0 MB 00:00 (16/137): gdbm-libs-1.23-2.fc38.x86_64.rpm 1.3 MB/s | 56 kB 00:00 (17/137): glib2-2.74.1-2.fc38.x86_64.rpm 60 MB/s | 2.7 MB 00:00 (18/137): gmp-6.2.1-3.fc38.x86_64.rpm 26 MB/s | 315 kB 00:00 (19/137): gnupg2-2.3.8-1.fc38.x86_64.rpm 50 MB/s | 2.5 MB 00:00 (20/137): gnutls-3.7.8-9.fc38.x86_64.rpm 23 MB/s | 1.1 MB 00:00 (21/137): gpgme-1.17.1-3.fc38.x86_64.rpm 5.1 MB/s | 210 kB 00:00 (22/137): grep-3.8-1.fc38.x86_64.rpm 23 MB/s | 282 kB 00:00 (23/137): ima-evm-utils-1.4-6.fc38.x86_64.rpm 4.7 MB/s | 63 kB 00:00 (24/137): json-c-0.16-3.fc38.x86_64.rpm 3.0 MB/s | 42 kB 00:00 (25/137): keyutils-libs-1.6.1-5.fc38.x86_64.rpm 3.6 MB/s | 32 kB 00:00 (26/137): krb5-libs-1.20.1-3.fc38.x86_64.rpm 45 MB/s | 719 kB 00:00 (27/137): libacl-2.3.1-4.fc38.x86_64.rpm 1.4 MB/s | 24 kB 00:00 (28/137): libarchive-3.6.1-3.fc38.x86_64.rpm 32 MB/s | 397 kB 00:00 (29/137): libassuan-2.5.5-5.fc38.x86_64.rpm 7.3 MB/s | 68 kB 00:00 (30/137): libattr-2.5.1-5.fc38.x86_64.rpm 2.1 MB/s | 18 kB 00:00 (31/137): libb2-0.98.1-7.fc38.x86_64.rpm 2.9 MB/s | 25 kB 00:00 (32/137): libbrotli-1.0.9-9.fc38.x86_64.rpm 23 MB/s | 316 kB 00:00 (33/137): libcap-2.48-5.fc38.x86_64.rpm 4.7 MB/s | 67 kB 00:00 (34/137): libcap-ng-0.8.3-4.fc38.x86_64.rpm 2.8 MB/s | 33 kB 00:00 (35/137): libcom_err-1.46.5-3.fc38.x86_64.rpm 3.1 MB/s | 26 kB 00:00 (36/137): libcomps-0.1.18-4.fc38.x86_64.rpm 8.4 MB/s | 77 kB 00:00 (37/137): libcurl-7.87.0-1.fc38.x86_64.rpm 25 MB/s | 302 kB 00:00 (38/137): libdnf-0.68.0-1.fc38.x86_64.rpm 43 MB/s | 659 kB 00:00 (39/137): libevent-2.1.12-7.fc38.x86_64.rpm 17 MB/s | 259 kB 00:00 (40/137): libffi-3.4.4-1.fc38.x86_64.rpm 2.9 MB/s | 38 kB 00:00 (41/137): libfsverity-1.4-8.fc38.x86_64.rpm 2.3 MB/s | 20 kB 00:00 (42/137): libgcrypt-1.10.1-6.fc38.x86_64.rpm 37 MB/s | 512 kB 00:00 (43/137): libgpg-error-1.46-1.fc38.x86_64.rpm 15 MB/s | 222 kB 00:00 (44/137): libidn2-2.3.4-1.fc38.x86_64.rpm 16 MB/s | 154 kB 00:00 (45/137): libksba-1.6.3-1.fc38.x86_64.rpm 16 MB/s | 158 kB 00:00 (46/137): libmodulemd-2.14.0-4.fc38.x86_64.rpm 21 MB/s | 237 kB 00:00 (47/137): libnghttp2-1.51.0-1.fc38.x86_64.rpm 7.1 MB/s | 75 kB 00:00 (48/137): libnsl2-2.0.0-4.fc38.x86_64.rpm 3.2 MB/s | 31 kB 00:00 (49/137): libpsl-0.21.1-6.fc38.x86_64.rpm 7.4 MB/s | 65 kB 00:00 (50/137): librepo-1.15.1-1.fc38.x86_64.rpm 10 MB/s | 97 kB 00:00 (51/137): libreport-filesystem-2.17.6-1.fc38.no 1.7 MB/s | 14 kB 00:00 (52/137): libselinux-3.4-6.fc38.x86_64.rpm 9.0 MB/s | 86 kB 00:00 (53/137): libsemanage-3.4-6.fc38.x86_64.rpm 11 MB/s | 120 kB 00:00 (54/137): libsepol-3.4-4.fc38.x86_64.rpm 27 MB/s | 321 kB 00:00 (55/137): libsigsegv-2.14-3.fc38.x86_64.rpm 2.9 MB/s | 27 kB 00:00 (56/137): libsolv-0.7.22-3.fc38.x86_64.rpm 32 MB/s | 406 kB 00:00 (57/137): libssh-0.10.4-2.fc38.x86_64.rpm 18 MB/s | 210 kB 00:00 (58/137): libssh-config-0.10.4-2.fc38.noarch.rp 824 kB/s | 9.2 kB 00:00 (59/137): libtasn1-4.19.0-1.fc38.x86_64.rpm 7.5 MB/s | 76 kB 00:00 (60/137): libtirpc-1.3.3-0.fc38.x86_64.rpm 9.7 MB/s | 94 kB 00:00 (61/137): libunistring-1.0-2.fc38.x86_64.rpm 36 MB/s | 541 kB 00:00 (62/137): libverto-0.3.2-4.fc38.x86_64.rpm 1.8 MB/s | 21 kB 00:00 (63/137): libxcrypt-4.4.33-5.fc38.x86_64.rpm 13 MB/s | 120 kB 00:00 (64/137): libxml2-2.10.3-2.fc38.x86_64.rpm 45 MB/s | 704 kB 00:00 (65/137): libyaml-0.2.5-8.fc38.x86_64.rpm 3.7 MB/s | 60 kB 00:00 (66/137): lua-libs-5.4.4-6.fc38.x86_64.rpm 11 MB/s | 133 kB 00:00 (67/137): lz4-libs-1.9.3-5.fc38.x86_64.rpm 7.8 MB/s | 70 kB 00:00 (68/137): mpdecimal-2.5.1-4.fc38.x86_64.rpm 11 MB/s | 102 kB 00:00 (69/137): mpfr-4.1.1-2.fc38.x86_64.rpm 39 MB/s | 599 kB 00:00 (70/137): ncurses-base-6.3-5.20221126.fc38.noar 6.9 MB/s | 62 kB 00:00 (71/137): ncurses-libs-6.3-5.20221126.fc38.x86_ 28 MB/s | 329 kB 00:00 (72/137): nettle-3.8-2.fc38.x86_64.rpm 32 MB/s | 414 kB 00:00 (73/137): npth-1.6-10.fc38.x86_64.rpm 2.1 MB/s | 25 kB 00:00 (74/137): openldap-2.6.3-1.fc38.x86_64.rpm 23 MB/s | 254 kB 00:00 (75/137): openssl-libs-3.0.5-6.fc38.x86_64.rpm 68 MB/s | 2.1 MB 00:00 (76/137): p11-kit-0.24.1-5.fc38.x86_64.rpm 11 MB/s | 360 kB 00:00 (77/137): p11-kit-trust-0.24.1-5.fc38.x86_64.rp 4.6 MB/s | 138 kB 00:00 (78/137): pcre2-10.40-1.fc38.1.x86_64.rpm 22 MB/s | 236 kB 00:00 (79/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp 13 MB/s | 143 kB 00:00 (80/137): popt-1.19-1.fc38.x86_64.rpm 5.4 MB/s | 59 kB 00:00 (81/137): python3-dbus-1.3.2-1.fc38.x86_64.rpm 15 MB/s | 147 kB 00:00 (82/137): python3-gpg-1.17.1-3.fc38.x86_64.rpm 24 MB/s | 282 kB 00:00 (83/137): python3-hawkey-0.68.0-1.fc38.x86_64.r 9.1 MB/s | 110 kB 00:00 (84/137): python3-libcomps-0.1.18-4.fc38.x86_64 5.5 MB/s | 48 kB 00:00 (85/137): python3-libdnf-0.68.0-1.fc38.x86_64.r 49 MB/s | 820 kB 00:00 (86/137): libgcc-13.0.0-0.4.fc38.x86_64.rpm 639 kB/s | 93 kB 00:00 (87/137): libgomp-13.0.0-0.4.fc38.x86_64.rpm 1.6 MB/s | 300 kB 00:00 (88/137): libstdc++-13.0.0-0.4.fc38.x86_64.rpm 3.9 MB/s | 799 kB 00:00 (89/137): basesystem-11-14.fc37.noarch.rpm 88 kB/s | 7.0 kB 00:00 (90/137): crypto-policies-20221215-1.gita4c31a3 675 kB/s | 90 kB 00:00 (91/137): audit-libs-3.0.9-2.fc38.x86_64.rpm 444 kB/s | 116 kB 00:00 (92/137): dnf-data-4.14.0-1.fc38.noarch.rpm 819 kB/s | 43 kB 00:00 (93/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 711 kB/s | 34 kB 00:00 (94/137): dnf-4.14.0-1.fc38.noarch.rpm 3.2 MB/s | 480 kB 00:00 (95/137): fedora-gpg-keys-38-0.3.noarch.rpm 1.7 MB/s | 125 kB 00:00 (96/137): ca-certificates-2022.2.54-5.fc37.noar 2.5 MB/s | 829 kB 00:00 (97/137): fedora-release-38-0.6.noarch.rpm 258 kB/s | 11 kB 00:00 (98/137): fedora-release-identity-basic-38-0.6. 280 kB/s | 11 kB 00:00 (99/137): fedora-release-common-38-0.6.noarch.r 471 kB/s | 21 kB 00:00 (100/137): fedora-repos-38-0.3.noarch.rpm 251 kB/s | 10 kB 00:00 (101/137): fedora-repos-rawhide-38-0.3.noarch.r 234 kB/s | 9.7 kB 00:00 (102/137): glibc-common-2.36.9000-19.fc38.x86_6 6.0 MB/s | 309 kB 00:00 (103/137): glibc-minimal-langpack-2.36.9000-19. 730 kB/s | 30 kB 00:00 (104/137): glibc-2.36.9000-19.fc38.x86_64.rpm 15 MB/s | 2.1 MB 00:00 (105/137): filesystem-3.18-2.fc37.x86_64.rpm 6.5 MB/s | 1.1 MB 00:00 (106/137): libblkid-2.38.1-3.fc38.x86_64.rpm 2.4 MB/s | 106 kB 00:00 (107/137): libmount-2.38.1-3.fc38.x86_64.rpm 3.1 MB/s | 135 kB 00:00 (108/137): libsmartcols-2.38.1-3.fc38.x86_64.rp 1.5 MB/s | 64 kB 00:00 (109/137): libuuid-2.38.1-3.fc38.x86_64.rpm 657 kB/s | 27 kB 00:00 (110/137): libzstd-1.5.2-3.fc37.x86_64.rpm 6.5 MB/s | 294 kB 00:00 (111/137): publicsuffix-list-dafsa-20221208-1.f 1.4 MB/s | 59 kB 00:00 (112/137): python-setuptools-wheel-65.5.1-1.fc3 14 MB/s | 715 kB 00:00 (113/137): python3-3.11.1-1.fc38.x86_64.rpm 642 kB/s | 27 kB 00:00 (114/137): python-pip-wheel-22.3.1-1.fc38.noarc 15 MB/s | 1.4 MB 00:00 (115/137): python3-dateutil-2.8.2-4.fc37.noarch 7.8 MB/s | 361 kB 00:00 (116/137): python3-distro-1.8.0-1.fc38.noarch.r 1.2 MB/s | 49 kB 00:00 (117/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 12 MB/s | 607 kB 00:00 (118/137): python3-dnf-plugins-core-4.3.1-1.fc3 6.1 MB/s | 277 kB 00:00 (119/137): python3-rpm-4.18.0-8.fc38.x86_64.rpm 2.1 MB/s | 94 kB 00:00 (120/137): python3-six-1.16.0-8.fc37.noarch.rpm 985 kB/s | 42 kB 00:00 (121/137): readline-8.2-2.fc38.x86_64.rpm 4.4 MB/s | 211 kB 00:00 (122/137): rpm-build-libs-4.18.0-8.fc38.x86_64. 2.1 MB/s | 94 kB 00:00 (123/137): rpm-4.18.0-8.fc38.x86_64.rpm 5.9 MB/s | 572 kB 00:00 (124/137): rpm-libs-4.18.0-8.fc38.x86_64.rpm 6.8 MB/s | 309 kB 00:00 (125/137): rpm-sign-libs-4.18.0-8.fc38.x86_64.r 646 kB/s | 27 kB 00:00 (126/137): sed-4.8-11.fc37.x86_64.rpm 6.7 MB/s | 306 kB 00:00 (127/137): python3-libs-3.11.1-1.fc38.x86_64.rp 31 MB/s | 9.6 MB 00:00 (128/137): rpm-sequoia-1.2.0-1.fc38.x86_64.rpm 6.3 MB/s | 829 kB 00:00 (129/137): setup-2.14.3-1.fc38.noarch.rpm 3.5 MB/s | 152 kB 00:00 (130/137): systemd-libs-252.4-598.fc38.x86_64.r 12 MB/s | 632 kB 00:00 (131/137): shadow-utils-4.13-3.fc38.x86_64.rpm 13 MB/s | 1.3 MB 00:00 (132/137): sqlite-libs-3.40.0-1.fc38.x86_64.rpm 6.7 MB/s | 661 kB 00:00 (133/137): tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64.r 13 MB/s | 710 kB 00:00 (134/137): zchunk-libs-1.2.3-1.fc38.x86_64.rpm 1.2 MB/s | 51 kB 00:00 (135/137): xz-libs-5.2.9-1.fc38.x86_64.rpm 1.1 MB/s | 93 kB 00:00 (136/137): tzdata-2022g-1.fc38.noarch.rpm 7.8 MB/s | 716 kB 00:00 (137/137): zlib-1.2.13-1.fc38.x86_64.rpm 2.1 MB/s | 94 kB 00:00 -------------------------------------------------------------------------------- Total 26 MB/s | 57 MB 00:02 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.x86_64 1/137 Running scriptlet: libgcc-13.0.0-0.4.fc38.x86_64 1/137 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/137 Installing : tzdata-2022g-1.fc38.noarch 3/137 Installing : fedora-release-identity-basic-38-0.6.noarch 4/137 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 5/137 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 6/137 Installing : fedora-gpg-keys-38-0.3.noarch 7/137 Installing : fedora-release-38-0.6.noarch 8/137 Installing : fedora-release-common-38-0.6.noarch 9/137 Installing : fedora-repos-rawhide-38-0.3.noarch 10/137 Installing : fedora-repos-38-0.3.noarch 11/137 Installing : setup-2.14.3-1.fc38.noarch 12/137 Running scriptlet: setup-2.14.3-1.fc38.noarch 12/137 Installing : filesystem-3.18-2.fc37.x86_64 13/137 Installing : basesystem-11-14.fc37.noarch 14/137 Installing : pcre2-syntax-10.40-1.fc38.1.noarch 15/137 Installing : ncurses-base-6.3-5.20221126.fc38.noarch 16/137 Installing : ncurses-libs-6.3-5.20221126.fc38.x86_64 17/137 Running scriptlet: glibc-2.36.9000-19.fc38.x86_64 18/137 Installing : glibc-2.36.9000-19.fc38.x86_64 18/137 Running scriptlet: glibc-2.36.9000-19.fc38.x86_64 18/137 Installing : bash-5.2.9-3.fc38.x86_64 19/137 Running scriptlet: bash-5.2.9-3.fc38.x86_64 19/137 Installing : glibc-common-2.36.9000-19.fc38.x86_64 20/137 Installing : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 21/137 Installing : zlib-1.2.13-1.fc38.x86_64 22/137 Installing : bzip2-libs-1.0.8-12.fc38.x86_64 23/137 Installing : xz-libs-5.2.9-1.fc38.x86_64 24/137 Installing : libzstd-1.5.2-3.fc37.x86_64 25/137 Installing : sqlite-libs-3.40.0-1.fc38.x86_64 26/137 Installing : gmp-1:6.2.1-3.fc38.x86_64 27/137 Installing : libcap-2.48-5.fc38.x86_64 28/137 Installing : libgpg-error-1.46-1.fc38.x86_64 29/137 Installing : popt-1.19-1.fc38.x86_64 30/137 Installing : libxml2-2.10.3-2.fc38.x86_64 31/137 Installing : lua-libs-5.4.4-6.fc38.x86_64 32/137 Installing : libstdc++-13.0.0-0.4.fc38.x86_64 33/137 Installing : libuuid-2.38.1-3.fc38.x86_64 34/137 Installing : elfutils-libelf-0.188-3.fc38.x86_64 35/137 Installing : file-libs-5.42-4.fc38.x86_64 36/137 Installing : libattr-2.5.1-5.fc38.x86_64 37/137 Installing : libacl-2.3.1-4.fc38.x86_64 38/137 Installing : libffi-3.4.4-1.fc38.x86_64 39/137 Installing : p11-kit-0.24.1-5.fc38.x86_64 40/137 Installing : libunistring-1.0-2.fc38.x86_64 41/137 Installing : libidn2-2.3.4-1.fc38.x86_64 42/137 Installing : libxcrypt-4.4.33-5.fc38.x86_64 43/137 Installing : pcre2-10.40-1.fc38.1.x86_64 44/137 Installing : readline-8.2-2.fc38.x86_64 45/137 Installing : libassuan-2.5.5-5.fc38.x86_64 46/137 Installing : nettle-3.8-2.fc38.x86_64 47/137 Installing : rpm-sequoia-1.2.0-1.fc38.x86_64 48/137 Installing : expat-2.5.0-1.fc38.x86_64 49/137 Installing : gdbm-libs-1:1.23-2.fc38.x86_64 50/137 Installing : json-c-0.16-3.fc38.x86_64 51/137 Installing : keyutils-libs-1.6.1-5.fc38.x86_64 52/137 Installing : libcom_err-1.46.5-3.fc38.x86_64 53/137 Installing : libsepol-3.4-4.fc38.x86_64 54/137 Installing : libselinux-3.4-6.fc38.x86_64 55/137 Installing : sed-4.8-11.fc37.x86_64 56/137 Installing : libtasn1-4.19.0-1.fc38.x86_64 57/137 Installing : lz4-libs-1.9.3-5.fc38.x86_64 58/137 Installing : libgomp-13.0.0-0.4.fc38.x86_64 59/137 Installing : libsmartcols-2.38.1-3.fc38.x86_64 60/137 Installing : libb2-0.98.1-7.fc38.x86_64 61/137 Installing : systemd-libs-252.4-598.fc38.x86_64 62/137 Installing : dbus-libs-1:1.14.4-1.fc38.x86_64 63/137 Installing : findutils-1:4.9.0-2.fc38.x86_64 64/137 Installing : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 65/137 Installing : libcomps-0.1.18-4.fc38.x86_64 66/137 Installing : grep-3.8-1.fc38.x86_64 67/137 Installing : libpsl-0.21.1-6.fc38.x86_64 68/137 Installing : libblkid-2.38.1-3.fc38.x86_64 69/137 Installing : libmount-2.38.1-3.fc38.x86_64 70/137 Installing : mpdecimal-2.5.1-4.fc38.x86_64 71/137 Installing : libgcrypt-1.10.1-6.fc38.x86_64 72/137 Installing : libksba-1.6.3-1.fc38.x86_64 73/137 Installing : mpfr-4.1.1-2.fc38.x86_64 74/137 Installing : elfutils-default-yama-scope-0.188-3.fc38.noarch 75/137 Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch 75/137 Installing : elfutils-libs-0.188-3.fc38.x86_64 76/137 Installing : alternatives-1.21-1.fc38.x86_64 77/137 Installing : p11-kit-trust-0.24.1-5.fc38.x86_64 78/137 Running scriptlet: p11-kit-trust-0.24.1-5.fc38.x86_64 78/137 Installing : gnutls-3.7.8-9.fc38.x86_64 79/137 Installing : glib2-2.74.1-2.fc38.x86_64 80/137 Installing : libbrotli-1.0.9-9.fc38.x86_64 81/137 Installing : libcap-ng-0.8.3-4.fc38.x86_64 82/137 Installing : audit-libs-3.0.9-2.fc38.x86_64 83/137 Installing : rpm-libs-4.18.0-8.fc38.x86_64 84/137 Installing : rpm-build-libs-4.18.0-8.fc38.x86_64 85/137 Installing : libsemanage-3.4-6.fc38.x86_64 86/137 Installing : shadow-utils-2:4.13-3.fc38.x86_64 87/137 Installing : libnghttp2-1.51.0-1.fc38.x86_64 88/137 Installing : libsigsegv-2.14-3.fc38.x86_64 89/137 Installing : gawk-5.1.1-4.fc38.x86_64 90/137 Installing : libverto-0.3.2-4.fc38.x86_64 91/137 Installing : libyaml-0.2.5-8.fc38.x86_64 92/137 Installing : libmodulemd-2.14.0-4.fc38.x86_64 93/137 Installing : npth-1.6-10.fc38.x86_64 94/137 Installing : libssh-config-0.10.4-2.fc38.noarch 95/137 Installing : libreport-filesystem-2.17.6-1.fc38.noarch 96/137 Installing : dnf-data-4.14.0-1.fc38.noarch 97/137 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : coreutils-common-9.1-8.fc38.x86_64 98/137 Installing : openssl-libs-1:3.0.5-6.fc38.x86_64 99/137 Installing : coreutils-9.1-8.fc38.x86_64 100/137 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 101/137 Installing : ca-certificates-2022.2.54-5.fc37.noarch 101/137 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 101/137 Installing : krb5-libs-1.20.1-3.fc38.x86_64 102/137 Installing : libtirpc-1.3.3-0.fc38.x86_64 103/137 Installing : libfsverity-1.4-8.fc38.x86_64 104/137 Installing : zchunk-libs-1.2.3-1.fc38.x86_64 105/137 Installing : libsolv-0.7.22-3.fc38.x86_64 106/137 Installing : libnsl2-2.0.0-4.fc38.x86_64 107/137 Installing : libssh-0.10.4-2.fc38.x86_64 108/137 Installing : python-pip-wheel-22.3.1-1.fc38.noarch 109/137 Installing : python3-3.11.1-1.fc38.x86_64 110/137 Installing : python3-libs-3.11.1-1.fc38.x86_64 111/137 Installing : python3-dbus-1.3.2-1.fc38.x86_64 112/137 Installing : python3-libcomps-0.1.18-4.fc38.x86_64 113/137 Installing : python3-distro-1.8.0-1.fc38.noarch 114/137 Installing : python3-six-1.16.0-8.fc37.noarch 115/137 Installing : python3-dateutil-1:2.8.2-4.fc37.noarch 116/137 Installing : libarchive-3.6.1-3.fc38.x86_64 117/137 Installing : libevent-2.1.12-7.fc38.x86_64 118/137 Installing : openldap-2.6.3-1.fc38.x86_64 119/137 Installing : libcurl-7.87.0-1.fc38.x86_64 120/137 Installing : gnupg2-2.3.8-1.fc38.x86_64 121/137 Installing : gpgme-1.17.1-3.fc38.x86_64 122/137 Installing : librepo-1.15.1-1.fc38.x86_64 123/137 Installing : libdnf-0.68.0-1.fc38.x86_64 124/137 Installing : python3-libdnf-0.68.0-1.fc38.x86_64 125/137 Installing : python3-hawkey-0.68.0-1.fc38.x86_64 126/137 Installing : python3-gpg-1.17.1-3.fc38.x86_64 127/137 Installing : curl-7.87.0-1.fc38.x86_64 128/137 Running scriptlet: tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 129/137 useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Installing : tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 129/137 Installing : ima-evm-utils-1.4-6.fc38.x86_64 130/137 Installing : rpm-sign-libs-4.18.0-8.fc38.x86_64 131/137 Installing : python3-rpm-4.18.0-8.fc38.x86_64 132/137 Installing : python3-dnf-4.14.0-1.fc38.noarch 133/137 Installing : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 134/137 Installing : dnf-plugins-core-4.3.1-1.fc38.noarch 135/137 Installing : dnf-4.14.0-1.fc38.noarch 136/137 Running scriptlet: dnf-4.14.0-1.fc38.noarch 136/137 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 137/137 Installing : rpm-4.18.0-8.fc38.x86_64 137/137 Running scriptlet: filesystem-3.18-2.fc37.x86_64 137/137 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 137/137 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 137/137 Verifying : alternatives-1.21-1.fc38.x86_64 1/137 Verifying : bash-5.2.9-3.fc38.x86_64 2/137 Verifying : bzip2-libs-1.0.8-12.fc38.x86_64 3/137 Verifying : coreutils-9.1-8.fc38.x86_64 4/137 Verifying : coreutils-common-9.1-8.fc38.x86_64 5/137 Verifying : curl-7.87.0-1.fc38.x86_64 6/137 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 7/137 Verifying : dbus-libs-1:1.14.4-1.fc38.x86_64 8/137 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 9/137 Verifying : elfutils-libelf-0.188-3.fc38.x86_64 10/137 Verifying : elfutils-libs-0.188-3.fc38.x86_64 11/137 Verifying : expat-2.5.0-1.fc38.x86_64 12/137 Verifying : file-libs-5.42-4.fc38.x86_64 13/137 Verifying : findutils-1:4.9.0-2.fc38.x86_64 14/137 Verifying : gawk-5.1.1-4.fc38.x86_64 15/137 Verifying : gdbm-libs-1:1.23-2.fc38.x86_64 16/137 Verifying : glib2-2.74.1-2.fc38.x86_64 17/137 Verifying : gmp-1:6.2.1-3.fc38.x86_64 18/137 Verifying : gnupg2-2.3.8-1.fc38.x86_64 19/137 Verifying : gnutls-3.7.8-9.fc38.x86_64 20/137 Verifying : gpgme-1.17.1-3.fc38.x86_64 21/137 Verifying : grep-3.8-1.fc38.x86_64 22/137 Verifying : ima-evm-utils-1.4-6.fc38.x86_64 23/137 Verifying : json-c-0.16-3.fc38.x86_64 24/137 Verifying : keyutils-libs-1.6.1-5.fc38.x86_64 25/137 Verifying : krb5-libs-1.20.1-3.fc38.x86_64 26/137 Verifying : libacl-2.3.1-4.fc38.x86_64 27/137 Verifying : libarchive-3.6.1-3.fc38.x86_64 28/137 Verifying : libassuan-2.5.5-5.fc38.x86_64 29/137 Verifying : libattr-2.5.1-5.fc38.x86_64 30/137 Verifying : libb2-0.98.1-7.fc38.x86_64 31/137 Verifying : libbrotli-1.0.9-9.fc38.x86_64 32/137 Verifying : libcap-2.48-5.fc38.x86_64 33/137 Verifying : libcap-ng-0.8.3-4.fc38.x86_64 34/137 Verifying : libcom_err-1.46.5-3.fc38.x86_64 35/137 Verifying : libcomps-0.1.18-4.fc38.x86_64 36/137 Verifying : libcurl-7.87.0-1.fc38.x86_64 37/137 Verifying : libdnf-0.68.0-1.fc38.x86_64 38/137 Verifying : libevent-2.1.12-7.fc38.x86_64 39/137 Verifying : libffi-3.4.4-1.fc38.x86_64 40/137 Verifying : libfsverity-1.4-8.fc38.x86_64 41/137 Verifying : libgcrypt-1.10.1-6.fc38.x86_64 42/137 Verifying : libgpg-error-1.46-1.fc38.x86_64 43/137 Verifying : libidn2-2.3.4-1.fc38.x86_64 44/137 Verifying : libksba-1.6.3-1.fc38.x86_64 45/137 Verifying : libmodulemd-2.14.0-4.fc38.x86_64 46/137 Verifying : libnghttp2-1.51.0-1.fc38.x86_64 47/137 Verifying : libnsl2-2.0.0-4.fc38.x86_64 48/137 Verifying : libpsl-0.21.1-6.fc38.x86_64 49/137 Verifying : librepo-1.15.1-1.fc38.x86_64 50/137 Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 51/137 Verifying : libselinux-3.4-6.fc38.x86_64 52/137 Verifying : libsemanage-3.4-6.fc38.x86_64 53/137 Verifying : libsepol-3.4-4.fc38.x86_64 54/137 Verifying : libsigsegv-2.14-3.fc38.x86_64 55/137 Verifying : libsolv-0.7.22-3.fc38.x86_64 56/137 Verifying : libssh-0.10.4-2.fc38.x86_64 57/137 Verifying : libssh-config-0.10.4-2.fc38.noarch 58/137 Verifying : libtasn1-4.19.0-1.fc38.x86_64 59/137 Verifying : libtirpc-1.3.3-0.fc38.x86_64 60/137 Verifying : libunistring-1.0-2.fc38.x86_64 61/137 Verifying : libverto-0.3.2-4.fc38.x86_64 62/137 Verifying : libxcrypt-4.4.33-5.fc38.x86_64 63/137 Verifying : libxml2-2.10.3-2.fc38.x86_64 64/137 Verifying : libyaml-0.2.5-8.fc38.x86_64 65/137 Verifying : lua-libs-5.4.4-6.fc38.x86_64 66/137 Verifying : lz4-libs-1.9.3-5.fc38.x86_64 67/137 Verifying : mpdecimal-2.5.1-4.fc38.x86_64 68/137 Verifying : mpfr-4.1.1-2.fc38.x86_64 69/137 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 70/137 Verifying : ncurses-libs-6.3-5.20221126.fc38.x86_64 71/137 Verifying : nettle-3.8-2.fc38.x86_64 72/137 Verifying : npth-1.6-10.fc38.x86_64 73/137 Verifying : openldap-2.6.3-1.fc38.x86_64 74/137 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 75/137 Verifying : p11-kit-0.24.1-5.fc38.x86_64 76/137 Verifying : p11-kit-trust-0.24.1-5.fc38.x86_64 77/137 Verifying : pcre2-10.40-1.fc38.1.x86_64 78/137 Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 79/137 Verifying : popt-1.19-1.fc38.x86_64 80/137 Verifying : python3-dbus-1.3.2-1.fc38.x86_64 81/137 Verifying : python3-gpg-1.17.1-3.fc38.x86_64 82/137 Verifying : python3-hawkey-0.68.0-1.fc38.x86_64 83/137 Verifying : python3-libcomps-0.1.18-4.fc38.x86_64 84/137 Verifying : python3-libdnf-0.68.0-1.fc38.x86_64 85/137 Verifying : libgcc-13.0.0-0.4.fc38.x86_64 86/137 Verifying : libgomp-13.0.0-0.4.fc38.x86_64 87/137 Verifying : libstdc++-13.0.0-0.4.fc38.x86_64 88/137 Verifying : audit-libs-3.0.9-2.fc38.x86_64 89/137 Verifying : basesystem-11-14.fc37.noarch 90/137 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 91/137 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 92/137 Verifying : dnf-4.14.0-1.fc38.noarch 93/137 Verifying : dnf-data-4.14.0-1.fc38.noarch 94/137 Verifying : dnf-plugins-core-4.3.1-1.fc38.noarch 95/137 Verifying : fedora-gpg-keys-38-0.3.noarch 96/137 Verifying : fedora-release-38-0.6.noarch 97/137 Verifying : fedora-release-common-38-0.6.noarch 98/137 Verifying : fedora-release-identity-basic-38-0.6.noarch 99/137 Verifying : fedora-repos-38-0.3.noarch 100/137 Verifying : fedora-repos-rawhide-38-0.3.noarch 101/137 Verifying : filesystem-3.18-2.fc37.x86_64 102/137 Verifying : glibc-2.36.9000-19.fc38.x86_64 103/137 Verifying : glibc-common-2.36.9000-19.fc38.x86_64 104/137 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 105/137 Verifying : libblkid-2.38.1-3.fc38.x86_64 106/137 Verifying : libmount-2.38.1-3.fc38.x86_64 107/137 Verifying : libsmartcols-2.38.1-3.fc38.x86_64 108/137 Verifying : libuuid-2.38.1-3.fc38.x86_64 109/137 Verifying : libzstd-1.5.2-3.fc37.x86_64 110/137 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 111/137 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 112/137 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 113/137 Verifying : python3-3.11.1-1.fc38.x86_64 114/137 Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 115/137 Verifying : python3-distro-1.8.0-1.fc38.noarch 116/137 Verifying : python3-dnf-4.14.0-1.fc38.noarch 117/137 Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 118/137 Verifying : python3-libs-3.11.1-1.fc38.x86_64 119/137 Verifying : python3-rpm-4.18.0-8.fc38.x86_64 120/137 Verifying : python3-six-1.16.0-8.fc37.noarch 121/137 Verifying : readline-8.2-2.fc38.x86_64 122/137 Verifying : rpm-4.18.0-8.fc38.x86_64 123/137 Verifying : rpm-build-libs-4.18.0-8.fc38.x86_64 124/137 Verifying : rpm-libs-4.18.0-8.fc38.x86_64 125/137 Verifying : rpm-sequoia-1.2.0-1.fc38.x86_64 126/137 Verifying : rpm-sign-libs-4.18.0-8.fc38.x86_64 127/137 Verifying : sed-4.8-11.fc37.x86_64 128/137 Verifying : setup-2.14.3-1.fc38.noarch 129/137 Verifying : shadow-utils-2:4.13-3.fc38.x86_64 130/137 Verifying : sqlite-libs-3.40.0-1.fc38.x86_64 131/137 Verifying : systemd-libs-252.4-598.fc38.x86_64 132/137 Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 133/137 Verifying : tzdata-2022g-1.fc38.noarch 134/137 Verifying : xz-libs-5.2.9-1.fc38.x86_64 135/137 Verifying : zchunk-libs-1.2.3-1.fc38.x86_64 136/137 Verifying : zlib-1.2.13-1.fc38.x86_64 137/137 Installed products updated. Installed: alternatives-1.21-1.fc38.x86_64 audit-libs-3.0.9-2.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 dbus-libs-1:1.14.4-1.fc38.x86_64 dnf-4.14.0-1.fc38.noarch dnf-data-4.14.0-1.fc38.noarch dnf-plugins-core-4.3.1-1.fc38.noarch elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 expat-2.5.0-1.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-libs-5.42-4.fc38.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc38.x86_64 gawk-5.1.1-4.fc38.x86_64 gdbm-libs-1:1.23-2.fc38.x86_64 glib2-2.74.1-2.fc38.x86_64 glibc-2.36.9000-19.fc38.x86_64 glibc-common-2.36.9000-19.fc38.x86_64 glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 gmp-1:6.2.1-3.fc38.x86_64 gnupg2-2.3.8-1.fc38.x86_64 gnutls-3.7.8-9.fc38.x86_64 gpgme-1.17.1-3.fc38.x86_64 grep-3.8-1.fc38.x86_64 ima-evm-utils-1.4-6.fc38.x86_64 json-c-0.16-3.fc38.x86_64 keyutils-libs-1.6.1-5.fc38.x86_64 krb5-libs-1.20.1-3.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-3.fc38.x86_64 libassuan-2.5.5-5.fc38.x86_64 libattr-2.5.1-5.fc38.x86_64 libb2-0.98.1-7.fc38.x86_64 libblkid-2.38.1-3.fc38.x86_64 libbrotli-1.0.9-9.fc38.x86_64 libcap-2.48-5.fc38.x86_64 libcap-ng-0.8.3-4.fc38.x86_64 libcom_err-1.46.5-3.fc38.x86_64 libcomps-0.1.18-4.fc38.x86_64 libcurl-7.87.0-1.fc38.x86_64 libdnf-0.68.0-1.fc38.x86_64 libevent-2.1.12-7.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 libfsverity-1.4-8.fc38.x86_64 libgcc-13.0.0-0.4.fc38.x86_64 libgcrypt-1.10.1-6.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 libgpg-error-1.46-1.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libksba-1.6.3-1.fc38.x86_64 libmodulemd-2.14.0-4.fc38.x86_64 libmount-2.38.1-3.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc38.x86_64 libpsl-0.21.1-6.fc38.x86_64 librepo-1.15.1-1.fc38.x86_64 libreport-filesystem-2.17.6-1.fc38.noarch libselinux-3.4-6.fc38.x86_64 libsemanage-3.4-6.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 libsigsegv-2.14-3.fc38.x86_64 libsmartcols-2.38.1-3.fc38.x86_64 libsolv-0.7.22-3.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.x86_64 libtasn1-4.19.0-1.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 libuuid-2.38.1-3.fc38.x86_64 libverto-0.3.2-4.fc38.x86_64 libxcrypt-4.4.33-5.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libyaml-0.2.5-8.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lz4-libs-1.9.3-5.fc38.x86_64 mpdecimal-2.5.1-4.fc38.x86_64 mpfr-4.1.1-2.fc38.x86_64 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.x86_64 nettle-3.8-2.fc38.x86_64 npth-1.6-10.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-5.fc38.x86_64 p11-kit-trust-0.24.1-5.fc38.x86_64 pcre2-10.40-1.fc38.1.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.x86_64 python3-dateutil-1:2.8.2-4.fc37.noarch python3-dbus-1.3.2-1.fc38.x86_64 python3-distro-1.8.0-1.fc38.noarch python3-dnf-4.14.0-1.fc38.noarch python3-dnf-plugins-core-4.3.1-1.fc38.noarch python3-gpg-1.17.1-3.fc38.x86_64 python3-hawkey-0.68.0-1.fc38.x86_64 python3-libcomps-0.1.18-4.fc38.x86_64 python3-libdnf-0.68.0-1.fc38.x86_64 python3-libs-3.11.1-1.fc38.x86_64 python3-rpm-4.18.0-8.fc38.x86_64 python3-six-1.16.0-8.fc37.noarch readline-8.2-2.fc38.x86_64 rpm-4.18.0-8.fc38.x86_64 rpm-build-libs-4.18.0-8.fc38.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 rpm-sign-libs-4.18.0-8.fc38.x86_64 sed-4.8-11.fc37.x86_64 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64 tzdata-2022g-1.fc38.noarch xz-libs-5.2.9-1.fc38.x86_64 zchunk-libs-1.2.3-1.fc38.x86_64 zlib-1.2.13-1.fc38.x86_64 Complete! Finish(bootstrap): dnf install 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_64-1672135248.183296/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 Copr repository 27 MB/s | 35 MB 00:01 Additional repo https_jakub_fedorapeople_org_fe 10 kB/s | 3.0 kB 00:00 fedora 408 kB/s | 23 kB 00:00 Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing group/module packages: bash x86_64 5.2.9-3.fc38 copr_base 1.8 M bzip2 x86_64 1.0.8-12.fc38 copr_base 53 k coreutils x86_64 9.1-8.fc38 copr_base 1.1 M cpio x86_64 2.13-13.fc38 copr_base 271 k diffutils x86_64 3.8-3.fc38 copr_base 371 k fedora-release-common noarch 38-0.6 fedora 21 k findutils x86_64 1:4.9.0-2.fc38 copr_base 483 k gawk x86_64 5.1.1-4.fc38 copr_base 1.0 M glibc-minimal-langpack x86_64 2.36.9000-19.fc38 fedora 30 k grep x86_64 3.8-1.fc38 copr_base 282 k gzip x86_64 1.12-2.fc38 copr_base 159 k info x86_64 7.0.1-1.fc38 fedora 181 k patch x86_64 2.7.6-17.fc38 copr_base 125 k redhat-rpm-config noarch 235-1.fc38 fedora 80 k rpm-build x86_64 4.18.0-8.fc38 fedora 77 k sed x86_64 4.8-11.fc37 fedora 306 k shadow-utils x86_64 2:4.13-3.fc38 fedora 1.3 M tar x86_64 2:1.34-5.fc38 fedora 885 k unzip x86_64 6.0-58.fc38 fedora 182 k util-linux x86_64 2.38.1-3.fc38 fedora 2.3 M which x86_64 2.21-36.fc38 fedora 41 k xz x86_64 5.2.9-1.fc38 fedora 306 k Installing dependencies: alternatives x86_64 1.21-1.fc38 copr_base 39 k ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k audit-libs x86_64 3.0.9-2.fc38 fedora 116 k authselect x86_64 1.4.2-1.fc38 copr_base 140 k authselect-libs x86_64 1.4.2-1.fc38 copr_base 237 k basesystem noarch 11-14.fc37 fedora 7.0 k binutils x86_64 2.39-6.fc38 copr_base 5.4 M binutils-gold x86_64 2.39-6.fc38 copr_base 787 k bzip2-libs x86_64 1.0.8-12.fc38 copr_base 42 k ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k coreutils-common x86_64 9.1-8.fc38 copr_base 2.0 M cracklib x86_64 2.9.7-30.fc38 copr_base 82 k crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-1.fc38 copr_base 346 k cyrus-sasl-lib x86_64 2.1.28-8.fc38 copr_base 793 k debugedit x86_64 5.0-5.fc37 fedora 77 k dwz x86_64 0.15-1.fc38 copr_base 137 k ed x86_64 1.18-2.fc38 copr_base 79 k efi-srpm-macros noarch 5-6.fc37 fedora 22 k elfutils x86_64 0.188-3.fc38 copr_base 524 k elfutils-debuginfod-client x86_64 0.188-3.fc38 copr_base 40 k elfutils-default-yama-scope noarch 0.188-3.fc38 copr_base 16 k elfutils-libelf x86_64 0.188-3.fc38 copr_base 196 k elfutils-libs x86_64 0.188-3.fc38 copr_base 257 k fedora-gpg-keys noarch 38-0.3 fedora 125 k fedora-release noarch 38-0.6 fedora 11 k fedora-release-identity-basic noarch 38-0.6 fedora 11 k fedora-repos noarch 38-0.3 fedora 10 k fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k file x86_64 5.42-4.fc38 copr_base 49 k file-libs x86_64 5.42-4.fc38 copr_base 676 k filesystem x86_64 3.18-2.fc37 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k gdb-minimal x86_64 12.1-10.fc38 fedora 3.7 M gdbm-libs x86_64 1:1.23-2.fc38 copr_base 56 k ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k glibc x86_64 2.36.9000-19.fc38 fedora 2.1 M glibc-common x86_64 2.36.9000-19.fc38 fedora 309 k glibc-gconv-extra x86_64 2.36.9000-19.fc38 fedora 1.6 M gmp x86_64 1:6.2.1-3.fc38 copr_base 315 k gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k jansson x86_64 2.13.1-5.fc38 copr_base 45 k kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k keyutils-libs x86_64 1.6.1-5.fc38 copr_base 32 k krb5-libs x86_64 1.20.1-3.fc38 copr_base 719 k libacl x86_64 2.3.1-4.fc38 copr_base 24 k libarchive x86_64 3.6.1-3.fc38 copr_base 397 k libattr x86_64 2.5.1-5.fc38 copr_base 18 k libblkid x86_64 2.38.1-3.fc38 fedora 106 k libbrotli x86_64 1.0.9-9.fc38 copr_base 316 k libcap x86_64 2.48-5.fc38 copr_base 67 k libcap-ng x86_64 0.8.3-4.fc38 copr_base 33 k libcom_err x86_64 1.46.5-3.fc38 copr_base 26 k libcurl x86_64 7.87.0-1.fc38 copr_base 302 k libdb x86_64 5.3.28-54.fc38 copr_base 763 k libeconf x86_64 0.4.0-4.fc38 copr_base 28 k libevent x86_64 2.1.12-7.fc38 copr_base 259 k libfdisk x86_64 2.38.1-3.fc38 fedora 160 k libffi x86_64 3.4.4-1.fc38 copr_base 38 k libgcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k libgomp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 300 k libidn2 x86_64 2.3.4-1.fc38 copr_base 154 k libmount x86_64 2.38.1-3.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-1.fc38 copr_base 75 k libnsl2 x86_64 2.0.0-4.fc38 copr_base 31 k libpkgconf x86_64 1.8.0-3.fc38 copr_base 36 k libpsl x86_64 0.21.1-6.fc38 copr_base 65 k libpwquality x86_64 1.4.5-1.fc38 fedora 119 k libselinux x86_64 3.4-6.fc38 copr_base 86 k libsemanage x86_64 3.4-6.fc38 copr_base 120 k libsepol x86_64 3.4-4.fc38 copr_base 321 k libsigsegv x86_64 2.14-3.fc38 copr_base 27 k libsmartcols x86_64 2.38.1-3.fc38 fedora 64 k libssh x86_64 0.10.4-2.fc38 copr_base 210 k libssh-config noarch 0.10.4-2.fc38 copr_base 9.2 k libstdc++ x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 799 k libtasn1 x86_64 4.19.0-1.fc38 copr_base 76 k libtirpc x86_64 1.3.3-0.fc38 copr_base 94 k libunistring x86_64 1.0-2.fc38 copr_base 541 k libutempter x86_64 1.2.1-7.fc38 copr_base 26 k libuuid x86_64 2.38.1-3.fc38 fedora 27 k libverto x86_64 0.3.2-4.fc38 copr_base 21 k libxcrypt x86_64 4.4.33-5.fc38 copr_base 120 k libxml2 x86_64 2.10.3-2.fc38 copr_base 704 k libzstd x86_64 1.5.2-3.fc37 fedora 294 k lua-libs x86_64 5.4.4-6.fc38 copr_base 133 k lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k lz4-libs x86_64 1.9.3-5.fc38 copr_base 70 k mpfr x86_64 4.1.1-2.fc38 copr_base 599 k ncurses-base noarch 6.3-5.20221126.fc38 copr_base 62 k ncurses-libs x86_64 6.3-5.20221126.fc38 copr_base 329 k nettle x86_64 3.8-2.fc38 copr_base 414 k nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k openldap x86_64 2.6.3-1.fc38 copr_base 254 k openssl-libs x86_64 1:3.0.5-6.fc38 copr_base 2.1 M p11-kit x86_64 0.24.1-5.fc38 copr_base 360 k p11-kit-trust x86_64 0.24.1-5.fc38 copr_base 138 k package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k pam x86_64 1.5.2-15.fc38 copr_base 521 k pam-libs x86_64 1.5.2-15.fc38 copr_base 57 k pcre2 x86_64 10.40-1.fc38.1 copr_base 236 k pcre2-syntax noarch 10.40-1.fc38.1 copr_base 143 k perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k pkgconf x86_64 1.8.0-3.fc38 copr_base 42 k pkgconf-m4 noarch 1.8.0-3.fc38 copr_base 15 k pkgconf-pkg-config x86_64 1.8.0-3.fc38 copr_base 11 k popt x86_64 1.19-1.fc38 copr_base 59 k publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k python-srpm-macros noarch 3.11-6.fc38 fedora 25 k qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k readline x86_64 8.2-2.fc38 fedora 211 k rpm x86_64 4.18.0-8.fc38 fedora 572 k rpm-build-libs x86_64 4.18.0-8.fc38 fedora 94 k rpm-libs x86_64 4.18.0-8.fc38 fedora 309 k rpm-sequoia x86_64 1.2.0-1.fc38 fedora 829 k rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k setup noarch 2.14.3-1.fc38 fedora 152 k sqlite-libs x86_64 3.40.0-1.fc38 fedora 661 k systemd-libs x86_64 252.4-598.fc38 fedora 632 k tzdata noarch 2022g-1.fc38 fedora 716 k util-linux-core x86_64 2.38.1-3.fc38 fedora 470 k xxhash-libs x86_64 0.8.1-3.fc37 fedora 41 k xz-libs x86_64 5.2.9-1.fc38 fedora 93 k zip x86_64 3.0-35.fc38 fedora 259 k zlib x86_64 1.2.13-1.fc38 fedora 94 k zstd x86_64 1.5.2-3.fc37 fedora 447 k Installing Groups: Buildsystem building group Transaction Summary ========================================================================================================================= Install 153 Packages Total size: 52 M Installed size: 181 M Downloading Packages: [SKIPPED] alternatives-1.21-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] bash-5.2.9-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.39-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.39-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-12.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.1-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.13-13.fc38.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.7-30.fc38.x86_64.rpm: Already downloaded [SKIPPED] curl-7.87.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.8-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] ed-1.18-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.188-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] file-5.42-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] file-libs-5.42-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] findutils-4.9.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gawk-5.1.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] gmp-6.2.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] grep-3.8-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.12-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] jansson-2.13.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] krb5-libs-1.20.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libacl-2.3.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.6.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.5.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-9.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.46.5-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libcurl-7.87.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-54.fc38.x86_64.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libevent-2.1.12-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.4.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnghttp2-1.51.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.21.1-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libselinux-3.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-3.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsepol-3.4-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.14-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-0.10.4-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded [SKIPPED] libtasn1-4.19.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtirpc-1.3.3-0.fc38.x86_64.rpm: Already downloaded [SKIPPED] libunistring-1.0-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.2.1-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.4.33-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.10.3-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.4.4-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] lz4-libs-1.9.3-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] mpfr-4.1.1-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded [SKIPPED] ncurses-libs-6.3-5.20221126.fc38.x86_64.rpm: Already downloaded [SKIPPED] nettle-3.8-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] openldap-2.6.3-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] openssl-libs-3.0.5-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.24.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.24.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] pam-1.5.2-15.fc38.x86_64.rpm: Already downloaded [SKIPPED] pam-libs-1.5.2-15.fc38.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-17.fc38.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.40-1.fc38.1.x86_64.rpm: Already downloaded [SKIPPED] pcre2-syntax-10.40-1.fc38.1.noarch.rpm: Already downloaded [SKIPPED] pkgconf-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.8.0-3.fc38.noarch.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.8.0-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] popt-1.19-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libgomp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libstdc++-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.0.9-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded [SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded [SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded [SKIPPED] debugedit-5.0-5.fc37.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded [SKIPPED] filesystem-3.18-2.fc37.x86_64.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded [SKIPPED] gdb-minimal-12.1-10.fc38.x86_64.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded [SKIPPED] glibc-2.36.9000-19.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-common-2.36.9000-19.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.x86_64.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded [SKIPPED] info-7.0.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded [SKIPPED] libblkid-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmount-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.5-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] libsmartcols-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libuuid-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded [SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded [SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded [SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded [SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded [SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded [SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded [SKIPPED] readline-8.2-2.fc38.x86_64.rpm: Already downloaded [SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rpm-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-libs-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-libs-4.18.0-8.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpm-sequoia-1.2.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded [SKIPPED] sed-4.8-11.fc37.x86_64.rpm: Already downloaded [SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded [SKIPPED] shadow-utils-4.13-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] sqlite-libs-3.40.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] systemd-libs-252.4-598.fc38.x86_64.rpm: Already downloaded [SKIPPED] tar-1.34-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded [SKIPPED] unzip-6.0-58.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] util-linux-core-2.38.1-3.fc38.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-36.fc38.x86_64.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.1-3.fc37.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.9-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-35.fc38.x86_64.rpm: Already downloaded [SKIPPED] zlib-1.2.13-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] zstd-1.5.2-3.fc37.x86_64.rpm: Already downloaded fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x5323552A: Userid : "Fedora (37) " Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-2.fc37.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.0-0.4.fc38.x86_64 1/153 Running scriptlet: libgcc-13.0.0-0.4.fc38.x86_64 1/153 Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/153 Installing : fedora-release-identity-basic-38-0.6.noarch 3/153 Installing : tzdata-2022g-1.fc38.noarch 4/153 Installing : rust-srpm-macros-23-1.fc38.noarch 5/153 Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/153 Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/153 Installing : perl-srpm-macros-1-47.fc38.noarch 8/153 Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 9/153 Installing : openblas-srpm-macros-2-12.fc37.noarch 10/153 Installing : ocaml-srpm-macros-7-2.fc37.noarch 11/153 Installing : nim-srpm-macros-3-7.fc37.noarch 12/153 Installing : kernel-srpm-macros-1.0-15.fc37.noarch 13/153 Installing : gnat-srpm-macros-4-16.fc37.noarch 14/153 Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 15/153 Installing : fpc-srpm-macros-1.3-6.fc37.noarch 16/153 Installing : fedora-gpg-keys-38-0.3.noarch 17/153 Installing : fedora-release-38-0.6.noarch 18/153 Installing : fedora-release-common-38-0.6.noarch 19/153 Installing : fedora-repos-rawhide-38-0.3.noarch 20/153 Installing : fedora-repos-38-0.3.noarch 21/153 Installing : setup-2.14.3-1.fc38.noarch 22/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.3-1.fc38.noarch 22/153 Installing : filesystem-3.18-2.fc37.x86_64 23/153 Installing : basesystem-11-14.fc37.noarch 24/153 Installing : ansible-srpm-macros-1-8.1.fc38.noarch 25/153 Installing : pkgconf-m4-1.8.0-3.fc38.noarch 26/153 Installing : pcre2-syntax-10.40-1.fc38.1.noarch 27/153 Installing : ncurses-base-6.3-5.20221126.fc38.noarch 28/153 Installing : ncurses-libs-6.3-5.20221126.fc38.x86_64 29/153 Installing : glibc-gconv-extra-2.36.9000-19.fc38.x86_64 30/153 Running scriptlet: glibc-gconv-extra-2.36.9000-19.fc38.x86_64 30/153 Running scriptlet: glibc-2.36.9000-19.fc38.x86_64 31/153 Installing : glibc-2.36.9000-19.fc38.x86_64 31/153 Running scriptlet: glibc-2.36.9000-19.fc38.x86_64 31/153 Installing : bash-5.2.9-3.fc38.x86_64 32/153 Running scriptlet: bash-5.2.9-3.fc38.x86_64 32/153 Installing : glibc-common-2.36.9000-19.fc38.x86_64 33/153 Installing : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 34/153 Installing : zlib-1.2.13-1.fc38.x86_64 35/153 Installing : xz-libs-5.2.9-1.fc38.x86_64 36/153 Installing : bzip2-libs-1.0.8-12.fc38.x86_64 37/153 Installing : elfutils-libelf-0.188-3.fc38.x86_64 38/153 Installing : gmp-1:6.2.1-3.fc38.x86_64 39/153 Installing : popt-1.19-1.fc38.x86_64 40/153 Installing : libstdc++-13.0.0-0.4.fc38.x86_64 41/153 Installing : libuuid-2.38.1-3.fc38.x86_64 42/153 Installing : libzstd-1.5.2-3.fc37.x86_64 43/153 Installing : libblkid-2.38.1-3.fc38.x86_64 44/153 Installing : libattr-2.5.1-5.fc38.x86_64 45/153 Installing : libacl-2.3.1-4.fc38.x86_64 46/153 Installing : libcap-2.48-5.fc38.x86_64 47/153 Installing : libxcrypt-4.4.33-5.fc38.x86_64 48/153 Installing : readline-8.2-2.fc38.x86_64 49/153 Installing : lz4-libs-1.9.3-5.fc38.x86_64 50/153 Installing : systemd-libs-252.4-598.fc38.x86_64 51/153 Installing : mpfr-4.1.1-2.fc38.x86_64 52/153 Installing : dwz-0.15-1.fc38.x86_64 53/153 Installing : unzip-6.0-58.fc38.x86_64 54/153 Installing : file-libs-5.42-4.fc38.x86_64 55/153 Installing : file-5.42-4.fc38.x86_64 56/153 Installing : sqlite-libs-3.40.0-1.fc38.x86_64 57/153 Installing : alternatives-1.21-1.fc38.x86_64 58/153 Installing : libcap-ng-0.8.3-4.fc38.x86_64 59/153 Installing : audit-libs-3.0.9-2.fc38.x86_64 60/153 Installing : libcom_err-1.46.5-3.fc38.x86_64 61/153 Installing : libeconf-0.4.0-4.fc38.x86_64 62/153 Installing : pam-libs-1.5.2-15.fc38.x86_64 63/153 Installing : libsepol-3.4-4.fc38.x86_64 64/153 Installing : libunistring-1.0-2.fc38.x86_64 65/153 Installing : libidn2-2.3.4-1.fc38.x86_64 66/153 Installing : lua-libs-5.4.4-6.fc38.x86_64 67/153 Installing : pcre2-10.40-1.fc38.1.x86_64 68/153 Installing : libselinux-3.4-6.fc38.x86_64 69/153 Installing : sed-4.8-11.fc37.x86_64 70/153 Installing : grep-3.8-1.fc38.x86_64 71/153 Installing : findutils-1:4.9.0-2.fc38.x86_64 72/153 Installing : xz-5.2.9-1.fc38.x86_64 73/153 Installing : libmount-2.38.1-3.fc38.x86_64 74/153 Installing : libsmartcols-2.38.1-3.fc38.x86_64 75/153 Installing : util-linux-core-2.38.1-3.fc38.x86_64 76/153 Installing : libsemanage-3.4-6.fc38.x86_64 77/153 Installing : shadow-utils-2:4.13-3.fc38.x86_64 78/153 Running scriptlet: libutempter-1.2.1-7.fc38.x86_64 79/153 Installing : libutempter-1.2.1-7.fc38.x86_64 79/153 Installing : tar-2:1.34-5.fc38.x86_64 80/153 Installing : libpsl-0.21.1-6.fc38.x86_64 81/153 Installing : zip-3.0-35.fc38.x86_64 82/153 Installing : zstd-1.5.2-3.fc37.x86_64 83/153 Installing : libfdisk-2.38.1-3.fc38.x86_64 84/153 Installing : nettle-3.8-2.fc38.x86_64 85/153 Installing : rpm-sequoia-1.2.0-1.fc38.x86_64 86/153 Installing : rpm-libs-4.18.0-8.fc38.x86_64 87/153 Installing : bzip2-1.0.8-12.fc38.x86_64 88/153 Installing : libxml2-2.10.3-2.fc38.x86_64 89/153 Installing : ed-1.18-2.fc38.x86_64 90/153 Installing : patch-2.7.6-17.fc38.x86_64 91/153 Installing : elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153 Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch 92/153 Installing : cpio-2.13-13.fc38.x86_64 93/153 Installing : diffutils-3.8-3.fc38.x86_64 94/153 Installing : gdbm-libs-1:1.23-2.fc38.x86_64 95/153 Installing : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 96/153 Installing : jansson-2.13.1-5.fc38.x86_64 97/153 Installing : keyutils-libs-1.6.1-5.fc38.x86_64 98/153 Installing : libbrotli-1.0.9-9.fc38.x86_64 99/153 Installing : libdb-5.3.28-54.fc38.x86_64 100/153 Installing : libffi-3.4.4-1.fc38.x86_64 101/153 Installing : p11-kit-0.24.1-5.fc38.x86_64 102/153 Installing : libnghttp2-1.51.0-1.fc38.x86_64 103/153 Installing : libpkgconf-1.8.0-3.fc38.x86_64 104/153 Installing : pkgconf-1.8.0-3.fc38.x86_64 105/153 Installing : pkgconf-pkg-config-1.8.0-3.fc38.x86_64 106/153 Installing : libsigsegv-2.14-3.fc38.x86_64 107/153 Installing : gawk-5.1.1-4.fc38.x86_64 108/153 Installing : libtasn1-4.19.0-1.fc38.x86_64 109/153 Installing : p11-kit-trust-0.24.1-5.fc38.x86_64 110/153 Running scriptlet: p11-kit-trust-0.24.1-5.fc38.x86_64 110/153 Installing : libverto-0.3.2-4.fc38.x86_64 111/153 Installing : libgomp-13.0.0-0.4.fc38.x86_64 112/153 Installing : xxhash-libs-0.8.1-3.fc37.x86_64 113/153 Installing : libssh-config-0.10.4-2.fc38.noarch 114/153 Installing : coreutils-common-9.1-8.fc38.x86_64 115/153 Installing : openssl-libs-1:3.0.5-6.fc38.x86_64 116/153 Installing : coreutils-9.1-8.fc38.x86_64 117/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153 Installing : ca-certificates-2022.2.54-5.fc37.noarch 118/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 118/153 Installing : krb5-libs-1.20.1-3.fc38.x86_64 119/153 Installing : libtirpc-1.3.3-0.fc38.x86_64 120/153 Running scriptlet: authselect-libs-1.4.2-1.fc38.x86_64 121/153 Installing : authselect-libs-1.4.2-1.fc38.x86_64 121/153 Installing : gzip-1.12-2.fc38.x86_64 122/153 Installing : cracklib-2.9.7-30.fc38.x86_64 123/153 Installing : libpwquality-1.4.5-1.fc38.x86_64 124/153 Installing : authselect-1.4.2-1.fc38.x86_64 125/153 Installing : libnsl2-2.0.0-4.fc38.x86_64 126/153 Installing : pam-1.5.2-15.fc38.x86_64 127/153 Installing : libssh-0.10.4-2.fc38.x86_64 128/153 Installing : libarchive-3.6.1-3.fc38.x86_64 129/153 Installing : libevent-2.1.12-7.fc38.x86_64 130/153 Installing : openldap-2.6.3-1.fc38.x86_64 131/153 Installing : libcurl-7.87.0-1.fc38.x86_64 132/153 Installing : elfutils-libs-0.188-3.fc38.x86_64 133/153 Installing : elfutils-debuginfod-client-0.188-3.fc38.x86_64 134/153 Installing : binutils-gold-2.39-6.fc38.x86_64 135/153 Installing : binutils-2.39-6.fc38.x86_64 136/153 Running scriptlet: binutils-2.39-6.fc38.x86_64 136/153 Installing : elfutils-0.188-3.fc38.x86_64 137/153 Installing : gdb-minimal-12.1-10.fc38.x86_64 138/153 Installing : debugedit-5.0-5.fc37.x86_64 139/153 Installing : rpm-build-libs-4.18.0-8.fc38.x86_64 140/153 Installing : curl-7.87.0-1.fc38.x86_64 141/153 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 142/153 Installing : rpm-4.18.0-8.fc38.x86_64 142/153 Installing : efi-srpm-macros-5-6.fc37.noarch 143/153 Installing : lua-srpm-macros-1-7.fc37.noarch 144/153 Installing : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 145/153 Installing : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 146/153 Installing : go-srpm-macros-3.2.0-1.fc38.noarch 147/153 Installing : python-srpm-macros-3.11-6.fc38.noarch 148/153 Installing : redhat-rpm-config-235-1.fc38.noarch 149/153 Installing : rpm-build-4.18.0-8.fc38.x86_64 150/153 Installing : util-linux-2.38.1-3.fc38.x86_64 151/153 Installing : which-2.21-36.fc38.x86_64 152/153 Installing : info-7.0.1-1.fc38.x86_64 153/153 Running scriptlet: filesystem-3.18-2.fc37.x86_64 153/153 Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-1.fc38.x86_64 153/153 Running scriptlet: rpm-4.18.0-8.fc38.x86_64 153/153 Running scriptlet: info-7.0.1-1.fc38.x86_64 153/153 Verifying : alternatives-1.21-1.fc38.x86_64 1/153 Verifying : authselect-1.4.2-1.fc38.x86_64 2/153 Verifying : authselect-libs-1.4.2-1.fc38.x86_64 3/153 Verifying : bash-5.2.9-3.fc38.x86_64 4/153 Verifying : binutils-2.39-6.fc38.x86_64 5/153 Verifying : binutils-gold-2.39-6.fc38.x86_64 6/153 Verifying : bzip2-1.0.8-12.fc38.x86_64 7/153 Verifying : bzip2-libs-1.0.8-12.fc38.x86_64 8/153 Verifying : coreutils-9.1-8.fc38.x86_64 9/153 Verifying : coreutils-common-9.1-8.fc38.x86_64 10/153 Verifying : cpio-2.13-13.fc38.x86_64 11/153 Verifying : cracklib-2.9.7-30.fc38.x86_64 12/153 Verifying : curl-7.87.0-1.fc38.x86_64 13/153 Verifying : cyrus-sasl-lib-2.1.28-8.fc38.x86_64 14/153 Verifying : diffutils-3.8-3.fc38.x86_64 15/153 Verifying : dwz-0.15-1.fc38.x86_64 16/153 Verifying : ed-1.18-2.fc38.x86_64 17/153 Verifying : elfutils-0.188-3.fc38.x86_64 18/153 Verifying : elfutils-debuginfod-client-0.188-3.fc38.x86_64 19/153 Verifying : elfutils-default-yama-scope-0.188-3.fc38.noarch 20/153 Verifying : elfutils-libelf-0.188-3.fc38.x86_64 21/153 Verifying : elfutils-libs-0.188-3.fc38.x86_64 22/153 Verifying : file-5.42-4.fc38.x86_64 23/153 Verifying : file-libs-5.42-4.fc38.x86_64 24/153 Verifying : findutils-1:4.9.0-2.fc38.x86_64 25/153 Verifying : gawk-5.1.1-4.fc38.x86_64 26/153 Verifying : gdbm-libs-1:1.23-2.fc38.x86_64 27/153 Verifying : gmp-1:6.2.1-3.fc38.x86_64 28/153 Verifying : grep-3.8-1.fc38.x86_64 29/153 Verifying : gzip-1.12-2.fc38.x86_64 30/153 Verifying : jansson-2.13.1-5.fc38.x86_64 31/153 Verifying : keyutils-libs-1.6.1-5.fc38.x86_64 32/153 Verifying : krb5-libs-1.20.1-3.fc38.x86_64 33/153 Verifying : libacl-2.3.1-4.fc38.x86_64 34/153 Verifying : libarchive-3.6.1-3.fc38.x86_64 35/153 Verifying : libattr-2.5.1-5.fc38.x86_64 36/153 Verifying : libbrotli-1.0.9-9.fc38.x86_64 37/153 Verifying : libcap-2.48-5.fc38.x86_64 38/153 Verifying : libcap-ng-0.8.3-4.fc38.x86_64 39/153 Verifying : libcom_err-1.46.5-3.fc38.x86_64 40/153 Verifying : libcurl-7.87.0-1.fc38.x86_64 41/153 Verifying : libdb-5.3.28-54.fc38.x86_64 42/153 Verifying : libeconf-0.4.0-4.fc38.x86_64 43/153 Verifying : libevent-2.1.12-7.fc38.x86_64 44/153 Verifying : libffi-3.4.4-1.fc38.x86_64 45/153 Verifying : libidn2-2.3.4-1.fc38.x86_64 46/153 Verifying : libnghttp2-1.51.0-1.fc38.x86_64 47/153 Verifying : libnsl2-2.0.0-4.fc38.x86_64 48/153 Verifying : libpkgconf-1.8.0-3.fc38.x86_64 49/153 Verifying : libpsl-0.21.1-6.fc38.x86_64 50/153 Verifying : libselinux-3.4-6.fc38.x86_64 51/153 Verifying : libsemanage-3.4-6.fc38.x86_64 52/153 Verifying : libsepol-3.4-4.fc38.x86_64 53/153 Verifying : libsigsegv-2.14-3.fc38.x86_64 54/153 Verifying : libssh-0.10.4-2.fc38.x86_64 55/153 Verifying : libssh-config-0.10.4-2.fc38.noarch 56/153 Verifying : libtasn1-4.19.0-1.fc38.x86_64 57/153 Verifying : libtirpc-1.3.3-0.fc38.x86_64 58/153 Verifying : libunistring-1.0-2.fc38.x86_64 59/153 Verifying : libutempter-1.2.1-7.fc38.x86_64 60/153 Verifying : libverto-0.3.2-4.fc38.x86_64 61/153 Verifying : libxcrypt-4.4.33-5.fc38.x86_64 62/153 Verifying : libxml2-2.10.3-2.fc38.x86_64 63/153 Verifying : lua-libs-5.4.4-6.fc38.x86_64 64/153 Verifying : lz4-libs-1.9.3-5.fc38.x86_64 65/153 Verifying : mpfr-4.1.1-2.fc38.x86_64 66/153 Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 67/153 Verifying : ncurses-libs-6.3-5.20221126.fc38.x86_64 68/153 Verifying : nettle-3.8-2.fc38.x86_64 69/153 Verifying : openldap-2.6.3-1.fc38.x86_64 70/153 Verifying : openssl-libs-1:3.0.5-6.fc38.x86_64 71/153 Verifying : p11-kit-0.24.1-5.fc38.x86_64 72/153 Verifying : p11-kit-trust-0.24.1-5.fc38.x86_64 73/153 Verifying : pam-1.5.2-15.fc38.x86_64 74/153 Verifying : pam-libs-1.5.2-15.fc38.x86_64 75/153 Verifying : patch-2.7.6-17.fc38.x86_64 76/153 Verifying : pcre2-10.40-1.fc38.1.x86_64 77/153 Verifying : pcre2-syntax-10.40-1.fc38.1.noarch 78/153 Verifying : pkgconf-1.8.0-3.fc38.x86_64 79/153 Verifying : pkgconf-m4-1.8.0-3.fc38.noarch 80/153 Verifying : pkgconf-pkg-config-1.8.0-3.fc38.x86_64 81/153 Verifying : popt-1.19-1.fc38.x86_64 82/153 Verifying : libgcc-13.0.0-0.4.fc38.x86_64 83/153 Verifying : libgomp-13.0.0-0.4.fc38.x86_64 84/153 Verifying : libstdc++-13.0.0-0.4.fc38.x86_64 85/153 Verifying : ansible-srpm-macros-1-8.1.fc38.noarch 86/153 Verifying : audit-libs-3.0.9-2.fc38.x86_64 87/153 Verifying : basesystem-11-14.fc37.noarch 88/153 Verifying : ca-certificates-2022.2.54-5.fc37.noarch 89/153 Verifying : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 90/153 Verifying : debugedit-5.0-5.fc37.x86_64 91/153 Verifying : efi-srpm-macros-5-6.fc37.noarch 92/153 Verifying : fedora-gpg-keys-38-0.3.noarch 93/153 Verifying : fedora-release-38-0.6.noarch 94/153 Verifying : fedora-release-common-38-0.6.noarch 95/153 Verifying : fedora-release-identity-basic-38-0.6.noarch 96/153 Verifying : fedora-repos-38-0.3.noarch 97/153 Verifying : fedora-repos-rawhide-38-0.3.noarch 98/153 Verifying : filesystem-3.18-2.fc37.x86_64 99/153 Verifying : fonts-srpm-macros-1:2.0.5-10.fc38.noarch 100/153 Verifying : fpc-srpm-macros-1.3-6.fc37.noarch 101/153 Verifying : gdb-minimal-12.1-10.fc38.x86_64 102/153 Verifying : ghc-srpm-macros-1.5.0-7.fc37.noarch 103/153 Verifying : glibc-2.36.9000-19.fc38.x86_64 104/153 Verifying : glibc-common-2.36.9000-19.fc38.x86_64 105/153 Verifying : glibc-gconv-extra-2.36.9000-19.fc38.x86_64 106/153 Verifying : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 107/153 Verifying : gnat-srpm-macros-4-16.fc37.noarch 108/153 Verifying : go-srpm-macros-3.2.0-1.fc38.noarch 109/153 Verifying : info-7.0.1-1.fc38.x86_64 110/153 Verifying : kernel-srpm-macros-1.0-15.fc37.noarch 111/153 Verifying : libblkid-2.38.1-3.fc38.x86_64 112/153 Verifying : libfdisk-2.38.1-3.fc38.x86_64 113/153 Verifying : libmount-2.38.1-3.fc38.x86_64 114/153 Verifying : libpwquality-1.4.5-1.fc38.x86_64 115/153 Verifying : libsmartcols-2.38.1-3.fc38.x86_64 116/153 Verifying : libuuid-2.38.1-3.fc38.x86_64 117/153 Verifying : libzstd-1.5.2-3.fc37.x86_64 118/153 Verifying : lua-srpm-macros-1-7.fc37.noarch 119/153 Verifying : nim-srpm-macros-3-7.fc37.noarch 120/153 Verifying : ocaml-srpm-macros-7-2.fc37.noarch 121/153 Verifying : openblas-srpm-macros-2-12.fc37.noarch 122/153 Verifying : package-notes-srpm-macros-0.5-6.fc38.noarch 123/153 Verifying : perl-srpm-macros-1-47.fc38.noarch 124/153 Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 125/153 Verifying : python-srpm-macros-3.11-6.fc38.noarch 126/153 Verifying : qt5-srpm-macros-5.15.7-1.fc38.noarch 127/153 Verifying : readline-8.2-2.fc38.x86_64 128/153 Verifying : redhat-rpm-config-235-1.fc38.noarch 129/153 Verifying : rpm-4.18.0-8.fc38.x86_64 130/153 Verifying : rpm-build-4.18.0-8.fc38.x86_64 131/153 Verifying : rpm-build-libs-4.18.0-8.fc38.x86_64 132/153 Verifying : rpm-libs-4.18.0-8.fc38.x86_64 133/153 Verifying : rpm-sequoia-1.2.0-1.fc38.x86_64 134/153 Verifying : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch 135/153 Verifying : rust-srpm-macros-23-1.fc38.noarch 136/153 Verifying : sed-4.8-11.fc37.x86_64 137/153 Verifying : setup-2.14.3-1.fc38.noarch 138/153 Verifying : shadow-utils-2:4.13-3.fc38.x86_64 139/153 Verifying : sqlite-libs-3.40.0-1.fc38.x86_64 140/153 Verifying : systemd-libs-252.4-598.fc38.x86_64 141/153 Verifying : tar-2:1.34-5.fc38.x86_64 142/153 Verifying : tzdata-2022g-1.fc38.noarch 143/153 Verifying : unzip-6.0-58.fc38.x86_64 144/153 Verifying : util-linux-2.38.1-3.fc38.x86_64 145/153 Verifying : util-linux-core-2.38.1-3.fc38.x86_64 146/153 Verifying : which-2.21-36.fc38.x86_64 147/153 Verifying : xxhash-libs-0.8.1-3.fc37.x86_64 148/153 Verifying : xz-5.2.9-1.fc38.x86_64 149/153 Verifying : xz-libs-5.2.9-1.fc38.x86_64 150/153 Verifying : zip-3.0-35.fc38.x86_64 151/153 Verifying : zlib-1.2.13-1.fc38.x86_64 152/153 Verifying : zstd-1.5.2-3.fc37.x86_64 153/153 Installed: alternatives-1.21-1.fc38.x86_64 ansible-srpm-macros-1-8.1.fc38.noarch audit-libs-3.0.9-2.fc38.x86_64 authselect-1.4.2-1.fc38.x86_64 authselect-libs-1.4.2-1.fc38.x86_64 basesystem-11-14.fc37.noarch bash-5.2.9-3.fc38.x86_64 binutils-2.39-6.fc38.x86_64 binutils-gold-2.39-6.fc38.x86_64 bzip2-1.0.8-12.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch coreutils-9.1-8.fc38.x86_64 coreutils-common-9.1-8.fc38.x86_64 cpio-2.13-13.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch curl-7.87.0-1.fc38.x86_64 cyrus-sasl-lib-2.1.28-8.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 diffutils-3.8-3.fc38.x86_64 dwz-0.15-1.fc38.x86_64 ed-1.18-2.fc38.x86_64 efi-srpm-macros-5-6.fc37.noarch elfutils-0.188-3.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch elfutils-libelf-0.188-3.fc38.x86_64 elfutils-libs-0.188-3.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch fedora-release-38-0.6.noarch fedora-release-common-38-0.6.noarch fedora-release-identity-basic-38-0.6.noarch fedora-repos-38-0.3.noarch fedora-repos-rawhide-38-0.3.noarch file-5.42-4.fc38.x86_64 file-libs-5.42-4.fc38.x86_64 filesystem-3.18-2.fc37.x86_64 findutils-1:4.9.0-2.fc38.x86_64 fonts-srpm-macros-1:2.0.5-10.fc38.noarch fpc-srpm-macros-1.3-6.fc37.noarch gawk-5.1.1-4.fc38.x86_64 gdb-minimal-12.1-10.fc38.x86_64 gdbm-libs-1:1.23-2.fc38.x86_64 ghc-srpm-macros-1.5.0-7.fc37.noarch glibc-2.36.9000-19.fc38.x86_64 glibc-common-2.36.9000-19.fc38.x86_64 glibc-gconv-extra-2.36.9000-19.fc38.x86_64 glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 gmp-1:6.2.1-3.fc38.x86_64 gnat-srpm-macros-4-16.fc37.noarch go-srpm-macros-3.2.0-1.fc38.noarch grep-3.8-1.fc38.x86_64 gzip-1.12-2.fc38.x86_64 info-7.0.1-1.fc38.x86_64 jansson-2.13.1-5.fc38.x86_64 kernel-srpm-macros-1.0-15.fc37.noarch keyutils-libs-1.6.1-5.fc38.x86_64 krb5-libs-1.20.1-3.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 libarchive-3.6.1-3.fc38.x86_64 libattr-2.5.1-5.fc38.x86_64 libblkid-2.38.1-3.fc38.x86_64 libbrotli-1.0.9-9.fc38.x86_64 libcap-2.48-5.fc38.x86_64 libcap-ng-0.8.3-4.fc38.x86_64 libcom_err-1.46.5-3.fc38.x86_64 libcurl-7.87.0-1.fc38.x86_64 libdb-5.3.28-54.fc38.x86_64 libeconf-0.4.0-4.fc38.x86_64 libevent-2.1.12-7.fc38.x86_64 libfdisk-2.38.1-3.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 libgcc-13.0.0-0.4.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 libidn2-2.3.4-1.fc38.x86_64 libmount-2.38.1-3.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 libnsl2-2.0.0-4.fc38.x86_64 libpkgconf-1.8.0-3.fc38.x86_64 libpsl-0.21.1-6.fc38.x86_64 libpwquality-1.4.5-1.fc38.x86_64 libselinux-3.4-6.fc38.x86_64 libsemanage-3.4-6.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 libsigsegv-2.14-3.fc38.x86_64 libsmartcols-2.38.1-3.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libstdc++-13.0.0-0.4.fc38.x86_64 libtasn1-4.19.0-1.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 libutempter-1.2.1-7.fc38.x86_64 libuuid-2.38.1-3.fc38.x86_64 libverto-0.3.2-4.fc38.x86_64 libxcrypt-4.4.33-5.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 lua-libs-5.4.4-6.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch lz4-libs-1.9.3-5.fc38.x86_64 mpfr-4.1.1-2.fc38.x86_64 ncurses-base-6.3-5.20221126.fc38.noarch ncurses-libs-6.3-5.20221126.fc38.x86_64 nettle-3.8-2.fc38.x86_64 nim-srpm-macros-3-7.fc37.noarch ocaml-srpm-macros-7-2.fc37.noarch openblas-srpm-macros-2-12.fc37.noarch openldap-2.6.3-1.fc38.x86_64 openssl-libs-1:3.0.5-6.fc38.x86_64 p11-kit-0.24.1-5.fc38.x86_64 p11-kit-trust-0.24.1-5.fc38.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch pam-1.5.2-15.fc38.x86_64 pam-libs-1.5.2-15.fc38.x86_64 patch-2.7.6-17.fc38.x86_64 pcre2-10.40-1.fc38.1.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch perl-srpm-macros-1-47.fc38.noarch pkgconf-1.8.0-3.fc38.x86_64 pkgconf-m4-1.8.0-3.fc38.noarch pkgconf-pkg-config-1.8.0-3.fc38.x86_64 popt-1.19-1.fc38.x86_64 publicsuffix-list-dafsa-20221208-1.fc38.noarch python-srpm-macros-3.11-6.fc38.noarch qt5-srpm-macros-5.15.7-1.fc38.noarch readline-8.2-2.fc38.x86_64 redhat-rpm-config-235-1.fc38.noarch rpm-4.18.0-8.fc38.x86_64 rpm-build-4.18.0-8.fc38.x86_64 rpm-build-libs-4.18.0-8.fc38.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch rust-srpm-macros-23-1.fc38.noarch sed-4.8-11.fc37.x86_64 setup-2.14.3-1.fc38.noarch shadow-utils-2:4.13-3.fc38.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 tar-2:1.34-5.fc38.x86_64 tzdata-2022g-1.fc38.noarch unzip-6.0-58.fc38.x86_64 util-linux-2.38.1-3.fc38.x86_64 util-linux-core-2.38.1-3.fc38.x86_64 which-2.21-36.fc38.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 xz-5.2.9-1.fc38.x86_64 xz-libs-5.2.9-1.fc38.x86_64 zip-3.0-35.fc38.x86_64 zlib-1.2.13-1.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: util-linux-2.38.1-3.fc38.x86_64 diffutils-3.8-3.fc38.x86_64 pam-libs-1.5.2-15.fc38.x86_64 p11-kit-trust-0.24.1-5.fc38.x86_64 ed-1.18-2.fc38.x86_64 fedora-release-common-38-0.6.noarch libevent-2.1.12-7.fc38.x86_64 bzip2-libs-1.0.8-12.fc38.x86_64 libpsl-0.21.1-6.fc38.x86_64 lz4-libs-1.9.3-5.fc38.x86_64 zstd-1.5.2-3.fc37.x86_64 libidn2-2.3.4-1.fc38.x86_64 bash-5.2.9-3.fc38.x86_64 libnsl2-2.0.0-4.fc38.x86_64 findutils-4.9.0-2.fc38.x86_64 pkgconf-1.8.0-3.fc38.x86_64 openldap-2.6.3-1.fc38.x86_64 glibc-2.36.9000-19.fc38.x86_64 lua-srpm-macros-1-7.fc37.noarch kernel-srpm-macros-1.0-15.fc37.noarch pcre2-10.40-1.fc38.1.x86_64 alternatives-1.21-1.fc38.x86_64 cracklib-2.9.7-30.fc38.x86_64 keyutils-libs-1.6.1-5.fc38.x86_64 elfutils-debuginfod-client-0.188-3.fc38.x86_64 basesystem-11-14.fc37.noarch ncurses-libs-6.3-5.20221126.fc38.x86_64 gmp-6.2.1-3.fc38.x86_64 pam-1.5.2-15.fc38.x86_64 rpm-build-libs-4.18.0-8.fc38.x86_64 redhat-rpm-config-235-1.fc38.noarch publicsuffix-list-dafsa-20221208-1.fc38.noarch krb5-libs-1.20.1-3.fc38.x86_64 mpfr-4.1.1-2.fc38.x86_64 gpg-pubkey-eb10b464-6202d9c6 shadow-utils-4.13-3.fc38.x86_64 libtirpc-1.3.3-0.fc38.x86_64 nettle-3.8-2.fc38.x86_64 fedora-gpg-keys-38-0.3.noarch python-srpm-macros-3.11-6.fc38.noarch rpm-build-4.18.0-8.fc38.x86_64 fedora-repos-rawhide-38-0.3.noarch libattr-2.5.1-5.fc38.x86_64 fedora-repos-38-0.3.noarch unzip-6.0-58.fc38.x86_64 sqlite-libs-3.40.0-1.fc38.x86_64 libsepol-3.4-4.fc38.x86_64 libsemanage-3.4-6.fc38.x86_64 binutils-gold-2.39-6.fc38.x86_64 efi-srpm-macros-5-6.fc37.noarch zlib-1.2.13-1.fc38.x86_64 jansson-2.13.1-5.fc38.x86_64 authselect-libs-1.4.2-1.fc38.x86_64 glibc-minimal-langpack-2.36.9000-19.fc38.x86_64 libblkid-2.38.1-3.fc38.x86_64 rpm-sequoia-1.2.0-1.fc38.x86_64 fpc-srpm-macros-1.3-6.fc37.noarch patch-2.7.6-17.fc38.x86_64 gzip-1.12-2.fc38.x86_64 libssh-0.10.4-2.fc38.x86_64 zip-3.0-35.fc38.x86_64 which-2.21-36.fc38.x86_64 libmount-2.38.1-3.fc38.x86_64 openssl-libs-3.0.5-6.fc38.x86_64 libacl-2.3.1-4.fc38.x86_64 gdb-minimal-12.1-10.fc38.x86_64 rpmautospec-rpm-macros-0.3.1-1.fc38.noarch coreutils-common-9.1-8.fc38.x86_64 gpg-pubkey-5323552a-6112bcdc libfdisk-2.38.1-3.fc38.x86_64 openblas-srpm-macros-2-12.fc37.noarch bzip2-1.0.8-12.fc38.x86_64 libunistring-1.0-2.fc38.x86_64 libgomp-13.0.0-0.4.fc38.x86_64 package-notes-srpm-macros-0.5-6.fc38.noarch libgcc-13.0.0-0.4.fc38.x86_64 libpkgconf-1.8.0-3.fc38.x86_64 fedora-release-identity-basic-38-0.6.noarch tar-1.34-5.fc38.x86_64 file-5.42-4.fc38.x86_64 libffi-3.4.4-1.fc38.x86_64 fonts-srpm-macros-2.0.5-10.fc38.noarch p11-kit-0.24.1-5.fc38.x86_64 libuuid-2.38.1-3.fc38.x86_64 setup-2.14.3-1.fc38.noarch ansible-srpm-macros-1-8.1.fc38.noarch libstdc++-13.0.0-0.4.fc38.x86_64 libsmartcols-2.38.1-3.fc38.x86_64 libverto-0.3.2-4.fc38.x86_64 rust-srpm-macros-23-1.fc38.noarch authselect-1.4.2-1.fc38.x86_64 crypto-policies-20221215-1.gita4c31a3.fc38.noarch dwz-0.15-1.fc38.x86_64 coreutils-9.1-8.fc38.x86_64 debugedit-5.0-5.fc37.x86_64 libcap-ng-0.8.3-4.fc38.x86_64 rpm-4.18.0-8.fc38.x86_64 fedora-release-38-0.6.noarch cyrus-sasl-lib-2.1.28-8.fc38.x86_64 pcre2-syntax-10.40-1.fc38.1.noarch libxcrypt-4.4.33-5.fc38.x86_64 xz-5.2.9-1.fc38.x86_64 audit-libs-3.0.9-2.fc38.x86_64 systemd-libs-252.4-598.fc38.x86_64 curl-7.87.0-1.fc38.x86_64 libbrotli-1.0.9-9.fc38.x86_64 libtasn1-4.19.0-1.fc38.x86_64 perl-srpm-macros-1-47.fc38.noarch ghc-srpm-macros-1.5.0-7.fc37.noarch readline-8.2-2.fc38.x86_64 elfutils-default-yama-scope-0.188-3.fc38.noarch grep-3.8-1.fc38.x86_64 ocaml-srpm-macros-7-2.fc37.noarch gawk-5.1.1-4.fc38.x86_64 libpwquality-1.4.5-1.fc38.x86_64 libutempter-1.2.1-7.fc38.x86_64 lua-libs-5.4.4-6.fc38.x86_64 nim-srpm-macros-3-7.fc37.noarch elfutils-libs-0.188-3.fc38.x86_64 libselinux-3.4-6.fc38.x86_64 libcurl-7.87.0-1.fc38.x86_64 libcap-2.48-5.fc38.x86_64 xz-libs-5.2.9-1.fc38.x86_64 libnghttp2-1.51.0-1.fc38.x86_64 libxml2-2.10.3-2.fc38.x86_64 binutils-2.39-6.fc38.x86_64 tzdata-2022g-1.fc38.noarch libeconf-0.4.0-4.fc38.x86_64 filesystem-3.18-2.fc37.x86_64 info-7.0.1-1.fc38.x86_64 libarchive-3.6.1-3.fc38.x86_64 glibc-common-2.36.9000-19.fc38.x86_64 sed-4.8-11.fc37.x86_64 cpio-2.13-13.fc38.x86_64 file-libs-5.42-4.fc38.x86_64 elfutils-libelf-0.188-3.fc38.x86_64 pkgconf-m4-1.8.0-3.fc38.noarch glibc-gconv-extra-2.36.9000-19.fc38.x86_64 ca-certificates-2022.2.54-5.fc37.noarch ncurses-base-6.3-5.20221126.fc38.noarch popt-1.19-1.fc38.x86_64 libdb-5.3.28-54.fc38.x86_64 pkgconf-pkg-config-1.8.0-3.fc38.x86_64 xxhash-libs-0.8.1-3.fc37.x86_64 gnat-srpm-macros-4-16.fc37.noarch elfutils-0.188-3.fc38.x86_64 libssh-config-0.10.4-2.fc38.noarch libcom_err-1.46.5-3.fc38.x86_64 gdbm-libs-1.23-2.fc38.x86_64 rpm-libs-4.18.0-8.fc38.x86_64 libzstd-1.5.2-3.fc37.x86_64 qt5-srpm-macros-5.15.7-1.fc38.noarch util-linux-core-2.38.1-3.fc38.x86_64 go-srpm-macros-3.2.0-1.fc38.noarch libsigsegv-2.14-3.fc38.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1669248000 Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-pxkg7ivm/python-biopython/python-biopython.spec) Config(child) 1 minutes 7 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672135248.183296 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/results/python-biopython-1.80-1.fc38.src.rpm) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672135248.183296/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672135248.183296/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 Additional repo https_jakub_fedorapeople_org_fe 11 kB/s | 3.0 kB 00:00 fedora 91 kB/s | 23 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for python-biopython-1.80-1.fc38.src.rpm Start: build setup for python-biopython-1.80-1.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1669248000 Wrote: /builddir/build/SRPMS/python-biopython-1.80-1.fc38.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 Additional repo https_jakub_fedorapeople_org_fe 4.3 kB/s | 3.0 kB 00:00 fedora 93 kB/s | 23 kB 00:00 Dependencies resolved. ============================================================================================================= Package Arch Version Repository Size ============================================================================================================= Installing: gcc x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 34 M mysql-connector-python3 noarch 8.0.21-7.fc37 fedora 590 k python3-devel x86_64 3.11.1-1.fc38 fedora 269 k python3-mysqlclient x86_64 2.1.1-2.fc38 fedora 106 k python3-numpy x86_64 1:1.23.5-1.fc38 copr_base 7.3 M python3-psycopg2 x86_64 2.9.3-6.fc37 fedora 208 k python3-rdflib noarch 6.2.0-1.fc38 fedora 965 k python3-reportlab x86_64 3.6.12-1.fc38 fedora 3.5 M python3-setuptools noarch 65.5.1-1.fc38 fedora 1.7 M Installing dependencies: annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k annobin-plugin-gcc x86_64 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 889 k cpp x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 11 M dejavu-sans-fonts noarch 2.37-19.fc37 fedora 1.3 M expat x86_64 2.5.0-1.fc38 copr_base 111 k flexiblas x86_64 3.2.1-3.fc38 fedora 32 k flexiblas-netlib x86_64 3.2.1-3.fc38 fedora 3.1 M flexiblas-openblas-openmp x86_64 3.2.1-3.fc38 fedora 17 k fonts-filesystem noarch 1:2.0.5-10.fc38 fedora 8.0 k freetype x86_64 2.12.1-3.fc38 copr_base 407 k fribidi x86_64 1.0.12-2.fc38 copr_base 89 k gc x86_64 8.2.2-1.fc38 copr_base 111 k gcc-plugin-annobin x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 29 k glib2 x86_64 2.74.1-2.fc38 copr_base 2.7 M glibc-devel x86_64 2.36.9000-19.fc38 fedora 47 k glibc-headers-x86 noarch 2.36.9000-19.fc38 fedora 525 k gnutls x86_64 3.7.8-9.fc38 copr_base 1.1 M graphite2 x86_64 1.3.14-10.fc38 copr_base 95 k guile22 x86_64 2.2.7-6.fc38 copr_base 6.4 M harfbuzz x86_64 6.0.0-1.fc38 copr_base 825 k jbigkit-libs x86_64 2.1-24.fc38 copr_base 53 k kernel-headers x86_64 6.1.0-1.fc38 fedora 1.5 M lcms2 x86_64 2.14-1.fc38 copr_base 177 k libXau x86_64 1.0.11-1.fc38 copr_base 32 k libart_lgpl x86_64 2.3.21-28.fc38 copr_base 73 k libb2 x86_64 0.98.1-7.fc38 copr_base 25 k libgfortran x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 890 k libimagequant x86_64 2.17.0-3.fc38 copr_base 63 k libjpeg-turbo x86_64 2.1.4-1.fc38 copr_base 182 k libmpc x86_64 1.2.1-5.fc38 copr_base 61 k libpng x86_64 2:1.6.37-13.fc38 copr_base 120 k libpq x86_64 15.0-2.fc38 copr_base 210 k libquadmath x86_64 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 178 k libraqm x86_64 0.8.0-2.fc38 copr_base 20 k libtiff x86_64 4.4.0-4.fc38 copr_base 198 k libtool-ltdl x86_64 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 37 k libwebp x86_64 1.2.4-2.fc38 copr_base 280 k libxcb x86_64 1.13.1-10.fc38 copr_base 227 k libxcrypt-devel x86_64 4.4.33-5.fc38 copr_base 31 k make x86_64 1:4.3-11.fc38 copr_base 534 k mariadb-connector-c x86_64 3.2.7-2.fc38 copr_base 196 k mariadb-connector-c-config noarch 3.2.7-2.fc38 copr_base 10 k mpdecimal x86_64 2.5.1-4.fc38 copr_base 102 k openblas x86_64 0.3.21-4.fc38 copr_base 35 k openblas-openmp x86_64 0.3.21-4.fc38 copr_base 5.0 M openjpeg2 x86_64 2.5.0-2.fc38 copr_base 178 k protobuf x86_64 3.19.6-1.fc38 fedora 984 k pyproject-rpm-macros noarch 1.5.0-1.fc38 fedora 40 k python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M python-rpm-macros noarch 3.11-6.fc38 fedora 19 k python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k python3 x86_64 3.11.1-1.fc38 fedora 27 k python3-isodate noarch 0.6.1-5.fc37 fedora 79 k python3-libs x86_64 3.11.1-1.fc38 fedora 9.6 M python3-olefile noarch 0.46-18.fc37 fedora 67 k python3-packaging noarch 21.3-7.fc38 fedora 98 k python3-pillow x86_64 9.3.0-2.fc38 fedora 921 k python3-protobuf x86_64 3.19.6-1.fc38 fedora 420 k python3-pyparsing noarch 3.0.9-2.fc37 fedora 262 k python3-rpm-generators noarch 13-2.fc37 fedora 30 k python3-rpm-macros noarch 3.11-6.fc38 fedora 15 k python3-six noarch 1.16.0-8.fc37 fedora 42 k Transaction Summary ============================================================================================================= Install 71 Packages Total size: 102 M Total download size: 33 M Installed size: 394 M Downloading Packages: [SKIPPED] expat-2.5.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] gc-8.2.2-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] guile22-2.2.7-6.fc38.x86_64.rpm: Already downloaded [SKIPPED] libb2-0.98.1-7.fc38.x86_64.rpm: Already downloaded [SKIPPED] libmpc-1.2.1-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.33-5.fc38.x86_64.rpm: Already downloaded [SKIPPED] make-4.3-11.fc38.x86_64.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-4.fc38.x86_64.rpm: Already downloaded [SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] cpp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.36.9000-19.fc38.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.36.9000-19.fc38.noarch.rpm: Already downloaded [SKIPPED] kernel-headers-6.1.0-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] pyproject-rpm-macros-1.5.0-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded [SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded [SKIPPED] python3-3.11.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-devel-3.11.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-libs-3.11.1-1.fc38.x86_64.rpm: Already downloaded [SKIPPED] python3-packaging-21.3-7.fc38.noarch.rpm: Already downloaded [SKIPPED] python3-pyparsing-3.0.9-2.fc37.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-generators-13-2.fc37.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded [SKIPPED] python3-setuptools-65.5.1-1.fc38.noarch.rpm: Already downloaded (30/71): fribidi-1.0.12-2.fc38.x86_64.rpm 349 kB/s | 89 kB 00:00 (31/71): freetype-2.12.1-3.fc38.x86_64.rpm 1.4 MB/s | 407 kB 00:00 (32/71): gnutls-3.7.8-9.fc38.x86_64.rpm 26 MB/s | 1.1 MB 00:00 (33/71): graphite2-1.3.14-10.fc38.x86_64.rpm 3.9 MB/s | 95 kB 00:00 (34/71): glib2-2.74.1-2.fc38.x86_64.rpm 8.8 MB/s | 2.7 MB 00:00 (35/71): harfbuzz-6.0.0-1.fc38.x86_64.rpm 48 MB/s | 825 kB 00:00 (36/71): jbigkit-libs-2.1-24.fc38.x86_64.rpm 3.2 MB/s | 53 kB 00:00 (37/71): lcms2-2.14-1.fc38.x86_64.rpm 16 MB/s | 177 kB 00:00 (38/71): libXau-1.0.11-1.fc38.x86_64.rpm 3.7 MB/s | 32 kB 00:00 (39/71): libart_lgpl-2.3.21-28.fc38.x86_64.rpm 7.2 MB/s | 73 kB 00:00 (40/71): libimagequant-2.17.0-3.fc38.x86_64.rpm 6.6 MB/s | 63 kB 00:00 (41/71): libjpeg-turbo-2.1.4-1.fc38.x86_64.rpm 18 MB/s | 182 kB 00:00 (42/71): libpng-1.6.37-13.fc38.x86_64.rpm 13 MB/s | 120 kB 00:00 (43/71): libpq-15.0-2.fc38.x86_64.rpm 19 MB/s | 210 kB 00:00 (44/71): libraqm-0.8.0-2.fc38.x86_64.rpm 2.2 MB/s | 20 kB 00:00 (45/71): libtiff-4.4.0-4.fc38.x86_64.rpm 19 MB/s | 198 kB 00:00 (46/71): libwebp-1.2.4-2.fc38.x86_64.rpm 25 MB/s | 280 kB 00:00 (47/71): libxcb-1.13.1-10.fc38.x86_64.rpm 21 MB/s | 227 kB 00:00 (48/71): mariadb-connector-c-3.2.7-2.fc38.x86_6 18 MB/s | 196 kB 00:00 (49/71): mariadb-connector-c-config-3.2.7-2.fc3 1.2 MB/s | 10 kB 00:00 (50/71): openblas-0.3.21-4.fc38.x86_64.rpm 3.9 MB/s | 35 kB 00:00 (51/71): openjpeg2-2.5.0-2.fc38.x86_64.rpm 9.9 MB/s | 178 kB 00:00 (52/71): openblas-openmp-0.3.21-4.fc38.x86_64.r 38 MB/s | 5.0 MB 00:00 (53/71): python3-numpy-1.23.5-1.fc38.x86_64.rpm 55 MB/s | 7.3 MB 00:00 (54/71): libgfortran-13.0.0-0.4.fc38.x86_64.rpm 4.3 MB/s | 890 kB 00:00 (55/71): libquadmath-13.0.0-0.4.fc38.x86_64.rpm 1.1 MB/s | 178 kB 00:00 (56/71): flexiblas-3.2.1-3.fc38.x86_64.rpm 118 kB/s | 32 kB 00:00 (57/71): flexiblas-openblas-openmp-3.2.1-3.fc38 145 kB/s | 17 kB 00:00 (58/71): fonts-filesystem-2.0.5-10.fc38.noarch. 92 kB/s | 8.0 kB 00:00 (59/71): dejavu-sans-fonts-2.37-19.fc37.noarch. 1.9 MB/s | 1.3 MB 00:00 (60/71): protobuf-3.19.6-1.fc38.x86_64.rpm 7.4 MB/s | 984 kB 00:00 (61/71): flexiblas-netlib-3.2.1-3.fc38.x86_64.r 4.0 MB/s | 3.1 MB 00:00 (62/71): python3-isodate-0.6.1-5.fc37.noarch.rp 507 kB/s | 79 kB 00:00 (63/71): mysql-connector-python3-8.0.21-7.fc37. 1.4 MB/s | 590 kB 00:00 (64/71): python3-mysqlclient-2.1.1-2.fc38.x86_6 1.1 MB/s | 106 kB 00:00 (65/71): python3-olefile-0.46-18.fc37.noarch.rp 805 kB/s | 67 kB 00:00 (66/71): python3-protobuf-3.19.6-1.fc38.x86_64. 4.6 MB/s | 420 kB 00:00 (67/71): python3-psycopg2-2.9.3-6.fc37.x86_64.r 2.1 MB/s | 208 kB 00:00 (68/71): python3-pillow-9.3.0-2.fc38.x86_64.rpm 4.8 MB/s | 921 kB 00:00 (69/71): python3-rdflib-6.2.0-1.fc38.noarch.rpm 9.7 MB/s | 965 kB 00:00 (70/71): python3-six-1.16.0-8.fc37.noarch.rpm 353 kB/s | 42 kB 00:00 (71/71): python3-reportlab-3.6.12-1.fc38.x86_64 15 MB/s | 3.5 MB 00:00 -------------------------------------------------------------------------------- Total 15 MB/s | 33 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.11-6.fc38.noarch 1/71 Installing : python3-rpm-macros-3.11-6.fc38.noarch 2/71 Installing : flexiblas-3.2.1-3.fc38.x86_64 3/71 Installing : libquadmath-13.0.0-0.4.fc38.x86_64 4/71 Installing : libgfortran-13.0.0-0.4.fc38.x86_64 5/71 Installing : libwebp-1.2.4-2.fc38.x86_64 6/71 Installing : libmpc-1.2.1-5.fc38.x86_64 7/71 Installing : libjpeg-turbo-2.1.4-1.fc38.x86_64 8/71 Installing : cpp-13.0.0-0.4.fc38.x86_64 9/71 Installing : pyproject-rpm-macros-1.5.0-1.fc38.noarch 10/71 Installing : python-setuptools-wheel-65.5.1-1.fc38.noarch 11/71 Installing : python-pip-wheel-22.3.1-1.fc38.noarch 12/71 Installing : protobuf-3.19.6-1.fc38.x86_64 13/71 Installing : kernel-headers-6.1.0-1.fc38.x86_64 14/71 Installing : glibc-headers-x86-2.36.9000-19.fc38.noarch 15/71 Installing : glibc-devel-2.36.9000-19.fc38.x86_64 16/71 Installing : libxcrypt-devel-4.4.33-5.fc38.x86_64 17/71 Installing : fonts-filesystem-1:2.0.5-10.fc38.noarch 18/71 Installing : dejavu-sans-fonts-2.37-19.fc37.noarch 19/71 Installing : libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 20/71 Installing : annobin-docs-10.99-1.0.1.fc38.noarch 21/71 Installing : openjpeg2-2.5.0-2.fc38.x86_64 22/71 Installing : openblas-0.3.21-4.fc38.x86_64 23/71 Installing : openblas-openmp-0.3.21-4.fc38.x86_64 24/71 Installing : flexiblas-netlib-3.2.1-3.fc38.x86_64 25/71 Installing : flexiblas-openblas-openmp-3.2.1-3.fc38.x86_64 26/71 Installing : mpdecimal-2.5.1-4.fc38.x86_64 27/71 Installing : mariadb-connector-c-config-3.2.7-2.fc38.noarch 28/71 Installing : mariadb-connector-c-3.2.7-2.fc38.x86_64 29/71 Installing : libpq-15.0-2.fc38.x86_64 30/71 Installing : libpng-2:1.6.37-13.fc38.x86_64 31/71 Installing : libimagequant-2.17.0-3.fc38.x86_64 32/71 Installing : libb2-0.98.1-7.fc38.x86_64 33/71 Installing : libart_lgpl-2.3.21-28.fc38.x86_64 34/71 Installing : libXau-1.0.11-1.fc38.x86_64 35/71 Installing : libxcb-1.13.1-10.fc38.x86_64 36/71 Installing : lcms2-2.14-1.fc38.x86_64 37/71 Installing : jbigkit-libs-2.1-24.fc38.x86_64 38/71 Installing : libtiff-4.4.0-4.fc38.x86_64 39/71 Installing : graphite2-1.3.14-10.fc38.x86_64 40/71 Installing : gnutls-3.7.8-9.fc38.x86_64 41/71 Installing : glib2-2.74.1-2.fc38.x86_64 42/71 Installing : harfbuzz-6.0.0-1.fc38.x86_64 43/71 Installing : freetype-2.12.1-3.fc38.x86_64 44/71 Installing : gc-8.2.2-1.fc38.x86_64 45/71 Installing : guile22-2.2.7-6.fc38.x86_64 46/71 Installing : make-1:4.3-11.fc38.x86_64 47/71 Installing : gcc-13.0.0-0.4.fc38.x86_64 48/71 Running scriptlet: gcc-13.0.0-0.4.fc38.x86_64 48/71 Installing : fribidi-1.0.12-2.fc38.x86_64 49/71 Installing : libraqm-0.8.0-2.fc38.x86_64 50/71 Installing : expat-2.5.0-1.fc38.x86_64 51/71 Installing : python3-3.11.1-1.fc38.x86_64 52/71 Installing : python3-libs-3.11.1-1.fc38.x86_64 53/71 Installing : python3-pyparsing-3.0.9-2.fc37.noarch 54/71 Installing : python3-packaging-21.3-7.fc38.noarch 55/71 Installing : python3-rpm-generators-13-2.fc37.noarch 56/71 Installing : python3-olefile-0.46-18.fc37.noarch 57/71 Installing : python3-pillow-9.3.0-2.fc38.x86_64 58/71 Installing : python3-protobuf-3.19.6-1.fc38.x86_64 59/71 Installing : python3-setuptools-65.5.1-1.fc38.noarch 60/71 Installing : python3-six-1.16.0-8.fc37.noarch 61/71 Installing : python3-isodate-0.6.1-5.fc37.noarch 62/71 Installing : python3-rdflib-6.2.0-1.fc38.noarch 63/71 Installing : mysql-connector-python3-8.0.21-7.fc37.noarch 64/71 Installing : python3-reportlab-3.6.12-1.fc38.x86_64 65/71 Installing : python3-devel-3.11.1-1.fc38.x86_64 66/71 Installing : python3-numpy-1:1.23.5-1.fc38.x86_64 67/71 Installing : python3-mysqlclient-2.1.1-2.fc38.x86_64 68/71 Installing : python3-psycopg2-2.9.3-6.fc37.x86_64 69/71 Installing : annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 70/71 Running scriptlet: annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 70/71 Installing : gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 71/71 Running scriptlet: gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 71/71 Verifying : expat-2.5.0-1.fc38.x86_64 1/71 Verifying : freetype-2.12.1-3.fc38.x86_64 2/71 Verifying : fribidi-1.0.12-2.fc38.x86_64 3/71 Verifying : gc-8.2.2-1.fc38.x86_64 4/71 Verifying : glib2-2.74.1-2.fc38.x86_64 5/71 Verifying : gnutls-3.7.8-9.fc38.x86_64 6/71 Verifying : graphite2-1.3.14-10.fc38.x86_64 7/71 Verifying : guile22-2.2.7-6.fc38.x86_64 8/71 Verifying : harfbuzz-6.0.0-1.fc38.x86_64 9/71 Verifying : jbigkit-libs-2.1-24.fc38.x86_64 10/71 Verifying : lcms2-2.14-1.fc38.x86_64 11/71 Verifying : libXau-1.0.11-1.fc38.x86_64 12/71 Verifying : libart_lgpl-2.3.21-28.fc38.x86_64 13/71 Verifying : libb2-0.98.1-7.fc38.x86_64 14/71 Verifying : libimagequant-2.17.0-3.fc38.x86_64 15/71 Verifying : libjpeg-turbo-2.1.4-1.fc38.x86_64 16/71 Verifying : libmpc-1.2.1-5.fc38.x86_64 17/71 Verifying : libpng-2:1.6.37-13.fc38.x86_64 18/71 Verifying : libpq-15.0-2.fc38.x86_64 19/71 Verifying : libraqm-0.8.0-2.fc38.x86_64 20/71 Verifying : libtiff-4.4.0-4.fc38.x86_64 21/71 Verifying : libwebp-1.2.4-2.fc38.x86_64 22/71 Verifying : libxcb-1.13.1-10.fc38.x86_64 23/71 Verifying : libxcrypt-devel-4.4.33-5.fc38.x86_64 24/71 Verifying : make-1:4.3-11.fc38.x86_64 25/71 Verifying : mariadb-connector-c-3.2.7-2.fc38.x86_64 26/71 Verifying : mariadb-connector-c-config-3.2.7-2.fc38.noarch 27/71 Verifying : mpdecimal-2.5.1-4.fc38.x86_64 28/71 Verifying : openblas-0.3.21-4.fc38.x86_64 29/71 Verifying : openblas-openmp-0.3.21-4.fc38.x86_64 30/71 Verifying : openjpeg2-2.5.0-2.fc38.x86_64 31/71 Verifying : python3-numpy-1:1.23.5-1.fc38.x86_64 32/71 Verifying : annobin-docs-10.99-1.0.1.fc38.noarch 33/71 Verifying : annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 34/71 Verifying : cpp-13.0.0-0.4.fc38.x86_64 35/71 Verifying : gcc-13.0.0-0.4.fc38.x86_64 36/71 Verifying : gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 37/71 Verifying : libgfortran-13.0.0-0.4.fc38.x86_64 38/71 Verifying : libquadmath-13.0.0-0.4.fc38.x86_64 39/71 Verifying : libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 40/71 Verifying : dejavu-sans-fonts-2.37-19.fc37.noarch 41/71 Verifying : flexiblas-3.2.1-3.fc38.x86_64 42/71 Verifying : flexiblas-netlib-3.2.1-3.fc38.x86_64 43/71 Verifying : flexiblas-openblas-openmp-3.2.1-3.fc38.x86_64 44/71 Verifying : fonts-filesystem-1:2.0.5-10.fc38.noarch 45/71 Verifying : glibc-devel-2.36.9000-19.fc38.x86_64 46/71 Verifying : glibc-headers-x86-2.36.9000-19.fc38.noarch 47/71 Verifying : kernel-headers-6.1.0-1.fc38.x86_64 48/71 Verifying : mysql-connector-python3-8.0.21-7.fc37.noarch 49/71 Verifying : protobuf-3.19.6-1.fc38.x86_64 50/71 Verifying : pyproject-rpm-macros-1.5.0-1.fc38.noarch 51/71 Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 52/71 Verifying : python-rpm-macros-3.11-6.fc38.noarch 53/71 Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 54/71 Verifying : python3-3.11.1-1.fc38.x86_64 55/71 Verifying : python3-devel-3.11.1-1.fc38.x86_64 56/71 Verifying : python3-isodate-0.6.1-5.fc37.noarch 57/71 Verifying : python3-libs-3.11.1-1.fc38.x86_64 58/71 Verifying : python3-mysqlclient-2.1.1-2.fc38.x86_64 59/71 Verifying : python3-olefile-0.46-18.fc37.noarch 60/71 Verifying : python3-packaging-21.3-7.fc38.noarch 61/71 Verifying : python3-pillow-9.3.0-2.fc38.x86_64 62/71 Verifying : python3-protobuf-3.19.6-1.fc38.x86_64 63/71 Verifying : python3-psycopg2-2.9.3-6.fc37.x86_64 64/71 Verifying : python3-pyparsing-3.0.9-2.fc37.noarch 65/71 Verifying : python3-rdflib-6.2.0-1.fc38.noarch 66/71 Verifying : python3-reportlab-3.6.12-1.fc38.x86_64 67/71 Verifying : python3-rpm-generators-13-2.fc37.noarch 68/71 Verifying : python3-rpm-macros-3.11-6.fc38.noarch 69/71 Verifying : python3-setuptools-65.5.1-1.fc38.noarch 70/71 Verifying : python3-six-1.16.0-8.fc37.noarch 71/71 Installed: annobin-docs-10.99-1.0.1.fc38.noarch annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64 cpp-13.0.0-0.4.fc38.x86_64 dejavu-sans-fonts-2.37-19.fc37.noarch expat-2.5.0-1.fc38.x86_64 flexiblas-3.2.1-3.fc38.x86_64 flexiblas-netlib-3.2.1-3.fc38.x86_64 flexiblas-openblas-openmp-3.2.1-3.fc38.x86_64 fonts-filesystem-1:2.0.5-10.fc38.noarch freetype-2.12.1-3.fc38.x86_64 fribidi-1.0.12-2.fc38.x86_64 gc-8.2.2-1.fc38.x86_64 gcc-13.0.0-0.4.fc38.x86_64 gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64 glib2-2.74.1-2.fc38.x86_64 glibc-devel-2.36.9000-19.fc38.x86_64 glibc-headers-x86-2.36.9000-19.fc38.noarch gnutls-3.7.8-9.fc38.x86_64 graphite2-1.3.14-10.fc38.x86_64 guile22-2.2.7-6.fc38.x86_64 harfbuzz-6.0.0-1.fc38.x86_64 jbigkit-libs-2.1-24.fc38.x86_64 kernel-headers-6.1.0-1.fc38.x86_64 lcms2-2.14-1.fc38.x86_64 libXau-1.0.11-1.fc38.x86_64 libart_lgpl-2.3.21-28.fc38.x86_64 libb2-0.98.1-7.fc38.x86_64 libgfortran-13.0.0-0.4.fc38.x86_64 libimagequant-2.17.0-3.fc38.x86_64 libjpeg-turbo-2.1.4-1.fc38.x86_64 libmpc-1.2.1-5.fc38.x86_64 libpng-2:1.6.37-13.fc38.x86_64 libpq-15.0-2.fc38.x86_64 libquadmath-13.0.0-0.4.fc38.x86_64 libraqm-0.8.0-2.fc38.x86_64 libtiff-4.4.0-4.fc38.x86_64 libtool-ltdl-2.4.7-3.0.1.fc38.x86_64 libwebp-1.2.4-2.fc38.x86_64 libxcb-1.13.1-10.fc38.x86_64 libxcrypt-devel-4.4.33-5.fc38.x86_64 make-1:4.3-11.fc38.x86_64 mariadb-connector-c-3.2.7-2.fc38.x86_64 mariadb-connector-c-config-3.2.7-2.fc38.noarch mpdecimal-2.5.1-4.fc38.x86_64 mysql-connector-python3-8.0.21-7.fc37.noarch openblas-0.3.21-4.fc38.x86_64 openblas-openmp-0.3.21-4.fc38.x86_64 openjpeg2-2.5.0-2.fc38.x86_64 protobuf-3.19.6-1.fc38.x86_64 pyproject-rpm-macros-1.5.0-1.fc38.noarch python-pip-wheel-22.3.1-1.fc38.noarch python-rpm-macros-3.11-6.fc38.noarch python-setuptools-wheel-65.5.1-1.fc38.noarch python3-3.11.1-1.fc38.x86_64 python3-devel-3.11.1-1.fc38.x86_64 python3-isodate-0.6.1-5.fc37.noarch python3-libs-3.11.1-1.fc38.x86_64 python3-mysqlclient-2.1.1-2.fc38.x86_64 python3-numpy-1:1.23.5-1.fc38.x86_64 python3-olefile-0.46-18.fc37.noarch python3-packaging-21.3-7.fc38.noarch python3-pillow-9.3.0-2.fc38.x86_64 python3-protobuf-3.19.6-1.fc38.x86_64 python3-psycopg2-2.9.3-6.fc37.x86_64 python3-pyparsing-3.0.9-2.fc37.noarch python3-rdflib-6.2.0-1.fc38.noarch python3-reportlab-3.6.12-1.fc38.x86_64 python3-rpm-generators-13-2.fc37.noarch python3-rpm-macros-3.11-6.fc38.noarch python3-setuptools-65.5.1-1.fc38.noarch python3-six-1.16.0-8.fc37.noarch Complete! Finish: build setup for python-biopython-1.80-1.fc38.src.rpm Start: rpmbuild python-biopython-1.80-1.fc38.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1669248000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fzyPSO + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf python-biopython-1.80 + /usr/bin/mkdir -p python-biopython-1.80 + cd python-biopython-1.80 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.80.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd biopython-1.80 ~/build/BUILD/python-biopython-1.80/biopython-1.80 ~/build/BUILD/python-biopython-1.80 + find Scripts -type f -exec chmod -x '{}' ';' + find Doc -type f -exec chmod -x '{}' ';' + find Doc -type f -exec sed -i 's/\r//' '{}' ';' + find Bio -type f -exec chmod -x '{}' ';' + find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';' + popd + cp -a biopython-1.80 python3 ~/build/BUILD/python-biopython-1.80 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.tlM6X6 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC ~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80 + CXX=g++ + export CXX + cd python-biopython-1.80 + pushd python3 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' running build running build_py creating build creating build/lib.linux-x86_64-cpython-311 creating build/lib.linux-x86_64-cpython-311/Bio copying Bio/File.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/LogisticRegression.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/MaxEntropy.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/NaiveBayes.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Seq.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqFeature.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/SeqRecord.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/bgzf.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/kNN.py -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/pairwise2.py -> build/lib.linux-x86_64-cpython-311/Bio creating build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Affy creating build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-x86_64-cpython-311/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices creating build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/AlignIO creating build/lib.linux-x86_64-cpython-311/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Alphabet creating build/lib.linux-x86_64-cpython-311/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Application creating build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Blast creating build/lib.linux-x86_64-cpython-311/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/CAPS creating build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-x86_64-cpython-311/Bio/codonalign creating build/lib.linux-x86_64-cpython-311/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Compass creating build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/SCOPData.py -> build/lib.linux-x86_64-cpython-311/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Data creating build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Emboss creating build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Entrez creating build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-x86_64-cpython-311/Bio/ExPASy creating build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-x86_64-cpython-311/Bio/GenBank creating build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Geo creating build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics creating build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram creating build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/HMM creating build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map creating build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf creating build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML creating build/lib.linux-x86_64-cpython-311/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Medline creating build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs creating build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/applications creating build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar creating build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Nexus creating build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-x86_64-cpython-311/Bio/NMR creating build/lib.linux-x86_64-cpython-311/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway creating build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB creating build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-x86_64-cpython-311/Bio/phenotype creating build/lib.linux-x86_64-cpython-311/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen creating build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop creating build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Restriction creating build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SCOP creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO creating build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO creating build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-x86_64-cpython-311/Bio/SeqUtils creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing creating build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications creating build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer creating build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer creating build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/SwissProt creating build/lib.linux-x86_64-cpython-311/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/TogoWS creating build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications creating build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML creating build/lib.linux-x86_64-cpython-311/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniGene creating build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/UniProt creating build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/__init__.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/dnal.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise copying Bio/Wise/psw.py -> build/lib.linux-x86_64-cpython-311/Bio/Wise creating build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/__init__.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/Loader.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-x86_64-cpython-311/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-x86_64-cpython-311/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Align.substitution_matrices.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Align.substitution_matrices.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Align.substitution_matrices.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.DTDs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Entrez.DTDs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Entrez.DTDs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3.11/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'Bio.Entrez.XSDs' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'Bio.Entrez.XSDs' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'Bio.Entrez.XSDs' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) copying Bio/cpairwise2module.c -> build/lib.linux-x86_64-cpython-311/Bio copying Bio/Align/_aligners.c -> build/lib.linux-x86_64-cpython-311/Bio/Align creating build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-x86_64-cpython-311/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-x86_64-cpython-311/Bio/Cluster creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs creating build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-x86_64-cpython-311/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-x86_64-cpython-311/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-x86_64-cpython-311/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/Bio creating build/temp.linux-x86_64-cpython-311/Bio/Align gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Align/_aligners.c -o build/temp.linux-x86_64-cpython-311/Bio/Align/_aligners.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Align/_aligners.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so building 'Bio.cpairwise2' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.11/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.11/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-x86_64-cpython-311/Bio/Nexus gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-x86_64-cpython-311/Bio/PDB creating build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-x86_64-cpython-311/Bio/motifs gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/motifs/_pwm.c -o build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-x86_64-cpython-311/Bio/Cluster gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/cluster.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/Cluster/clustermodule.c -o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/Cluster/cluster.o build/temp.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/kdtrees.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so building 'Bio.PDB.ccealign' extension gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealign.cpython-311-x86_64-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-x86_64-cpython-311/Bio/SeqIO gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/usr/include/python3.11 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so ~/build/BUILD/python-biopython-1.80 + popd + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.xeVmA6 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 ++ dirname /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.80 + pushd python3 ~/build/BUILD/python-biopython-1.80/python3 ~/build/BUILD/python-biopython-1.80 + /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 --install-data=/usr/share/python-biopython running install /usr/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running install_lib creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11 creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL copying build/lib.linux-x86_64-cpython-311/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise copying build/lib.linux-x86_64-cpython-311/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt copying build/lib.linux-x86_64-cpython-311/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene copying build/lib.linux-x86_64-cpython-311/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo copying build/lib.linux-x86_64-cpython-311/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS copying build/lib.linux-x86_64-cpython-311/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt copying build/lib.linux-x86_64-cpython-311/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing copying build/lib.linux-x86_64-cpython-311/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils copying build/lib.linux-x86_64-cpython-311/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO copying build/lib.linux-x86_64-cpython-311/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO copying build/lib.linux-x86_64-cpython-311/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP copying build/lib.linux-x86_64-cpython-311/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction copying build/lib.linux-x86_64-cpython-311/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop copying build/lib.linux-x86_64-cpython-311/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype copying build/lib.linux-x86_64-cpython-311/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep copying build/lib.linux-x86_64-cpython-311/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR copying build/lib.linux-x86_64-cpython-311/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus copying build/lib.linux-x86_64-cpython-311/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar copying build/lib.linux-x86_64-cpython-311/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications copying build/lib.linux-x86_64-cpython-311/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs copying build/lib.linux-x86_64-cpython-311/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline copying build/lib.linux-x86_64-cpython-311/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealign.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-x86_64-cpython-311/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB copying build/lib.linux-x86_64-cpython-311/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf copying build/lib.linux-x86_64-cpython-311/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG copying build/lib.linux-x86_64-cpython-311/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM copying build/lib.linux-x86_64-cpython-311/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics copying build/lib.linux-x86_64-cpython-311/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo copying build/lib.linux-x86_64-cpython-311/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank copying build/lib.linux-x86_64-cpython-311/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy copying build/lib.linux-x86_64-cpython-311/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/XSDs creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/DTDs copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez copying build/lib.linux-x86_64-cpython-311/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss copying build/lib.linux-x86_64-cpython-311/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data copying build/lib.linux-x86_64-cpython-311/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass copying build/lib.linux-x86_64-cpython-311/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign copying build/lib.linux-x86_64-cpython-311/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster copying build/lib.linux-x86_64-cpython-311/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS copying build/lib.linux-x86_64-cpython-311/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast copying build/lib.linux-x86_64-cpython-311/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application copying build/lib.linux-x86_64-cpython-311/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet copying build/lib.linux-x86_64-cpython-311/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO copying build/lib.linux-x86_64-cpython-311/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-x86_64-cpython-311/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications copying build/lib.linux-x86_64-cpython-311/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align copying build/lib.linux-x86_64-cpython-311/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy copying build/lib.linux-x86_64-cpython-311/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio copying build/lib.linux-x86_64-cpython-311/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/Loader.py to Loader.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/BioSQL/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/psw.py to psw.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/dnal.py to dnal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Wise/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniProt/GOA.py to GOA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/UniGene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_io.py to _io.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Newick.py to Newick.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/query.py to query.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_index.py to _index.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Residues.py to Residues.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Raf.py to Raf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Hie.py to Hie.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Dom.py to Dom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Des.py to Des.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SCOP/Cla.py to Cla.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/Restriction.py to Restriction.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PopGen/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/phenotype/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Pathway/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/xpktools.py to xpktools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Trees.py to Trees.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/StandardData.py to StandardData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nodes.py to Nodes.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/Nexus.py to Nexus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/db.py to db.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/xms.py to xms.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/transfac.py to transfac.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/thresholds.py to thresholds.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/pfm.py to pfm.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/minimal.py to minimal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/meme.py to meme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/matrix.py to matrix.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/mast.py to mast.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/alignace.py to alignace.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Medline/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/vectors.py to vectors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/qcprot.py to qcprot.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ic_data.py to ic_data.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/cealign.py to cealign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Structure.py to Structure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Selection.py to Selection.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/SASA.py to SASA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Residue.py to Residue.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PSEA.py to PSEA.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PICIO.py to PICIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBList.py to PDBList.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Model.py to Model.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Entity.py to Entity.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Dice.py to Dice.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/DSSP.py to DSSP.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Chain.py to Chain.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/Atom.py to Atom.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/KEGG/REST.py to REST.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/Utilities.py to Utilities.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/Trainer.py to Trainer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Geo/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/utils.py to utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/Parser.py to Parser.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Emboss/Applications.py to Applications.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/SCOPData.py to SCOPData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/PDBData.py to PDBData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Compass/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/CAPS/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/Record.py to Record.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Blast/Applications.py to Applications.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Application/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/tabular.py to tabular.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/stockholm.py to stockholm.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/sam.py to sam.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/psl.py to psl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/phylip.py to phylip.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/nexus.py to nexus.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/msf.py to msf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/mauve.py to mauve.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/maf.py to maf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/interfaces.py to interfaces.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/hhr.py to hhr.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/fasta.py to fasta.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/exonerate.py to exonerate.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/emboss.py to emboss.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/clustal.py to clustal.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/bigbed.py to bigbed.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/bed.py to bed.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/a2m.py to a2m.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/pairwise2.py to pairwise2.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/kNN.py to kNN.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/bgzf.py to bgzf.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/_utils.py to _utils.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/__init__.py to __init__.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Seq.py to Seq.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/File.py to File.cpython-311.pyc writing byte-compilation script '/tmp/tmpvn8jjppf.py' /usr/bin/python3 /tmp/tmpvn8jjppf.py removing /tmp/tmpvn8jjppf.py running install_egg_info running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' Copying biopython.egg-info to /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/biopython-1.80-py3.11.egg-info running install_scripts + xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 + find Scripts -name '*.py' Scripts/xbbtools/xbbtools.py: updating Scripts/xbbtools/xbb_widget.py: updating Scripts/xbbtools/xbb_utils.py: updating Scripts/xbbtools/xbb_translations.py: updating Scripts/xbbtools/xbb_search.py: updating Scripts/xbbtools/xbb_help.py: updating Scripts/xbbtools/xbb_blastbg.py: updating Scripts/xbbtools/xbb_blast.py: updating Scripts/xbbtools/nextorf.py: updating Scripts/update_ncbi_codon_table.py: no change Scripts/scop_pdb.py: updating Scripts/query_pubmed.py: updating Scripts/SeqGui/SeqGui.py: no change Scripts/Restriction/rebase_update.py: updating Scripts/Restriction/ranacompiler.py: updating Scripts/Performance/biosql_performance_read.py: updating Scripts/Performance/biosql_performance_load.py: updating Scripts/PDB/hsexpo.py: updating Scripts/PDB/generate_three_to_one_dict.py: no change Scripts/GenBank/check_output_simple.py: updating Scripts/GenBank/check_output.py: updating ~/build/BUILD/python-biopython-1.80 + popd + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.80-1.fc38 --unique-debug-suffix -1.80-1.fc38.x86_64 --unique-debug-src-base python-biopython-1.80-1.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.80 extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Align/_aligners.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Cluster/_cluster.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Nexus/cnexus.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/ccealign.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/PDB/kdtrees.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/_twoBitIO.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/cpairwise2.cpython-311-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/motifs/_pwm.cpython-311-x86_64-linux-gnu.so original debug info size: 1000kB, size after compression: 940kB /usr/bin/sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. 1192 blocks + /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 + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib/debug/usr/lib64/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.RPeVsk + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FFLAGS ~/build/BUILD/python-biopython-1.80/python3/Tests ~/build/BUILD/python-biopython-1.80 + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd python-biopython-1.80 + pushd python3/Tests + xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 + find . -name run_tests.py ./run_tests.py: updating + find ../ -name __init__.py + xargs rm -f ++ ls test_Ace.py test_Affy.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_MauveIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_AlignInfo.py test_Align_Alignment.py test_Align_a2m.py test_Align_bed.py test_Align_bigbed.py test_Align_bigmaf.py test_Align_bigpsl.py test_Align_clustal.py test_Align_emboss.py test_Align_exonerate.py test_Align_fasta.py test_Align_hhr.py test_Align_maf.py test_Align_mauve.py test_Align_msf.py test_Align_nexus.py test_Align_phylip.py test_Align_psl.py test_Align_sam.py test_Align_stockholm.py test_Align_tabular.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb_online.py test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector_online.py test_BioSQL_psycopg2.py test_BioSQL_psycopg2_online.py test_BioSQL_sqlite3.py test_BioSQL_sqlite3_online.py test_Blast_Record.py test_CAPS.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Dialign_tool.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Entrez_parser.py test_Enzyme.py test_ExPASy.py test_Fasttree_tool.py test_File.py test_GenBank.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_LogisticRegression.py test_MSAProbs_tool.py test_MafIO_index.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Muscle_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_QCSuperimposer.py test_PDB_ResidueDepth.py test_PDB_SASA.py test_PDB_SMCRA.py test_PDB_Selection.py test_PDB_StructureAlignment.py test_PDB_Superimposer.py test_PDB_internal_coords.py test_PDB_parse_pdb_header.py test_PDB_vectors.py test_PQR.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_matplotlib.py test_Phylo_networkx.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_RCSBFormats.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.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_legacy.py test_SearchIO_model.py test_SearchIO_write.py test_SeqFeature.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Gck.py test_SeqIO_Insdc.py test_SeqIO_NibIO.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_SnapGene.py test_SeqIO_TwoBitIO.py test_SeqIO_Xdna.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_UniProt_GOA.py test_Uniprot.py test_Wise.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 SubsMat ++ grep -v SearchIO_blast ++ grep -v Phylo ++ grep -v Nexus ++ grep -v pairwise_aligner ++ grep -v Tutorial ++ grep -v bgzf + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Ace.py test_Ace ... ok test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser) Test to check that contig parser parses each contig into a contig. ... ok test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.040 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Affy.py test_Affy ... ok testAffy3 (test_Affy.AffyTest.testAffy3) ... ok testAffy4 (test_Affy.AffyTest.testAffy4) ... ok testAffyBadHeader (test_Affy.AffyTest.testAffyBadHeader) ... ok testAffyWrongModeReadV3 (test_Affy.AffyTest.testAffyWrongModeReadV3) ... ok testAffyWrongModeReadV4 (test_Affy.AffyTest.testAffyWrongModeReadV4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py test_AlignIO ... ok test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files) Check that parsing an empty file returns an empty list. ... ok test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate) Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files) Check that writers can cope with no alignments. ... ok test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments) Check that writers reject records that are not alignments. ... ok test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.944 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py test_AlignIO_ClustalIO ... ok test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header) Make sure we can parse the Biopython header. ... ok test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok test_empy (test_AlignIO_ClustalIO.TestClustalIO.test_empy) 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 0.058 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.064 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py test_AlignIO_PhylipIO ... ok test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py test_AlignIO_convert ... ok test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type) Converting Clustal to NEXUS with a molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type) Converting Clustal to NEXUS without a molecule type. ... ok test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.173 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py C test_AlignInfo ... ok test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_Alignment.py test_Align_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_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_aligned_indices (test_Align_Alignment.TestPairwiseAlignment.test_aligned_indices) ... ok test_indexing_slicing (test_Align_Alignment.TestPairwiseAlignment.test_indexing_slicing) ... 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 0.178 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_a2m.py test_Align_a2m ... ok test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_bed.py test_Align_bed ... ok test_reading (test_Align_bed.TestAlign_bed12.test_reading) Test parsing alignments in file formats BED3 through BED12. ... ok test_writing (test_Align_bed.TestAlign_bed12.test_writing) Test writing the alignments in bed12.bed as BED3 through BED12. ... ok test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.bed. ... ok test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.bed. ... ok test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.bed. ... ok test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.bed. ... ok test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.bed. ... ok test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.bed. ... ok test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.bed. ... ok test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.bed. ... ok test_reading (test_Align_bed.TestAlign_dna_rna.test_reading) Test parsing dna_rna.bed. ... ok test_writing (test_Align_bed.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.bed. ... ok test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.bed. ... ok test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.bed. ... ok test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.bed. ... ok test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.bed. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_bigbed.py test_Align_bigbed ... ok test_reading (test_Align_bigbed.TestAlign_bed12.test_reading) Test parsing alignments in file formats BED3 through BED12. ... ok test_reading_psl_34_001 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.bb. ... ok test_reading_psl_34_003 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.bb. ... ok test_reading_psl_34_004 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.bb. ... ok test_reading_psl_34_005 (test_Align_bigbed.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.bb. ... ok test_reading (test_Align_bigbed.TestAlign_dna_rna.test_reading) Test parsing dna_rna.bb. ... ok test_reading_psl_35_001 (test_Align_bigbed.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.bb. ... ok test_reading (test_Align_bigbed.TestAlign_extended_bed.test_reading) Test parsing bigbed_extended.bb. ... ok test_search_chromosome (test_Align_bigbed.TestAlign_searching.test_search_chromosome) ... ok test_search_position (test_Align_bigbed.TestAlign_searching.test_search_position) ... ok test_search_region (test_Align_bigbed.TestAlign_searching.test_search_region) ... ok test_three_iterators (test_Align_bigbed.TestAlign_searching.test_three_iterators) Create three iterators and use them concurrently. ... ok Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.106 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_bigmaf.py test_Align_bigmaf ... ok test_reading_bundle_without_target (test_Align_bigmaf.TestAlign_reading.test_reading_bundle_without_target) Test parsing bundle_without_target.bb. ... ok test_reading_ucsc_mm9_chr10 (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_mm9_chr10) Test parsing MAF file ucsc_mm9_chr10.bb. ... ok test_reading_ucsc_test (test_Align_bigmaf.TestAlign_reading.test_reading_ucsc_test) Test parsing ucsc_test.bb. ... 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 ---------------------------------------------------------------------- Ran 1 test in 0.208 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_bigpsl.py test_Align_bigpsl ... ok test_reading_bigpsl (test_Align_bigpsl.TestAlign_bigpsl.test_reading_bigpsl) Test parsing bigPsl.bb. ... 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_reading (test_Align_bigpsl.TestAlign_dna_rna.test_reading) Test parsing 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_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 0.189 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_clustal.py test_Align_clustal ... ok test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign) Make sure we can parse the Kalign header. ... ok test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_emboss.py test_Align_emboss ... ok test_local_water2 (test_Align_emboss.TestEmboss.test_local_water2) Test parsing a local alignment. ... ok test_matcher_pair (test_Align_emboss.TestEmboss.test_matcher_pair) ... ok test_matcher_simple (test_Align_emboss.TestEmboss.test_matcher_simple) ... ok test_needle_asis (test_Align_emboss.TestEmboss.test_needle_asis) ... ok test_pair_aln_full_blank_line (test_Align_emboss.TestEmboss.test_pair_aln_full_blank_line) ... ok test_pair_example (test_Align_emboss.TestEmboss.test_pair_example) ... ok test_pair_example2 (test_Align_emboss.TestEmboss.test_pair_example2) ... ok test_pair_example3 (test_Align_emboss.TestEmboss.test_pair_example3) ... ok test_pair_example_nobrief (test_Align_emboss.TestEmboss.test_pair_example_nobrief) ... ok test_water_reverse1 (test_Align_emboss.TestEmboss.test_water_reverse1) ... ok test_water_reverse2 (test_Align_emboss.TestEmboss.test_water_reverse2) ... ok test_water_reverse3 (test_Align_emboss.TestEmboss.test_water_reverse3) ... ok test_water_reverse4 (test_Align_emboss.TestEmboss.test_water_reverse4) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_exonerate.py test_Align_exonerate ... ok test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar) Test parsing exn_22_m_affine_local_cigar.exn. ... ok test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar) Test parsing exn_22_m_affine_local_vulgar.exn. ... ok test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar) Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar) Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar) Test parsing exn_22_m_coding2coding_cigar.exn. ... ok test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar) Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar) Test parsing exn_22_m_cigar_fshifts.exn). ... ok test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar) Test parsing exn_22_o_vulgar_fshifts.exn. ... ok test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar) Test parsing exn_22_m_coding2genome_cigar.exn. ... ok test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar) Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar) Test parsing exn_22_m_dna2protein_cigar.exn. ... ok test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar) Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar) Test parsing exn_22_m_est2genome_cigar.exn. ... ok test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar) Test parsing exn_22_m_est2genome_vulgar.exn. ... ok test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar) Test parsing exn_22_o_vulgar_cigar.exn. ... ok test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar) Test parsing exn_22_o_vulgar.exn. ... ok test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar) Test parsing exn_22_q_multiple_cigar.exn. ... ok test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar) Test parsing exn_22_q_multiple_vulgar.exn. ... ok test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar) Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar) Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar) Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar) Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar) Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar) Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar) Test parsing exn_22_m_protein2genome_cigar.exn. ... ok test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar) Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar) Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar) Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar) Test parsing exn_22_m_ungapped_cigar.exn. ... ok test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar) Test parsing exn_22_m_ungapped_vulgar.exn. ... ok test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar) Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar) Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.137 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_fasta.py test_Align_fasta ... ok test_clustalw (test_Align_fasta.TestFASTAReadingWriting.test_clustalw) ... ok test_empty (test_Align_fasta.TestFASTAReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_fasta.TestFASTAReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_fasta.TestFASTAReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_fasta.TestFASTAReadingWriting.test_muscle) ... ok test_probcons (test_Align_fasta.TestFASTAReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.064 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_hhr.py test_Align_hhr ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_emptytable.test_reading) ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhblits_onlyheader.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_2uvo_hhsearch.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4p79_hhsearch_server_NOssm.test_reading) ... ok test_length (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_length) Test getting the number of alignments without parsing the file. ... ok test_reading (test_Align_hhr.Align_hhr_4y9h_hhsearch_server_NOssm.test_reading) ... ok test_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 0.220 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_maf.py test_Align_maf ... ok test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453) Test parsing bug2453.maf. ... ok test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target) Test parsing bundle_without_target.maf. ... ok test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch) Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature) Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10) Test parsing MAF file ucsc_mm9_chr10.maf. ... ok test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad) Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test) Test parsing ucsc_test.maf. ... ok test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453) Test reading and writing bug2453.maf. ... ok test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target) Test reading and writing bundle_without_target.maf. ... ok test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10) Test reading and writing ucsc_mm9_chr10.maf. ... ok test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test) Test reading and writing ucsc_test.maf. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.282 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_mauve.py test_Align_mauve ... ok test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok test_parse (test_Align_mauve.TestDSeparateFiles.test_parse) ... ok test_write_read (test_Align_mauve.TestDSeparateFiles.test_write_read) ... ok test_empty (test_Align_mauve.TestMauveBasic.test_empty) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_Align_msf.py test_Align_msf ... ok test_protein1 (test_Align_msf.TestMSF.test_protein1) ... ok test_protein2 (test_Align_msf.TestMSF.test_protein2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_nexus.py C 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 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_phylip.py test_Align_phylip ... ok test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok test_one (test_Align_phylip.TestPhylipReading.test_one) ... ok test_two_and_three (test_Align_phylip.TestPhylipReading.test_two_and_three) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_psl.py test_Align_psl ... ok test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002) Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.psl. ... ok test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.psl. ... ok test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.psl. ... ok test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.psl. ... ok test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.psl. ... ok test_reading (test_Align_psl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl. ... ok test_writing (test_Align_psl.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.psl. ... ok test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl. ... ok test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.psl. ... ok test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.psl. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.217 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_sam.py test_Align_sam ... ok test_4D8I6M (test_Align_sam.TestAlign_clippping.test_4D8I6M) Test alignment starting with deletion followed by insertion. ... ok test_4I8D6M (test_Align_sam.TestAlign_clippping.test_4I8D6M) Test alignment starting with insertion followed by deletion. ... ok test_4S6M (test_Align_sam.TestAlign_clippping.test_4S6M) Test alignment starting with soft clip at non-zero position. ... ok test_4S8D6M (test_Align_sam.TestAlign_clippping.test_4S8D6M) Test alignment starting with soft clip followed by deletion. ... ok test_4S8I6M (test_Align_sam.TestAlign_clippping.test_4S8I6M) Test alignment starting with soft clip followed by insertion. ... ok test_6M (test_Align_sam.TestAlign_clippping.test_6M) Test alignment starting at non-zero position. ... ok test_8D6M_ex1 (test_Align_sam.TestAlign_clippping.test_8D6M_ex1) Test alignment starting with deletion. ... ok test_8D6M_ex2 (test_Align_sam.TestAlign_clippping.test_8D6M_ex2) Test alignment starting with deletion at non-zero position. ... ok test_8I6M_ex1 (test_Align_sam.TestAlign_clippping.test_8I6M_ex1) Test alignment starting with insertion. ... ok test_8I6M_ex2 (test_Align_sam.TestAlign_clippping.test_8I6M_ex2) Test alignment starting with insertion at non-zero position. ... ok test_8S6M (test_Align_sam.TestAlign_clippping.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 ---------------------------------------------------------------------- Ran 1 test in 0.249 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_stockholm.py test_Align_stockholm ... ok test_reading_alignments_cath1 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath1) Test parsing CATH record 3.30.160.60/FF/004774. ... ok test_reading_alignments_cath2 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath2) Test parsing CATH record 2.105.10.10/FF/000002. ... ok test_reading_alignments_cath3 (test_Align_stockholm.TestStockholm_reading.test_reading_alignments_cath3) Test parsing CATH record 1.10.275.10/FF/000026. ... ok test_reading_example (test_Align_stockholm.TestStockholm_reading.test_reading_example) Test parsing Pfam record HAT as the docstring example. ... ok test_reading_writing_alignments_globins45 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_globins45) Test parsing hmmalign output. ... ok test_reading_writing_alignments_pfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam1) Test parsing Pfam record 120_Rick_ant. ... ok test_reading_writing_alignments_pfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam2) Test parsing Pfam record 7kD_DNA_binding. ... ok test_reading_writing_alignments_pfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam3) Test parsing Pfam record 12TM_1. ... ok test_reading_writing_alignments_pfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam4) Test parsing Pfam record 3Beta_HSD. ... ok test_reading_writing_alignments_pfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam5) Test parsing Pfam record ArsP_1. ... ok test_reading_writing_alignments_pfam6 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam6) Test parsing Pfam record COX2_TM. ... ok test_reading_writing_alignments_pfam7 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam7) Test parsing Pfam record Alpha_E1_glycop. ... ok test_reading_writing_alignments_pfam8 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam8) Test parsing Pfam record Cyclin_N. ... ok test_reading_writing_alignments_pfam9 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_pfam9) Test parsing Pfam record SH3_11. ... ok test_reading_writing_alignments_rfam1 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam1) Test parsing Rfam record BTnc005. ... ok test_reading_writing_alignments_rfam2 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam2) Test parsing Rfam record SraC_RyeA. ... ok test_reading_writing_alignments_rfam3 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam3) Test parsing Rfam record McaS. ... ok test_reading_writing_alignments_rfam4 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam4) Test parsing Rfam record IRES_KSHV. ... ok test_reading_writing_alignments_rfam5 (test_Align_stockholm.TestStockholm_reading.test_reading_writing_alignments_rfam5) Test parsing Rfam record BMV3_UPD-PK3. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.218 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_tabular.py test_Align_tabular ... ok test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.320 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Application.py test_Application ... ok test_echo (test_Application.TestApp.test_echo) ... ok test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.023 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.119 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py C test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.087 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.084 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py C test_BioSQL_psycopg2_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py test_BioSQL_sqlite3 ... ok test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility) Check can re-use an old BioSQL SQLite3 database. ... ok test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932) From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816) From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265) From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1) From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6) From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref) From GenBank file to BioSQL and back to a GenBank file, noref. ... ok test_one_of (common_BioSQL.ClosedLoopTest.test_one_of) From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2) From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items) Check all associated data is deleted from an item. ... ok test_server (common_BioSQL.DeleteTest.test_server) Check BioSeqDatabase methods. ... ok test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load) Make sure can't import records with same ID (in one go). ... ok test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load) Make sure can't import a single record twice (in one go). ... ok test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2) Make sure can't import a single record twice (in steps). ... ok test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading) Make sure all records are correctly loaded. ... ok test_reload (common_BioSQL.InDepthLoadTest.test_reload) Make sure can't reimport existing records. ... ok test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature) In depth check that SeqFeatures are transmitted through the db. ... ok test_transfer (common_BioSQL.InDepthLoadTest.test_transfer) Make sure can load record into another namespace. ... ok test_load_database (common_BioSQL.LoaderTest.test_load_database) Load SeqRecord objects into a BioSQL database. ... ok test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items) Test that valid ids can't be retrieved between namespaces. ... ok test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_server (common_BioSQL.MultiReadTest.test_server) Check BioSeqDatabase methods. ... ok test_get_db_items (common_BioSQL.ReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_lookup_items (common_BioSQL.ReadTest.test_lookup_items) Test retrieval of items using various ids. ... ok test_server (common_BioSQL.ReadTest.test_server) Check BioSeqDatabase methods. ... ok test_addition (common_BioSQL.SeqInterfaceTest.test_addition) Check can add Seq objects from BioSQL together. ... ok test_convert (common_BioSQL.SeqInterfaceTest.test_convert) Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication) Check can multiply Seq objects from BioSQL by integers. ... ok test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing) Check that slices of DBSeqRecord are retrieved properly. ... ok test_seq (common_BioSQL.SeqInterfaceTest.test_seq) Make sure Seqs from BioSQL implement the right interface. ... ok test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features) Check SeqFeatures of a sequence. ... ok test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record) Make sure SeqRecords from BioSQL implement the right interface. ... ok test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing) Check that slices of sequences are retrieved properly. ... ok test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location) Loaded uniprot-xml with ambiguous location in BioSQL. ... ok test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932) From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816) From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265) From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok test_arab1 (common_BioSQL.TransferTest.test_arab1) From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6) From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok test_no_ref (common_BioSQL.TransferTest.test_no_ref) From GenBank file to BioSQL, then again to a new namespace, noref. ... ok test_one_of (common_BioSQL.TransferTest.test_one_of) From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2) From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.692 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.084 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py test_Blast_Record ... ok test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.051 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CAPS.py test_CAPS ... ok test (test_CAPS.TestCAPS.test) ... ok testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.145 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Chi2.py test_Chi2 ... ok test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Cluster.py test_Cluster ... ok test_clusterdistance (test_Cluster.TestCluster.test_clusterdistance) ... ok test_clusterdistance_arguments (test_Cluster.TestCluster.test_clusterdistance_arguments) ... ok test_distancematrix_arguments (test_Cluster.TestCluster.test_distancematrix_arguments) ... ok test_distancematrix_kmedoids (test_Cluster.TestCluster.test_distancematrix_kmedoids) ... ok test_kcluster (test_Cluster.TestCluster.test_kcluster) ... ok test_kcluster_arguments (test_Cluster.TestCluster.test_kcluster_arguments) ... ok test_kmedoids_arguments (test_Cluster.TestCluster.test_kmedoids_arguments) ... ok test_mask_parse (test_Cluster.TestCluster.test_mask_parse) ... ok test_matrix_parse (test_Cluster.TestCluster.test_matrix_parse) ... ok test_pca (test_Cluster.TestCluster.test_pca) ... ok test_pca_arguments (test_Cluster.TestCluster.test_pca_arguments) ... ok test_somcluster (test_Cluster.TestCluster.test_somcluster) ... ok test_somcluster_arguments (test_Cluster.TestCluster.test_somcluster_arguments) ... ok test_tree (test_Cluster.TestCluster.test_tree) ... ok test_tree_arguments (test_Cluster.TestCluster.test_tree_arguments) ... ok test_treecluster (test_Cluster.TestCluster.test_treecluster) ... ok test_treecluster_arguments (test_Cluster.TestCluster.test_treecluster_arguments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CodonTable.py test_CodonTable ... ok test_coding (test_CodonTable.AmbiguousCodonsTests.test_coding) Check a few ambiguous codons for correct coding. ... ok test_list_ambiguous_codons (test_CodonTable.AmbiguousCodonsTests.test_list_ambiguous_codons) Check if stop codons are properly extended. ... ok test_start_codons (test_CodonTable.AmbiguousCodonsTests.test_start_codons) Test various ambiguous codons as start codon. ... ok test_stop_codons (test_CodonTable.AmbiguousCodonsTests.test_stop_codons) Test various ambiguous codons as stop codon. ... ok test_ambiguous_tables (test_CodonTable.BasicSanityTests.test_ambiguous_tables) Check if all IDs and all names are present in ambiguous tables. ... ok test_complete_tables (test_CodonTable.BasicSanityTests.test_complete_tables) Check if all unambiguous codon tables have all entries. ... ok test_number_of_tables (test_CodonTable.BasicSanityTests.test_number_of_tables) Check if we have the same number of tables for each type. ... ok test_ambiguous_forward_table (test_CodonTable.ErrorConditions.test_ambiguous_forward_table) Raise errors in AmbiguousForwardTable. ... ok test_list_possible_proteins (test_CodonTable.ErrorConditions.test_list_possible_proteins) Raise errors in list_possible proteins. ... ok test_print_table (test_CodonTable.PrintTable.test_print_table) Test output of __str__ function. ... ok test_table01 (test_CodonTable.SingleTableTests.test_table01) Check table 1: Standard. ... ok test_table02 (test_CodonTable.SingleTableTests.test_table02) Check table 2: Vertebrate Mitochondrial. ... ok test_table03 (test_CodonTable.SingleTableTests.test_table03) Check table 3: Yeast Mitochondrial. ... ok test_table04 (test_CodonTable.SingleTableTests.test_table04) Check table 4: Mold Mitochondrial and others. ... ok test_table05 (test_CodonTable.SingleTableTests.test_table05) Check table 5: Invertebrate Mitochondrial. ... ok test_table06 (test_CodonTable.SingleTableTests.test_table06) Check table 6: Ciliate and Other Nuclear. ... ok test_table09 (test_CodonTable.SingleTableTests.test_table09) Check table 9: Echinoderm and Flatworm Mitochondrial. ... ok test_table10 (test_CodonTable.SingleTableTests.test_table10) Check table 10: Euplotid Nuclear. ... ok test_table11 (test_CodonTable.SingleTableTests.test_table11) Check table 11: Bacterial, Archaeal and Plant Plastid. ... ok test_table12 (test_CodonTable.SingleTableTests.test_table12) Check table 12: Alternative Yeast Nuclear. ... ok test_table13 (test_CodonTable.SingleTableTests.test_table13) Check table 13: Ascidian Mitochondrial. ... ok test_table14 (test_CodonTable.SingleTableTests.test_table14) Check table 14: Alternative Flatworm Mitochondrial. ... ok test_table16 (test_CodonTable.SingleTableTests.test_table16) Check table 16: Chlorophycean Mitochondrial. ... ok test_table21 (test_CodonTable.SingleTableTests.test_table21) Check table 21: Trematode Mitochondrial. ... ok test_table22 (test_CodonTable.SingleTableTests.test_table22) Check table 22: Scenedesmus obliquus Mitochondrial. ... ok test_table23 (test_CodonTable.SingleTableTests.test_table23) Check table 9: Thraustochytrium Mitochondrial. ... ok test_table24 (test_CodonTable.SingleTableTests.test_table24) Check table 24: Pterobranchia Mitochondrial. ... ok test_table25 (test_CodonTable.SingleTableTests.test_table25) Check table 25: Candidate Division SR1 and Gracilibacteria. ... ok test_table26 (test_CodonTable.SingleTableTests.test_table26) Check table 26: Pachysolen tannophilus Nuclear. ... ok test_table27 (test_CodonTable.SingleTableTests.test_table27) Check table 27: Karyorelict Nuclear. ... ok test_table28 (test_CodonTable.SingleTableTests.test_table28) Check table 28: Condylostoma Nuclear. ... ok test_table29 (test_CodonTable.SingleTableTests.test_table29) Check table 29: Mesodinium Nuclear. ... ok test_table30 (test_CodonTable.SingleTableTests.test_table30) Check table 30: Peritrich Nuclear. ... ok test_table31 (test_CodonTable.SingleTableTests.test_table31) Check table 31: Blastocrithidia Nuclear. ... ok test_table32 (test_CodonTable.SingleTableTests.test_table32) Check table 32: Balanophoraceae Plastid. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py test_ColorSpiral ... ok test_dict (test_ColorSpiral.DictTest.test_dict) get_color_dict() for classes A-D, no jitter. ... ok test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist) Get set of eight colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral) Get set of 16 colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral) Set of 625 colours, with jitter, using get_colors(). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Compass.py test_Compass ... ok testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Consensus.py test_Consensus ... ok test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.667 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.054 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py test_EMBL_unittest ... ok test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line) Test SQ line with 0 length sequence. ... ok test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co) Test a ValueError is thrown by content after a CO line. ... ok test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords) Test sequence lines without coordinates. ... ok test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line) Test files with wrong DR lines. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Emboss.py test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss. ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools. ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py test_EmbossPrimer ... ok test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse) Make sure we get info right from a single primer find. ... ok test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse) Make sure we get the data from normal primer3 files okay. ... ok test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse) Make sure we can parse an internal oligo file correctly. ... ok test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full) Test parsing multiple primer sets (NirK full). ... ok test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd) Test parsing multiple primer sets (NirK forward). ... ok test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse) Make sure that we can use all single target primer3 files. ... ok test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation) Make sure we can output primer information correctly. ... ok test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse) Make sure the output from a simple primersearch file is correct. ... ok test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse) Make sure that we can parse all primersearch files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez.py test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Entrez/__init__.py:686: UserWarning: Email address is not specified. To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. As an example, if your email address is A.N.Other@example.com, you can specify it as follows: from Bio import Entrez Entrez.email = 'A.N.Other@example.com' In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities. warnings.warn( ok test_custom_directory (test_Entrez.CustomDirectoryTest.test_custom_directory) ... ok test_construct_cgi_ecitmatch (test_Entrez.TestURLConstruction.test_construct_cgi_ecitmatch) ... ok test_construct_cgi_efetch (test_Entrez.TestURLConstruction.test_construct_cgi_efetch) ... ok test_construct_cgi_einfo (test_Entrez.TestURLConstruction.test_construct_cgi_einfo) Test constructed url for request to Entrez. ... ok test_construct_cgi_elink1 (test_Entrez.TestURLConstruction.test_construct_cgi_elink1) ... ok test_construct_cgi_elink2 (test_Entrez.TestURLConstruction.test_construct_cgi_elink2) Commas: Link from protein to gene. ... ok test_construct_cgi_elink3 (test_Entrez.TestURLConstruction.test_construct_cgi_elink3) Multiple ID entries: Find one-to-one links from protein to gene. ... ok test_construct_cgi_epost1 (test_Entrez.TestURLConstruction.test_construct_cgi_epost1) ... ok test_construct_cgi_epost2 (test_Entrez.TestURLConstruction.test_construct_cgi_epost2) ... ok test_default_params (test_Entrez.TestURLConstruction.test_default_params) Test overriding default values for the "email", "api_key", and "tool" parameters. ... ok test_email_warning (test_Entrez.TestURLConstruction.test_email_warning) Test issuing warning when user does not specify email address. ... ok test_format_ids (test_Entrez.TestURLConstruction.test_format_ids) ... ok test_has_api_key (test_Entrez.TestURLConstruction.test_has_api_key) Test checking whether a Request object specifies an API key. ... ok ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux Ran 1 test in 4.160 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py test_Entrez_parser ... ok test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas) Test parsing XML using Schemas. ... ok test_fasta (test_Entrez_parser.EFetchTest.test_fasta) Test error handling when presented with Fasta non-XML data. ... ok test_genbank (test_Entrez_parser.EFetchTest.test_genbank) Test error handling when presented with GenBank non-XML data. ... ok test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ... ok test_pmc (test_Entrez_parser.EFetchTest.test_pmc) Test parsing XML returned by EFetch from PubMed Central. ... ok test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ... ok test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ... ok test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ... ok test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html) Test error handling when presented with HTML (so XML-like) data. ... ok test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping) Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags) Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ... ok test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ... ok test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration) Test error handling for a missing XML declaration. ... ok test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition) Test error handling for a missing DTD or XML Schema. ... ok test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ... ok test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ... ok test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ... ok test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ... ok test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ... ok test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ... ok test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ... ok test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ... ok test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ... ok test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ... ok test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ... ok test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ... ok test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ... ok test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ... ok test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ... ok test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ... ok test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ... ok test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ... ok test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ... ok test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ... ok test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ... ok test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ... ok test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ... ok test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ... ok test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ... ok test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ... ok test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ... ok test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none) Test parsing ESummary XML where an Integer is not defined. ... ok test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ... ok test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ... ok test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ... ok test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ... ok test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ... ok test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ... ok test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ... ok test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ... ok test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO handle (bytes not string). ... ok test_closed_handle (test_Entrez_parser.GeneralTests.test_closed_handle) Test parsing closed handle fails gracefully. ... ok test_parse_bytes_handle (test_Entrez_parser.GeneralTests.test_parse_bytes_handle) Test parsing a handle opened in binary mode. ... ok test_parse_text_handle (test_Entrez_parser.GeneralTests.test_parse_text_handle) Test parsing a handle opened in text mode. ... ok test_pickle (test_Entrez_parser.GeneralTests.test_pickle) Test if records created by the parser can be pickled. ... ok test_read_bytes_handle (test_Entrez_parser.GeneralTests.test_read_bytes_handle) Test reading a handle opened in binary mode. ... ok test_read_text_handle (test_Entrez_parser.GeneralTests.test_read_text_handle) Test reading a handle opened in text mode. ... ok ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux Ran 1 test in 0.440 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py test_Enzyme ... ok test_lactate (test_Enzyme.TestEnzyme.test_lactate) Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein) Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok test_parse_many (test_Enzyme.TestEnzyme.test_parse_many) Check parse function with multiple records. ... ok test_parse_one (test_Enzyme.TestEnzyme.test_parse_one) Check parse function with one record. ... ok test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok test_proline (test_Enzyme.TestEnzyme.test_proline) Parsing ENZYME record for proline racemase (5.1.1.4). ... ok test_valine (test_Enzyme.TestEnzyme.test_valine) Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py test_ExPASy ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.111 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_File.py test_File ... ok test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object) Test as_handle with a custom path-like object. ... ok test_handle (test_File.AsHandleTestCase.test_handle) Test as_handle with a file-like object argument. ... ok test_path_object (test_File.AsHandleTestCase.test_path_object) Test as_handle with a pathlib.Path object. ... ok test_string_path (test_File.AsHandleTestCase.test_string_path) Test as_handle with a string path argument. ... ok test_stringio (test_File.AsHandleTestCase.test_stringio) Testing passing StringIO handles. ... ok test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok test_bgzf (test_File.RandomAccess.test_bgzf) Test BGZF compressed file. ... ok test_gzip (test_File.RandomAccess.test_gzip) Test gzip compressed file. ... ok test_plain (test_File.RandomAccess.test_plain) Test plain text file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenBank.py test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_embl_cds_interaction (test_GenBank.GenBankScannerTests.test_embl_cds_interaction) Test EMBL CDS interaction, parse CDS features on embl files. ... ok test_embl_record_interaction (test_GenBank.GenBankScannerTests.test_embl_record_interaction) Test EMBL Record interaction on embl files. ... ok test_genbank_cds_interaction (test_GenBank.GenBankScannerTests.test_genbank_cds_interaction) Test CDS interaction, parse CDS features on gb(k) files. ... ok test_genbank_interaction (test_GenBank.GenBankScannerTests.test_genbank_interaction) Test GenBank records interaction on gbk files. ... ok test_000_genbank_bad_loc_wrap_warning (test_GenBank.GenBankTests.test_000_genbank_bad_loc_wrap_warning) Feature line wrapping warning. ... ok test_001_genbank_bad_origin_wrapping_location (test_GenBank.GenBankTests.test_001_genbank_bad_origin_wrapping_location) Bad origin wrapping. ... ok test_001_implicit_orign_wrap_fix (test_GenBank.GenBankTests.test_001_implicit_orign_wrap_fix) Attempt to fix implied origin wrapping. ... ok test_001_negative_location_warning (test_GenBank.GenBankTests.test_001_negative_location_warning) Un-parsable feature location warning. ... ok test_compound_complex_origin_wrap (test_GenBank.GenBankTests.test_compound_complex_origin_wrap) Test the attempts to fix compound complex origin wrapping. ... ok test_dbline_embl_gb (test_GenBank.GenBankTests.test_dbline_embl_gb) Parse GenBank/EMBL paired records with PR project entry: EMBL. ... ok test_dbline_gb_embl (test_GenBank.GenBankTests.test_dbline_gb_embl) Parse GenBank/EMBL paired records with PR project entry: GenBank. ... ok test_dblink (test_GenBank.GenBankTests.test_dblink) Parse GenBank record with old DBLINK project entry. ... ok test_dblink_two (test_GenBank.GenBankTests.test_dblink_two) Parse GenBank record with old and new DBLINK project entries. ... ok test_dot_lineage (test_GenBank.GenBankTests.test_dot_lineage) Missing taxonomy lineage. ... ok test_extremely_long_sequence (test_GenBank.GenBankTests.test_extremely_long_sequence) Tests if extremely long sequences can be read. ... ok test_fuzzy_origin_wrap (test_GenBank.GenBankTests.test_fuzzy_origin_wrap) Test features that wrap an origin, and have fuzzy location. ... ok test_genbank_bad_loc_wrap_parsing (test_GenBank.GenBankTests.test_genbank_bad_loc_wrap_parsing) Bad location wrapping. ... ok test_genbank_date_correct (test_GenBank.GenBankTests.test_genbank_date_correct) Check if user provided date is inserted correctly. ... ok test_genbank_date_datetime (test_GenBank.GenBankTests.test_genbank_date_datetime) Check if datetime objects are handled correctly. ... ok test_genbank_date_default (test_GenBank.GenBankTests.test_genbank_date_default) Check if default date is handled correctly. ... ok test_genbank_date_invalid (test_GenBank.GenBankTests.test_genbank_date_invalid) Check if invalid dates are treated as default. ... ok test_genbank_date_list (test_GenBank.GenBankTests.test_genbank_date_list) Check if date lists are handled correctly. ... ok test_genbank_read (test_GenBank.GenBankTests.test_genbank_read) GenBank.read(...) simple test. ... ok test_genbank_read_invalid (test_GenBank.GenBankTests.test_genbank_read_invalid) GenBank.read(...) error on invalid file (e.g. FASTA file). ... ok test_genbank_read_multirecord (test_GenBank.GenBankTests.test_genbank_read_multirecord) GenBank.read(...) error on multiple record input. ... ok test_genbank_read_no_origin_no_end (test_GenBank.GenBankTests.test_genbank_read_no_origin_no_end) GenBank.read(...) error on malformed file. ... ok test_implicit_orign_wrap_extract_and_translate (test_GenBank.GenBankTests.test_implicit_orign_wrap_extract_and_translate) Test that features wrapped around origin give expected data. ... ok test_invalid_product_line_raises_value_error (test_GenBank.GenBankTests.test_invalid_product_line_raises_value_error) Parsing invalid product line. ... ok test_locus_line_topogoly (test_GenBank.GenBankTests.test_locus_line_topogoly) Test if chromosome topology is conserved. ... ok test_long_names (test_GenBank.GenBankTests.test_long_names) Various GenBank names which push the column based LOCUS line. ... ok test_longer_locus_line (test_GenBank.GenBankTests.test_longer_locus_line) Check that we can read and write files with longer locus lines. ... ok test_malformed_structured_comment_parsing (test_GenBank.GenBankTests.test_malformed_structured_comment_parsing) Test malformed structured comment gives warning. ... ok test_multiline_structured_comment_parsing (test_GenBank.GenBankTests.test_multiline_structured_comment_parsing) Multiline structured comment parsing. ... ok test_negative_location (test_GenBank.GenBankTests.test_negative_location) Negative feature locations. ... ok test_qualifier_escaping_read (test_GenBank.GenBankTests.test_qualifier_escaping_read) Check qualifier escaping is preserved when parsing. ... ok test_qualifier_escaping_write (test_GenBank.GenBankTests.test_qualifier_escaping_write) Check qualifier escaping is preserved when writing. ... ok test_qualifier_order (test_GenBank.GenBankTests.test_qualifier_order) Check the qualifier order is preserved. ... ok test_structured_comment_parsing (test_GenBank.GenBankTests.test_structured_comment_parsing) Structured comment parsing. ... ok test_tsa (test_GenBank.GenBankTests.test_tsa) Test TSA annotation parsing. ... ok test_first_line_imgt (test_GenBank.LineOneTests.test_first_line_imgt) Check IMGT ID line parsing. ... ok test_topology_embl (test_GenBank.LineOneTests.test_topology_embl) Check EMBL ID line parsing. ... ok test_topology_genbank (test_GenBank.LineOneTests.test_topology_genbank) Check GenBank LOCUS line parsing. ... ok test_000_write_invalid_but_parsed_locus_line (test_GenBank.OutputTests.test_000_write_invalid_but_parsed_locus_line) Make sure we survive writing slightly invalid LOCUS lines we could parse. ... ok test_mad_dots (test_GenBank.OutputTests.test_mad_dots) Writing and reading back accesssion.version variants. ... ok test_seqrecord_default_description (test_GenBank.OutputTests.test_seqrecord_default_description) Read in file using SeqRecord default description. ... ok test_write_tsa_data_division (test_GenBank.OutputTests.test_write_tsa_data_division) Make sure we don't kill the TSA data_file_division for TSA files. ... ok test_cleaning_features (test_GenBank.TestBasics.test_cleaning_features) Test the ability to clean up feature values. ... ok test_ensembl_locus (test_GenBank.TestBasics.test_ensembl_locus) Test the ENSEMBL locus line. ... ok test_write_format (test_GenBank.TestBasics.test_write_format) Test writing to the difference formats. ... ok test_feature_parser_01 (test_GenBank.TestFeatureParser.test_feature_parser_01) ... ok test_feature_parser_02 (test_GenBank.TestFeatureParser.test_feature_parser_02) ... ok test_feature_parser_03 (test_GenBank.TestFeatureParser.test_feature_parser_03) ... ok test_feature_parser_04 (test_GenBank.TestFeatureParser.test_feature_parser_04) ... ok test_feature_parser_05 (test_GenBank.TestFeatureParser.test_feature_parser_05) ... ok test_feature_parser_06 (test_GenBank.TestFeatureParser.test_feature_parser_06) ... ok test_feature_parser_07 (test_GenBank.TestFeatureParser.test_feature_parser_07) ... ok test_feature_parser_08 (test_GenBank.TestFeatureParser.test_feature_parser_08) ... ok test_feature_parser_09 (test_GenBank.TestFeatureParser.test_feature_parser_09) ... ok test_feature_parser_10 (test_GenBank.TestFeatureParser.test_feature_parser_10) ... ok test_feature_parser_11 (test_GenBank.TestFeatureParser.test_feature_parser_11) ... ok test_feature_parser_12 (test_GenBank.TestFeatureParser.test_feature_parser_12) ... ok test_feature_parser_13 (test_GenBank.TestFeatureParser.test_feature_parser_13) ... ok test_feature_parser_14 (test_GenBank.TestFeatureParser.test_feature_parser_14) ... ok test_feature_parser_15 (test_GenBank.TestFeatureParser.test_feature_parser_15) ... ok test_feature_parser_16 (test_GenBank.TestFeatureParser.test_feature_parser_16) ... ok test_feature_parser_17 (test_GenBank.TestFeatureParser.test_feature_parser_17) ... ok test_feature_parser_18 (test_GenBank.TestFeatureParser.test_feature_parser_18) ... ok test_feature_parser_19 (test_GenBank.TestFeatureParser.test_feature_parser_19) ... ok test_feature_parser_20 (test_GenBank.TestFeatureParser.test_feature_parser_20) ... ok test_features_spanning_origin (test_GenBank.TestFeatureParser.test_features_spanning_origin) Test that features that span the origin on circular DNA are included correctly for different ways of specifying the topology. ... ok test_record_parser_01 (test_GenBank.TestRecordParser.test_record_parser_01) ... ok test_record_parser_02 (test_GenBank.TestRecordParser.test_record_parser_02) ... ok test_record_parser_03 (test_GenBank.TestRecordParser.test_record_parser_03) ... ok test_record_parser_04 (test_GenBank.TestRecordParser.test_record_parser_04) ... ok test_record_parser_05 (test_GenBank.TestRecordParser.test_record_parser_05) ... ok test_record_parser_06 (test_GenBank.TestRecordParser.test_record_parser_06) ... ok test_record_parser_07 (test_GenBank.TestRecordParser.test_record_parser_07) ... ok test_record_parser_08 (test_GenBank.TestRecordParser.test_record_parser_08) ... ok test_record_parser_09 (test_GenBank.TestRecordParser.test_record_parser_09) ... ok test_record_parser_10 (test_GenBank.TestRecordParser.test_record_parser_10) ... ok test_record_parser_11 (test_GenBank.TestRecordParser.test_record_parser_11) ... ok test_record_parser_12 (test_GenBank.TestRecordParser.test_record_parser_12) ... ok test_record_parser_13 (test_GenBank.TestRecordParser.test_record_parser_13) ... ok test_record_parser_14 (test_GenBank.TestRecordParser.test_record_parser_14) ... ok test_record_parser_15 (test_GenBank.TestRecordParser.test_record_parser_15) ... ok test_record_parser_16 (test_GenBank.TestRecordParser.test_record_parser_16) ... ok test_record_parser_17 (test_GenBank.TestRecordParser.test_record_parser_17) ... ok test_record_parser_18 (test_GenBank.TestRecordParser.test_record_parser_18) ... ok test_record_parser_19 (test_GenBank.TestRecordParser.test_record_parser_19) ... ok test_record_parser_20 (test_GenBank.TestRecordParser.test_record_parser_20) ... ok test_record_parser_tls (test_GenBank.TestRecordParser.test_record_parser_tls) ... ok test_record_parser_tsa (test_GenBank.TestRecordParser.test_record_parser_tsa) ... ok Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.278 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! x_order_2: colinear! test_GenomeDiagram ... ok test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions) Test color translations. ... ok test_add_track (test_GenomeDiagram.DiagramTest.test_add_track) Add track. ... ok test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error) Test adding unspecified track. ... ok test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level) Add track to occupied level. ... ok test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks) Delete track. ... ok test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf) Construct and draw PDF using method approach. ... ok test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf) Construct and draw PDF using object approach. ... ok test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks) Get track. ... ok test_move_track (test_GenomeDiagram.DiagramTest.test_move_track) Move a track. ... ok test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram) Construct and draw SVG and PDF for just part of a SeqRecord. ... ok test_renumber (test_GenomeDiagram.DiagramTest.test_renumber) Test renumbering tracks. ... ok test_str (test_GenomeDiagram.DiagramTest.test_str) Test diagram's info as string. ... ok test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments) Check how the write methods respond to output format arguments. ... ok test_limits (test_GenomeDiagram.GraphTest.test_limits) Check line graphs. ... ok test_slicing (test_GenomeDiagram.GraphTest.test_slicing) Check GraphData slicing. ... ok test_label_default (test_GenomeDiagram.LabelTest.test_label_default) Feature labels - default. ... ok test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils) All sigils. ... ok test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads) Feature arrow sigils, varying heads. ... ok test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts) Feature arrow sigils, varying shafts. ... ok test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts) Feature big-arrow sigils, varying shafts. ... ok test_labels (test_GenomeDiagram.SigilsTest.test_labels) Feature labels. ... ok test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads) Feature ARROW sigil heads within bounding box. ... ok test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads) Feature BIGARROW sigil heads within bounding box. ... ok test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy) Feature JAGGY sigil heads within bounding box. ... ok test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads) Feature OCTO sigil heads within bounding box. ... ok test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow) Feature arrow sigil heads within bounding box. ... ok test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow) Feature big-arrow sigil heads within bounding box. ... ok test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy) Feature arrow sigil heads within bounding box. ... ok test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo) Feature big-arrow sigil heads within bounding box. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.914 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py test_GraphicsBitmaps ... ok test_simple_scatter_plot (test_GraphicsBitmaps.ComparativeTest.test_simple_scatter_plot) Test creation of a simple PNG scatter plot. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.230 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py test_GraphicsChromosome ... ok test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count) Add counts to specific chromosome segments. ... ok test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label) Add labels to chromosome segments. ... ok test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count) Retrieve a color from a count number with the default color scheme. ... ok test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome) Test filling out the information on a chromosome. ... ok test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info) Test retrieval of segment information. ... ok test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale) Set the scale for a chromosome segment. ... ok test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism) Generate an organism with random chromosome info. ... ok test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism) Test the basic functionality of drawing an organism. ... ok test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf) Output a simple organism to a PDF file. ... ok test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps) Output a simple organism to a postscript file. ... ok test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg) Output a simple organism to an SVG file. ... ok test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget) Try widget derived functionality. ... ok test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures) Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples) Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.593 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py test_GraphicsDistribution ... ok test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page) Create a page with multiple distributions on it. ... ok test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page) Test displaying a page with single distribution. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.149 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py test_GraphicsGeneral ... ok test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1) Test creation of a simple ScatterPlot with one list. ... ok test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7) Test creation of a simple ScatterPlot with more lists. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.613 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py test_HMMCasino ... ok test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard) Standard Training with known states. ... ok test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without) Baum-Welch training without known state sequences. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.343 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py test_HMMGeneral ... ok test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood) Calculate log likelihood. ... ok test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator) Test the maximum likelihood estimator for simple cases. ... ok test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition) Testing allow_transition. ... ok test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic) Non-ergodic model (meaning that some transitions are not allowed). ... ok test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm) Test a simple model with 2 states and 2 symbols. ... ok test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from) Testing the calculation of transitions_from. ... ok test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to) Testing the calculation of transitions_to. ... ok test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions) Testing allow_all_transitions. ... ok test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize) Making sure MarkovModelBuilder is initialized correctly. ... ok test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value) Testing the calculation of s values. ... ok test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG.py test_KEGG ... ok test_irregular (test_KEGG.CompoundTests.test_irregular) compound.irregular tests. ... ok test_mass (test_KEGG.CompoundTests.test_mass) record.mass tests. ... ok test_sample (test_KEGG.CompoundTests.test_sample) compound.sample tests. ... ok test_4letter (test_KEGG.EnzymeTests.test_4letter) enzyme.4letter tests. ... ok test_exceptions (test_KEGG.EnzymeTests.test_exceptions) enzyme.exceptions tests. ... ok test_irregular (test_KEGG.EnzymeTests.test_irregular) enzyme.irregular tests. ... ok test_new (test_KEGG.EnzymeTests.test_new) enzyme.new tests. ... ok test_sample (test_KEGG.EnzymeTests.test_sample) enzyme.sample tests. ... ok test_map00950 (test_KEGG.MapTests.test_map00950) map00950.rea tests. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.095 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py test_KGML_graphics ... ok test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic) Basic rendering of KGML: write to PDF without modification. ... ok test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify) Rendering of KGML to PDF, with modification. ... ok test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency) Rendering of KGML to PDF, with color alpha channel. ... ok ---------------------------------------------------------------------- Ran 1 test in 4.232 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py test_KGML_graphics_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.042 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py test_KGML_nographics ... ok test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files) Read KGML from, and write KGML to, local files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.788 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py test_KeyWList ... ok test_parse (test_KeyWList.KeyWListTest.test_parse) Test parsing keywlist.txt works. ... ok test_parse2 (test_KeyWList.KeyWListTest.test_parse2) Parsing keywlist2.txt (without header and footer). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py test_LogisticRegression ... ok test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.048 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py test_MafIO_index ... ok test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary) Following issues 504 and 1086. ... ok test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length) Following issues 504 and 1086. ... ok test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3) Following issue 1083. ... ok test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1) Checking that spliced sequences are correct. ... ok test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2) Checking that spliced sequences are correct. ... ok test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.677 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.055 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py test_MarkovModel ... ok test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.170 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Medline.py test_Medline ... ok test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok test_parse (test_Medline.TestMedline.test_parse) ... ok test_read (test_Medline.TestMedline.test_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBITextParser.py test_NCBITextParser ... ok test_conversion (test_NCBITextParser.TestBlastRecord.test_conversion) Converting a Blast record multiple alignment. ... ok test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_001) Parsing BLASTN 2.0.10 output (text_2010L_blastn_001). ... ok test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_002) Parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002). ... ok test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_003) Parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003). ... ok test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastn_004) Parsing BLASTN 2.0.10 output (text_2010L_blastn_004). ... ok test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_001) Parsing BLASTP 2.0.10 output (text_2010L_blastp_001). ... ok test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_002) Parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002). ... ok test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_003) Parsing BLASTP 2.0.10 output (text_2010L_blastp_003). ... ok test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_004) Parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004). ... ok test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_005) Parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005). ... ok test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_006) Parsing BLASTP 2.0.10 output (text_2010L_blastp_006). ... ok test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastp_007) Parsing BLASTP 2.0.10 output (text_2010L_blastp_007). ... ok test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_001) Parsing BLASTX 2.0.10 output (text_2010L_blastx_001). ... ok test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_blastx_002) Parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002). ... ok test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_001) Parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001). ... ok test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_002) Parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002). ... ok test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_phiblast_003) Parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003). ... ok test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_001) Parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001). ... ok test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastn_002) Parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002). ... ok test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2010L_tblastx_001) Parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001). ... ok test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_001) Parsing BLASTN 2.0.11 output (text_2011L_blastn_001). ... ok test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_002) Parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002). ... ok test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_003) Parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003). ... ok test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastn_004) Parsing BLASTN 2.0.11 output (text_2011L_blastn_004). ... ok test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_001) Parsing BLASTP 2.0.11 output (text_2011L_blastp_001). ... ok test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_002) Parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002). ... ok test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_003) Parsing BLASTP 2.0.11 output (text_2011L_blastp_003). ... ok test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_004) Parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004). ... ok test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_005) Parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005). ... ok test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_006) Parsing BLASTP 2.0.11 output (text_2011L_blastp_006). ... ok test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastp_007) Parsing BLASTP 2.0.11 output (text_2011L_blastp_007). ... ok test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_001) Parsing BLASTX 2.0.11 output (text_2011L_blastx_001). ... ok test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_blastx_002) Parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002). ... ok test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_001) Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001). ... ok test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_002) Parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002). ... ok test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_psiblast_003) Parsing BLASTP 2.0.11 output (text_2011L_psiblast_003). ... ok test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_001) Parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001). ... ok test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastn_002) Parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002). ... ok test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2011L_tblastx_001) Parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001). ... ok test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2012L_psiblast_001) Parsing BLASTP 2.0.12 output (text_2012L_psiblast_001). ... ok test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_blastn_001) Parsing BLASTN 2.0.14 output (text_2014L_blastn_001). ... ok test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2014L_psiblast_001) Parsing BLASTP 2.0.14 output (text_2014L_psiblast_001). ... ok test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2201L_blastx_001) Parsing BLASTX 2.2.1 output (text_2201L_blastx_001). ... ok test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_001) Parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001). ... ok test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastn_002) Parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002). ... ok test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2202L_blastp_001) Parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001). ... ok test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser.test_text_2208L_psiblast_001) Parsing BLASTP 2.2.8 output (text_2208L_psiblast_001). ... ok test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2215L_blastx_001) Parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001). ... ok test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2216L_tblastn_001) Parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001). ... ok test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_001) Parsing BLASTX 2.2.20 output (text_2220L_blastx_001). ... ok test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2220L_blastx_002) Parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002). ... ok test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2221L_blastp_001) Parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001). ... ok test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222L_blastx_001) Parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001). ... ok test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2222_blastx_001) Parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001). ... ok test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_001) Parsing BLASTN 2.2.26+ output with no results. ... ok test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_002) Parsing BLASTN 2.2.26+ output with single hsp results. ... ok test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastn_003) Parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_001) Parsing BLASTP 2.2.26+ with no results. ... ok test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_002) Parsing BLASTP 2.2.26+ with single hsp results. ... ok test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastp_003) Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_001) Parsing BLASTX 2.2.26+ with no results. ... ok test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_002) Parsing BLASTX 2.2.26+ with single hsp results. ... ok test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_blastx_003) Parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_001) Parsing TBLASTN 2.2.26+ output with no results. ... ok test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_002) Parsing TBLASTN 2.2.26+ output with single hsp results. ... ok test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastn_003) Parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_001) Parsing TBLASTX 2.2.26+ output with no results. ... ok test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_002) Parsing TBLASTX 2.2.26+ output with single hsp results. ... ok test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser.test_text_2226_tblastx_003) Parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser.test_text_2230_blastp_001) Parsing BLASTP 2.2.30+ output with line of dashes. ... ok Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.387 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py test_NCBIXML ... ok test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001) Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001) Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001) Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001) Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001) Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001) Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001) Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001) Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002) Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001) Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001) Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.510 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NMR.py test_NMR ... ok test_noetools (test_NMR.NmrTests.test_noetools) Self test for NMR.NOEtools. ... ok test_xpktools (test_NMR.NmrTests.test_xpktools) Self test for NMR.xpktools. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py test_NaiveBayes ... ok test_car_data (test_NaiveBayes.CarTest.test_car_data) Simple example using car data. ... ok test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py test_PAML_baseml ... ok testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.151 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py test_PAML_codeml ... ok testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise) Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility) Test finding trees in the results. ... ok testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.795 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py test_PAML_yn00 ... ok testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.101 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDBList.py test_PDBList ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_CEAligner.py test_PDB_CEAligner ... ok test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner) Test aligning 7CFN on 6WQA. ... ok test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform) Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic) Test aligning 1LCD on 1LCD. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.098 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py test_PDB_DSSP ... ok test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA) Tests the usage of different ASA tables. ... ok test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file) Test parsing of pregenerated DSSP. ... ok test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds) Test parsing of DSSP hydrogen bond information. ... ok test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj) All elements correctly added to xtra attribute of input model object. ... ok test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file) Test parsing of pregenerated DSSP missing header information. ... ok setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.' ---------------------------------------------------------------------- Ran 1 test in 0.159 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py test_PDB_Dice ... ok test_dice (test_PDB_Dice.DiceTests.test_dice) Self test for PDB.Dice module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Disordered.py test_PDB_Disordered ... ok test_copy_and_write_disordered (test_PDB_Disordered.TestDisordered.test_copy_and_write_disordered) Extract, save, and parse again disordered atoms. ... ok test_copy_disordered_atom (test_PDB_Disordered.TestDisordered.test_copy_disordered_atom) Copies disordered atoms and all their children. ... ok test_copy_entire_chain (test_PDB_Disordered.TestDisordered.test_copy_entire_chain) Copy propagates throughout SMCRA object. ... ok test_disordered_cog (test_PDB_Disordered.TestDisordered.test_disordered_cog) Calculate DisorderedAtom center of geometry. ... ok test_empty_disordered (test_PDB_Disordered.TestDisordered.test_empty_disordered) Raise ValueError on center of mass calculation of empty DisorderedAtom. ... ok test_remove_disordered_atom (test_PDB_Disordered.TestDisordered.test_remove_disordered_atom) Remove altlocs from DisorderedAtom entities. ... ok test_remove_disordered_residue (test_PDB_Disordered.TestDisordered.test_remove_disordered_residue) Remove residues from DisorderedResidue entities. ... ok test_structure_w_disordered_com (test_PDB_Disordered.TestDisordered.test_structure_w_disordered_com) Calculate center of mass of structure including DisorderedAtoms. ... ok test_transform_disordered (test_PDB_Disordered.TestDisordered.test_transform_disordered) Transform propagates through disordered atoms. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py test_PDB_Exposure ... ok test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN) HSExposureCN. ... ok test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA) HSExposureCA. ... ok test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB) HSExposureCB. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.318 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py test_PDB_FragmentMapper ... ok test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper) Self test for FragmentMapper module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.112 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py test_PDB_KDTree ... ok test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual) Test all fixed radius neighbor search. ... ok test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple) Test all fixed radius neighbor search. ... ok test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search) Test searching all points within a certain radius of center. ... ok test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search) NeighborSearch: Find nearby randomly generated coordinates. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.656 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py test_PDB_MMCIF2Dict ... ok test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments) Comments may begin outside of column 1 if preceded by whitespace. ... ok test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive) Comments may begin outside of column 1. ... ok test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline) Multi-line string followed by token on the same line. ... ok test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block) Verbatim blocks parsed correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFIO.py test_PDB_MMCIFIO ... ok test_mmcifio_multimodel (test_PDB_MMCIFIO.WriteTest.test_mmcifio_multimodel) Write a multi-model, multi-chain mmCIF file. ... ok test_mmcifio_select (test_PDB_MMCIFIO.WriteTest.test_mmcifio_select) Write a selection of the structure using a Select subclass. ... ok test_mmcifio_write_custom_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_mmcifio_write_dict (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_dict) Write an mmCIF dictionary out, read it in and compare them. ... ok test_mmcifio_write_residue (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue) Write a single residue using MMCIFIO. ... ok test_mmcifio_write_residue_w_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_w_chain) Write a single residue (chain id == X) using MMCIFIO. ... ok test_mmcifio_write_residue_wout_chain (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_residue_wout_chain) Write a single orphan residue using MMCIFIO. ... ok test_mmcifio_write_structure (test_PDB_MMCIFIO.WriteTest.test_mmcifio_write_structure) Write a full structure using MMCIFIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.231 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py test_PDB_MMCIFParser ... ok test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion) Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering) Convert mmCIF to PDB and renumber atom serials. ... ok test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering) Convert mmCIF to PDB and preserve original serial numbering. ... ok testModels (test_PDB_MMCIFParser.ParseReal.testModels) Test file with multiple models. ... ok test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle) Test if the parser can handle file handle as well as filename. ... ok test_header (test_PDB_MMCIFParser.ParseReal.test_header) Test if the parser populates header data. ... ok test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions) Test file with residue insertion codes. ... ok test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers) Extract polypeptides from 1A80. ... ok test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast) Test if FastMMCIFParser can parse point mutations correctly. ... ok test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main) Test if MMCIFParser parse point mutations correctly. ... ok test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.030 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py test_PDB_NACCESS ... ok test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS) Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.' test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file) Test parsing of pregenerated asa NACCESS file. ... ok test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file) Test parsing of pregenerated rsa NACCESS file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py test_PDB_PDBIO ... ok test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering) Preserve model serial numbers during I/O. ... ok test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy) Write PDB file with missing occupancy. ... ok test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits) Test raising error when structure cannot meet PDB format limits. ... ok test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select) Write a selection of the structure using a Select subclass. ... ok test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering) Test writing PDB and do not preserve atom numbering. ... ok test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering) Test writing PDB and preserve atom numbering. ... ok test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue) Write a single residue using PDBIO. ... ok test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain) Write a single residue (chain id == X) using PDBIO. ... ok test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain) Write a single orphan residue using PDBIO. ... ok test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure) Write a full structure using PDBIO. ... ok test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated) Test parsing of truncated lines. ... ok test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element) PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element) Write a structure with atomic element X with PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.205 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py test_PDB_PDBParser ... ok test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive) Parse a flawed PDB file in permissive mode: check warnings. ... ok test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict) Parse a flawed PDB file in permissive mode: check errors. ... ok test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive) Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict) Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive) Parse file with missing occupancy with PERMISSIVE=True. ... ok test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict) Parse file with missing occupancy with PERMISSIVE=False. ... ok test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details) Verify details of the parsed example PDB file. ... ok test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity) Verify the structure of the parsed example PDB file. ... ok test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict) Parse 1A8O.pdb file in strict mode. ... ok test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA) Walk down the structure hierarchy and test parser reliability. ... ok test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive) Catch exception on duplicated residue. ... ok test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict) Throw exception on duplicated residue. ... ok test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty) Parse an empty file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PSEA.py test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py test_PDB_Polypeptide ... ok test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real) Test CaPPBuilder on real PDB file. ... ok test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd) Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau) Test tau angles calculated with CaPPBuilder. ... ok test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real) Test PPBuilder on real PDB file. ... ok test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd) Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion) Test phi/psi angles calculated with PPBuilder. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_QCSuperimposer.py test_PDB_QCSuperimposer ... ok test_get_init_rms (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_init_rms) Test initial RMS calculation. ... ok test_get_transformed (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_get_transformed) Test transformation of coordinates after QCP. ... ok test_on_pdb (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_on_pdb) Align a PDB to itself. ... ok test_run (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_run) Test QCP on dummy data. ... ok test_set (test_PDB_QCSuperimposer.QCPSuperimposerTest.test_set) Test setting of initial parameters. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py test_PDB_ResidueDepth ... ok setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.' test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr) Test generation of xyzr (atomic radii) file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py test_PDB_SASA ... ok test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii) Run Shrake-Rupley with custom radii. ... ok test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm) Run Shrake-Rupley with default parameters. ... ok test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level) Raise exception on input Atom entity. ... ok test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type) Raise exception on unsupported entity type. ... ok test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1) Raise exception on invalid level parameter: X. ... ok test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2) Raise exception on invalid level parameter: S > C. ... ok test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity) Raise exception on invalid level parameter: S > C. ... ok test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points) Raise exception on bad n_points parameter. ... ok test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius) Raise exception on bad probe_radius parameter. ... ok test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution) Run Shrake-Rupley with 960 points per sphere. ... ok test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C) Run Shrake-Rupley with level C. ... ok test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R) Run Shrake-Rupley with level R. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.062 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py test_PDB_SMCRA ... ok test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element) Unknown element is assigned 'X'. ... ok test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment) Atom Element. ... ok test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok test_ions (test_PDB_SMCRA.Atom_Element.test_ions) Element for magnesium is assigned correctly. ... ok test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog) Calculate center of geometry of individual chains. ... ok test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure) Center of mass of empty structure raises ValueError. ... ok test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog) Calculate Structure center of geometry. ... ok test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com) Calculate Structure center of mass. ... ok test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id) Change the id of a model. ... ok test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self) Changing the id to itself does nothing (does not raise). ... ok test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id) Change the id of a model. ... ok test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises) Cannot change id to a value already in use by another child. ... ok test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id) Change the id of a residue. ... ok test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain) Invalidate cached full_ids if an id is changed. ... ok test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue) Invalidate cached full_ids if an id is changed. ... ok test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy) Make a copy of a residue. ... ok test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms) Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains) Yields chains from different models separately. ... ok test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues) Yields all residues from all models. ... ok test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities) Test comparing and sorting the several SMCRA objects. ... ok test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort) Test atoms are sorted correctly in residues. ... ok test_transform (test_PDB_SMCRA.TransformTests.test_transform) Transform entities (rotation and translation). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.341 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Selection.py test_PDB_Selection ... ok test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level) Unfold from lowest level to all levels. ... ok test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level) Unfold from chain level to all levels. ... ok test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level) Unfold from model to all levels. ... ok test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level) Unfold from chain level to all levels. ... ok test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level) Unfold from highest level to all levels. ... ok test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py test_PDB_StructureAlignment ... ok test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign) Tests on module to align two proteins according to a FASTA alignment file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.218 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py test_PDB_Superimposer ... ok test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer) Test on module that superimpose two protein structures. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py test_PDB_parse_pdb_header ... ok test_1 (test_PDB_parse_pdb_header.ParseReal.test_1) Parse the header of a known PDB file (1A8O). ... ok test_2 (test_PDB_parse_pdb_header.ParseReal.test_2) Parse the header of another PDB file (2BEG). ... ok test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line) Unit test for parsing and converting fields in HEADER record. ... ok test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title) Unit test for sensible result with no TITLE line. ... ok test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465) Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99) Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465) A UNIT-test for the private function _parse_remark_465. ... ok test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line) Unit test for correct parsing of multiline title records. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.098 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py test_PDB_vectors ... ok test_Vector (test_PDB_vectors.VectorTests.test_Vector) Test Vector object. ... ok test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles) Test Vector angles. ... ok test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) Confirm can generate coordinate space transform for 3 points. ... ok test_division (test_PDB_vectors.VectorTests.test_division) Confirm division works. ... ok test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates) Test spherical coordinates. ... ok test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0) Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180) Test 180 deg rotation. ... ok test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90) Test 90 deg rotation. ... ok test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space) Confirm multi_coord_space computes forward, reverse transforms. ... ok test_normalization (test_PDB_vectors.VectorTests.test_normalization) Test Vector normalization. ... ok test_refmat (test_PDB_vectors.VectorTests.test_refmat) Test refmat can mirror one matrix to another. ... ok test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0) Test rotmat when the rotation is 0 deg (singularity). ... ok test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180) Test rotmat when the rotation is 180 deg (singularity). ... ok test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90) Test regular 90 deg rotation. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PQR.py test_PQR ... ok test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge) Test if missing or malformed charge case is handled correctly. ... ok test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius) Test if missing, malformed or negative radius case is handled correctly. ... ok test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz) Test if bad coordinates exception is raised. ... ok test_single_input (test_PQR.ParseSimplePQR.test_single_input) Test if a single ATOM entry correctly parsed. ... ok test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure) Write a full structure using PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.094 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Pathway.py test_Pathway ... ok testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.014 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Phd.py test_Phd ... ok test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO) Test phd_454 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO) Test phd1 using parser via SeqIO. ... ok test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser) Test phd1 file in detail. ... ok test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py test_PopGen_GenePop_nodepend ... ok test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser) Basic operation of the File Record Parser. ... ok test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features) Testing the ability to remove population/loci via class methods. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser) Basic operation of the Record Parser. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic) Basic test on Record. ... ok test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils) Basic operation of GenePop Utils. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.021 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.073 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py test_ProtParam ... ok test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity) Calculate protein aromaticity. ... ok test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH) Test charge_at_pH function. ... ok test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids) Calculate amino acid counts. ... ok test_flexibility (test_ProtParam.ProtParamTest.test_flexibility) Calculate protein flexibility. ... ok test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent) Calculate amino acid percentages. ... ok test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight) Calculate protein molecular weight. ... ok test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight) Calculate monoisotopic molecular weight. ... ok test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_gravy (test_ProtParam.ProtParamTest.test_gravy) Calculate gravy. Tests all pre-defined scales. ... ok test_instability_index (test_ProtParam.ProtParamTest.test_instability_index) Calculate protein instability index. ... ok test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point) Calculate the isoelectric point. ... ok test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient) Molar extinction coefficient. ... ok test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale) Calculate the Kite Doolittle scale. ... ok test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction) Calculate secondary structure fractions. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.064 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py test_RCSBFormats ... ok test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains) Compare parsed chains. ... ok test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models) Compared parsed models. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.430 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Restriction.py test_Restriction ... ok test_basic_isochizomers (test_Restriction.EnzymeComparison.test_basic_isochizomers) Test to be sure isochizomer and neoschizomers are as expected. ... ok test_comparisons (test_Restriction.EnzymeComparison.test_comparisons) Test comparison operators between different enzymes. ... ok test_change (test_Restriction.RestrictionBatchPrintTest.test_change) Test that change() changes something. ... ok test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map1) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map2) Test that print_as('map'); print_that() correctly wraps round. ... ok test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest.test_make_format_map3) Test that print_as('map'); print_that() correctly wraps round. ... ok test_analysis_restrictions (test_Restriction.RestrictionBatches.test_analysis_restrictions) Test Fancier restriction analysis. ... ok test_batch_analysis (test_Restriction.RestrictionBatches.test_batch_analysis) Sequence analysis with a restriction batch. ... ok test_creating_batch (test_Restriction.RestrictionBatches.test_creating_batch) Creating and modifying a restriction batch. ... ok test_premade_batches (test_Restriction.RestrictionBatches.test_premade_batches) Test content of premade batches CommOnly, NoComm, AllEnzymes. ... ok test_search_premade_batches (test_Restriction.RestrictionBatches.test_search_premade_batches) Test search with pre-made batches CommOnly, NoComm, AllEnzymes. ... ok test_formatted_seq (test_Restriction.SequenceTesting.test_formatted_seq) Test several methods of FormattedSeq. ... ok test_non_iupac_letters (test_Restriction.SequenceTesting.test_non_iupac_letters) Test if non-IUPAC letters raise a TypeError. ... ok test_sequence_object (test_Restriction.SequenceTesting.test_sequence_object) Test if sequence must be a Seq or MutableSeq object. ... ok test_circular_sequences (test_Restriction.SimpleEnzyme.test_circular_sequences) Deal with cutting circular sequences. ... ok test_cutting_border_positions (test_Restriction.SimpleEnzyme.test_cutting_border_positions) Check if cutting after first and penultimate position works. ... ok test_ear_cutting (test_Restriction.SimpleEnzyme.test_ear_cutting) Test basic cutting with EarI (ambiguous overhang). ... ok test_eco_cutting (test_Restriction.SimpleEnzyme.test_eco_cutting) Test basic cutting with EcoRI (5'overhang). ... ok test_init (test_Restriction.SimpleEnzyme.test_init) Check for error during __init__. ... ok test_kpn_cutting (test_Restriction.SimpleEnzyme.test_kpn_cutting) Test basic cutting with KpnI (3'overhang). ... ok test_overlapping_cut_sites (test_Restriction.SimpleEnzyme.test_overlapping_cut_sites) Check if overlapping recognition sites are properly handled. ... ok test_recognition_site_on_both_strands (test_Restriction.SimpleEnzyme.test_recognition_site_on_both_strands) Check if recognition sites on both strands are properly handled. ... ok test_shortcuts (test_Restriction.SimpleEnzyme.test_shortcuts) Check if '/' and '//' work as '.search' and '.catalyse'. ... ok test_sma_cutting (test_Restriction.SimpleEnzyme.test_sma_cutting) Test basic cutting with SmaI (blunt cutter). ... ok test_sna_cutting (test_Restriction.SimpleEnzyme.test_sna_cutting) Test basic cutting with SnaI (unknown). ... ok test_print_that (test_Restriction.TestPrintOutputs.test_print_that) Test print_that function. ... ok test_str_method (test_Restriction.TestPrintOutputs.test_str_method) Test __str__ and __repr__ outputs. ... ok test_supplier (test_Restriction.TestPrintOutputs.test_supplier) Test output of supplier list for different enzyme types. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.163 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py test_SCOP_Astral ... ok testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py test_SCOP_Cla ... ok testError (test_SCOP_Cla.ClaTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testIndex (test_SCOP_Cla.ClaTests.testIndex) Test CLA file indexing. ... ok testParse (test_SCOP_Cla.ClaTests.testParse) Test if all records in a CLA file are being read. ... ok testRecord (test_SCOP_Cla.ClaTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Cla.ClaTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py test_SCOP_Des ... ok testError (test_SCOP_Des.DesTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Des.DesTests.testParse) Test if all records in a DES file are being read. ... ok testRecord (test_SCOP_Des.DesTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Des.DesTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py test_SCOP_Dom ... ok testError (test_SCOP_Dom.DomTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Dom.DomTests.testParse) Test if all records in a DOM file are being read. ... ok testRecord (test_SCOP_Dom.DomTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Dom.DomTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.067 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py test_SCOP_Hie ... ok testError (test_SCOP_Hie.HieTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Hie.HieTests.testParse) Test if all records in a HIE file are being read. ... ok testStr (test_SCOP_Hie.HieTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py test_SCOP_Raf ... ok testParse (test_SCOP_Raf.RafTests.testParse) Parse a RAF record. ... ok testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py test_SCOP_Residues ... ok testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse) Test if we can parse residue subsets enclosed in brackets. ... ok testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.066 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py test_SCOP_Scop ... ok testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok testParse (test_SCOP_Scop.ScopTests.testParse) ... ok testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents) Test getDescendents method. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py test_SVDSuperimposer ... ok test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py test_SearchIO_blat_psl ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001) Test parsing blat output (pslx_34_001.pslx). ... ok test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002) Test parsing blat output (pslx_34_002.pslx). ... ok test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003) Test parsing blat output (pslx_34_003.pslx). ... ok test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004) Test parsing blat output (pslx_34_004.pslx). ... ok test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005) Test parsing blat output (pslx_34_005.pslx). ... ok test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002) Test parsing blat output (pslx_35_002.pslx). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.088 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001) Test blat-psl indexing, multiple queries. ... ok test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002) Test blat-psl indexing, single query, no hits. ... ok test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003) Test blat-psl indexing, single query, single hit. ... ok test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004) Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005) Test blat-psl indexing, multiple queries, no header. ... ok test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006) Test blat-pslx indexing, multiple queries. ... ok test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007) Test blat-pslx indexing, single query, no hits. ... ok test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008) Test blat-pslx indexing, single query, single hit. ... ok test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009) Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010) Test blat-pslx indexing, multiple queries, no header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.110 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate.py test_SearchIO_exonerate ... ok test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases.test_exn_22_o_vulgar_cigar) Test parsing exonerate output (exn_22_o_vulgar_cigar.exn). ... ok test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_c2c) Compares vulgar-text coordinate parsing for the coding2coding model. ... ok test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_g2g) Compares vulgar-text coordinate parsing for the genome2genome model. ... ok test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases.test_vulgar_text_similar_p2d) Compares vulgar-text coordinate parsing for the protein2dna model. ... ok test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_affine_local) Test parsing exonerate output (exn_22_m_affine_local.exn). ... ok test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_cdna2genome) Test parsing exonerate output (exn_22_m_cdna2genome.exn). ... ok test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding) Test parsing exonerate output (exn_22_m_coding2coding.exn). ... ok test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2coding_fshifts) Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn). ... ok test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_coding2genome) Test parsing exonerate output (exn_22_m_coding2genome.exn). ... ok test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_dna2protein) Test parsing exonerate output (exn_22_m_dna2protein.exn). ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_est2genome) Test parsing exonerate output (exn_22_m_est2genome.exn). ... ok test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_genome2genome) Test parsing exonerate output (exn_22_m_genome2genome.exn). ... ok test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ner) Test parsing exonerate output (exn_22_m_ner.exn). ... ok test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2dna_fshifts) Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn). ... ok test_exn_22_m_protein2genome (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_protein2genome) Test parsing exonerate output (exn_22_m_protein2genome.exn). ... ok test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped) Test parsing exonerate output (exn_22_m_ungapped.exn). ... ok test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_m_ungapped_trans) Test parsing exonerate output (exn_22_m_ungapped_trans.exn). ... ok test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_multiple) Test parsing exonerate output (exn_22_q_multiple.exn). ... ok test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_24_m_protein2genome_revcomp_fshifts (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_m_protein2genome_revcomp_fshifts) Test parsing exonerate output (exn_24_m_protein2genome_revcomp_fshifts.exn). ... ok test_exn_24_protein2genome_met_intron (test_SearchIO_exonerate.ExonerateTextCases.test_exn_24_protein2genome_met_intron) Test parsing exonerate output (exn_24_m_protein2genome_met_intron.exn). ... ok test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar) Test parsing exonerate output (exn_22_o_vulgar.exn). ... ok test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases.test_exn_22_o_vulgar_fshifts) Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.119 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_text_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome) Test exonerate-text indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple) Test exonerate-text indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py test_SearchIO_exonerate_vulgar_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome) Test exonerate-vulgar indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple) Test exonerate-vulgar indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.063 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10 ... ok test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002) Test parsing fasta34 output (output002.m10). ... ok test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003) Test parsing fasta34 output (output003.m10). ... ok test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001) Test parsing fasta35 output (output001.m10). ... ok test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004) Test parsing fasta35 output (output004.m10). ... ok test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005) Test parsing ssearch35 output (output005.m10). ... ok test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006) Test parsing fasta35 output (output006.m10). ... ok test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007) Test parsing fasta36 output (output007.m10). ... ok test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008) Test parsing tfastx36 output (output008.m10). ... ok test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009) Test parsing fasta36 output (output009.m10). ... ok test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010) Test parsing fasta36 output (output010.m10). ... ok test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011) Test parsing fasta36 output (output011.m10). ... ok test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012) Test parsing fasta36 output (output012.m10). ... ok test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013) Test parsing fasta36 output (output013.m10). ... ok test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014) Test parsing fasta36 output (output014.m10). ... ok test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015) Test parsing fasta36 output (output015.m10). ... ok test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016) Test parsing fasta36 output (output016.m10). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py test_SearchIO_fasta_m10_index ... ok test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001) Test fasta-m10 indexing, fasta35, multiple queries. ... ok test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002) Test fasta-m10 indexing, fasta34, multiple queries. ... ok test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005) Test fasta-m10 indexing, ssearch35, multiple queries. ... ok test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008) Test fasta-m10 indexing, tfastx36, multiple queries. ... ok test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009) Test fasta-m10 indexing, fasta36, multiple queries. ... ok test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010) Test fasta-m10 indexing, fasta36, single query, no hits. ... ok test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011) Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012) Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.101 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py C test_SearchIO_hhsuite2_text ... ok test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo) Parsing 2uvo. ... ok test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable) Parsing 4uvo with empty results table. ... ok test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader) Parsing 4uvo with only header present. ... ok test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79) Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm) Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198) Parsing hhpred_9590198.hhr file. ... ok test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx) Parsing allx.hhr file. ... ok test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1) Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py C test_SearchIO_hmmer2_text ... ok test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21) Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22) Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq) Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24) Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20) Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22) Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.136 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer2_text_index ... ok test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.1. ... ok test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.3. ... ok test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.4. ... ok test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam) Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch) Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.108 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab ... ok test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002) Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_domtab_index ... ok test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_001) Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002) Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003) Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004) Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001) Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_last) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_middle) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_single) Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.070 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002) Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003) Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004) Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001) Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.062 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_tab_index ... ok test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_001) Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002) Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003) Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004) Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_last) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_middle) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_single) Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text ... ok test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001) Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002) Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003) Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004) Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005) Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001) Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001) Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001) Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002) Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003) Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004) Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005) Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006) Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007) Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008) Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009) Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010) Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_31b1_hmmscan_001) Parsing hmmscan 3.1b1 (text_31b1_hmmscan_001). ... ok test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases.test_31b2_phmmer_001) Parsing phmmer 3.1b2 (text_31b2_phmmer_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.132 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py test_SearchIO_hmmer3_text_index ... ok test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002) Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_006) Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_007) Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_008) Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmsearch_005) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_last) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_middle) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_single) Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.056 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_legacy.py test_SearchIO_legacy ... ok test_TaggingConsumer (test_SearchIO_legacy.TestParserSupport.test_TaggingConsumer) ... ok test_attempt_read_and_call (test_SearchIO_legacy.TestParserSupport.test_attempt_read_and_call) ... ok test_is_blank_line (test_SearchIO_legacy.TestParserSupport.test_is_blank_line) ... ok test_read_and_call (test_SearchIO_legacy.TestParserSupport.test_read_and_call) ... ok test_safe_peekline (test_SearchIO_legacy.TestParserSupport.test_safe_peekline) ... ok test_safe_readline (test_SearchIO_legacy.TestParserSupport.test_safe_readline) ... ok test_one (test_SearchIO_legacy.UndoHandleTests.test_one) First test. ... ok test_read (test_SearchIO_legacy.UndoHandleTests.test_read) Test read method. ... ok test_undohandle_read_block (test_SearchIO_legacy.UndoHandleTests.test_undohandle_read_block) Test reading in blocks. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_model.py test_SearchIO_model ... ok test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases.test_coords_setters_getters) Test HSPFragment query and hit coordinate-related setters and getters. ... ok test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases.test_coords_setters_readonly) Test HSPFragment query and hit coordinate-related read-only getters. ... ok test_default_attrs (test_SearchIO_model.HSPFragmentCases.test_default_attrs) Test HSPFragment attributes' default values. ... ok test_frame_set_error (test_SearchIO_model.HSPFragmentCases.test_frame_set_error) Test HSPFragment query and hit frame setters, invalid values. ... ok test_frame_set_ok (test_SearchIO_model.HSPFragmentCases.test_frame_set_ok) Test HSPFragment query and hit frame setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentCases.test_getitem) Test HSPFragment.__getitem__. ... ok test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases.test_getitem_alignment_annot) Test HSPFragment.__getitem__, with alignment annotation. ... ok test_getitem_attrs (test_SearchIO_model.HSPFragmentCases.test_getitem_attrs) Test HSPFragment.__getitem__, with attributes. ... ok test_id_desc_set (test_SearchIO_model.HSPFragmentCases.test_id_desc_set) Test HSPFragment query and hit id and description setters. ... ok test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases.test_init_with_seqrecord) Test HSPFragment.__init__, with SeqRecord. ... ok test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases.test_init_wrong_seqtypes) Test HSPFragment.__init__, wrong sequence argument types. ... ok test_len (test_SearchIO_model.HSPFragmentCases.test_len) Test HSPFragment.__len__. ... ok test_molecule_type_no_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_no_seq) Test HSPFragment molecule_type property, query and hit sequences not present. ... ok test_molecule_type_with_seq (test_SearchIO_model.HSPFragmentCases.test_molecule_type_with_seq) Test HSPFragment molecule_type property, query or hit sequences present. ... ok test_pickle (test_SearchIO_model.HSPFragmentCases.test_pickle) Test pickling and unpickling of HSPFragment. ... ok test_repr (test_SearchIO_model.HSPFragmentCases.test_repr) Test HSPFragment.__repr__. ... ok test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases.test_seq_unequal_hit_query_len) Test HSPFragment sequence setter with unequal hit and query lengths. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentCases.test_seqmodel) Test HSPFragment sequence attribute types and default values. ... ok test_strand_set_error (test_SearchIO_model.HSPFragmentCases.test_strand_set_error) Test HSPFragment query and hit strand setters, invalid values. ... ok test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_minus_frame) Test HSPFragment query and hit strand getters, from minus frame. ... ok test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_plus_frame) Test HSPFragment query and hit strand getters, from plus frame. ... ok test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases.test_strand_set_from_zero_frame) Test HSPFragment query and hit strand getters, from zero frame. ... ok test_strand_set_ok (test_SearchIO_model.HSPFragmentCases.test_strand_set_ok) Test HSPFragment query and hit strand setters. ... ok test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem) Test HSPFragment.__getitem__, no alignments. ... ok test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_hit) Test HSPFragment.__getitem__, only hit. ... ok test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_getitem_only_query) Test HSPFragment.__getitem__, only query. ... ok test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_init) Test HSPFragment.__init__ attributes. ... ok test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_iter) Test HSP.__iter__, no alignments. ... ok test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_len) Test HSPFragment.__len__, no alignments. ... ok test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_repr) Test HSPFragment.__repr__, no alignments. ... ok test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases.test_seqmodel) Test HSPFragment sequence attributes, no alignments. ... ok test_contains (test_SearchIO_model.HSPMultipleFragmentCases.test_contains) Test HSP.__contains__. ... ok test_delitem (test_SearchIO_model.HSPMultipleFragmentCases.test_delitem) Test HSP.__delitem__. ... ok test_fragments (test_SearchIO_model.HSPMultipleFragmentCases.test_fragments) Test HSP.fragments property. ... ok test_getitem (test_SearchIO_model.HSPMultipleFragmentCases.test_getitem) Test HSP.__getitem__. ... ok test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases.test_id_desc_set) Test HSP query and hit id and description setters. ... ok test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPMultipleFragmentCases.test_len) Test HSP.__len__. ... ok test_molecule_type (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type) Test HSP.molecule_type getter. ... ok test_molecule_type_set (test_SearchIO_model.HSPMultipleFragmentCases.test_molecule_type_set) Test HSP.molecule_type setter. ... ok test_pickle (test_SearchIO_model.HSPMultipleFragmentCases.test_pickle) Test pickling and unpickling of HSP. ... ok test_range (test_SearchIO_model.HSPMultipleFragmentCases.test_range) Test HSP range properties. ... ok test_ranges (test_SearchIO_model.HSPMultipleFragmentCases.test_ranges) Test HSP ranges properties. ... ok test_seqs (test_SearchIO_model.HSPMultipleFragmentCases.test_seqs) Test HSP sequence properties. ... ok test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_multiple) Test HSP.__setitem__, multiple items. ... ok test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases.test_setitem_single) Test HSP.__setitem__, single item. ... ok test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPMultipleFragmentCases.test_span) Test HSP span properties. ... ok test_alignment (test_SearchIO_model.HSPSingleFragmentCases.test_alignment) Test HSP.alignment property. ... ok test_aln_span (test_SearchIO_model.HSPSingleFragmentCases.test_aln_span) Test HSP.aln_span property. ... ok test_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_fragment) Test HSP.fragment property. ... ok test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases.test_init_no_fragment) Test HSP.__init__ without fragments. ... ok test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases.test_is_fragmented) Test HSP.is_fragmented property. ... ok test_len (test_SearchIO_model.HSPSingleFragmentCases.test_len) Test HSP.__len__. ... ok test_range (test_SearchIO_model.HSPSingleFragmentCases.test_range) Test HSP range properties. ... ok test_seq (test_SearchIO_model.HSPSingleFragmentCases.test_seq) Test HSP sequence properties. ... ok test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases.test_setters_readonly) Test HSP read-only properties. ... ok test_span (test_SearchIO_model.HSPSingleFragmentCases.test_span) Test HSP span properties. ... ok test_append (test_SearchIO_model.HitCases.test_append) Test Hit.append. ... ok test_bool (test_SearchIO_model.HitCases.test_bool) Test Hit.__bool__. ... ok test_delitem (test_SearchIO_model.HitCases.test_delitem) Test Hit.__delitem__. ... ok test_desc_set (test_SearchIO_model.HitCases.test_desc_set) Test Hit.description setter. ... ok test_desc_set_no_seqrecord (test_SearchIO_model.HitCases.test_desc_set_no_seqrecord) Test Hit.description setter, without HSP SeqRecords. ... ok test_filter (test_SearchIO_model.HitCases.test_filter) Test Hit.filter. ... ok test_filter_no_filtered (test_SearchIO_model.HitCases.test_filter_no_filtered) Test Hit.hit_filter, all hits filtered out. ... ok test_filter_no_func (test_SearchIO_model.HitCases.test_filter_no_func) Test Hit.filter, without arguments. ... ok test_fragments (test_SearchIO_model.HitCases.test_fragments) Test Hit.fragments. ... ok test_getitem_multiple (test_SearchIO_model.HitCases.test_getitem_multiple) Test Hit.__getitem__, multiple items. ... ok test_getitem_single (test_SearchIO_model.HitCases.test_getitem_single) Test Hit.__getitem__, single item. ... ok test_hsp_map_no_func (test_SearchIO_model.HitCases.test_hsp_map_no_func) Test Hit.map, without arguments. ... ok test_hsps (test_SearchIO_model.HitCases.test_hsps) Test Hit.hsps. ... ok test_id_set (test_SearchIO_model.HitCases.test_id_set) Test Hit.id setter. ... ok test_index (test_SearchIO_model.HitCases.test_index) Test Hit.index. ... ok test_index_not_present (test_SearchIO_model.HitCases.test_index_not_present) Test Hit.index, when index is not present. ... ok test_init_hsps_only (test_SearchIO_model.HitCases.test_init_hsps_only) Test Hit.__init__, with hsps only. ... ok test_init_id_only (test_SearchIO_model.HitCases.test_init_id_only) Test Hit.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.HitCases.test_init_none) Test Hit.__init__, no arguments. ... ok test_item_multiple (test_SearchIO_model.HitCases.test_item_multiple) Test Hit.__setitem__, multiple items. ... ok test_iter (test_SearchIO_model.HitCases.test_iter) Test Hit.__iter__. ... ok test_len (test_SearchIO_model.HitCases.test_len) Test Hit.__len__. ... ok test_map (test_SearchIO_model.HitCases.test_map) Test Hit.hsp_map. ... ok test_pickle (test_SearchIO_model.HitCases.test_pickle) Test pickling and unpickling of Hit. ... ok test_pop (test_SearchIO_model.HitCases.test_pop) Test Hit.pop. ... ok test_repr (test_SearchIO_model.HitCases.test_repr) Test Hit.__repr__. ... ok test_setitem_single (test_SearchIO_model.HitCases.test_setitem_single) Test Hit.__setitem__, single item. ... ok test_sort (test_SearchIO_model.HitCases.test_sort) Test Hit.sort. ... ok test_sort_not_in_place (test_SearchIO_model.HitCases.test_sort_not_in_place) Test Hit.sort, not in place. ... ok test_validate_hsp_ok (test_SearchIO_model.HitCases.test_validate_hsp_ok) Test Hit._validate_hsp. ... ok test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_hit_id) Test Hit._validate_hsp, wrong hit ID. ... ok test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases.test_validate_hsp_wrong_query_id) Test Hit._validate_hsp, wrong query ID. ... ok test_validate_hsp_wrong_type (test_SearchIO_model.HitCases.test_validate_hsp_wrong_type) Test Hit._validate_hsp, wrong type. ... ok test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases.test_absorb_hit_does_not_exist) Test QueryResult.absorb, hit does not exist. ... ok test_absorb_hit_exists (test_SearchIO_model.QueryResultCases.test_absorb_hit_exists) Test QueryResult.absorb, hit with the same ID exists. ... ok test_append_alt_id_exists (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists) Test QueryResult.append, when alt ID exists. ... ok test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases.test_append_alt_id_exists_alt) Test QueryResult.append, when alt ID exists as primary. ... ok test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases.test_append_custom_hit_key_function_ok) Test QueryResult.append, with custom hit key function. ... ok test_append_id_exists (test_SearchIO_model.QueryResultCases.test_append_id_exists) Test QueryResult.append, when ID exists. ... ok test_append_ok (test_SearchIO_model.QueryResultCases.test_append_ok) Test QueryResult.append. ... ok test_bool (test_SearchIO_model.QueryResultCases.test_bool) Test QueryResult.__bool__. ... ok test_contains (test_SearchIO_model.QueryResultCases.test_contains) Test QueryResult.__contains__. ... ok test_contains_alt (test_SearchIO_model.QueryResultCases.test_contains_alt) Test QueryResult.__contains__, with alternative IDs. ... ok test_delitem_alt_ok (test_SearchIO_model.QueryResultCases.test_delitem_alt_ok) Test QueryResult.__delitem__, with alt ID. ... ok test_delitem_int_ok (test_SearchIO_model.QueryResultCases.test_delitem_int_ok) Test QueryResult.__delitem__. ... ok test_delitem_slice_ok (test_SearchIO_model.QueryResultCases.test_delitem_slice_ok) Test QueryResult.__delitem__, with slice. ... ok test_delitem_string_ok (test_SearchIO_model.QueryResultCases.test_delitem_string_ok) Test QueryResult.__getitem__, with string. ... ok test_description_set (test_SearchIO_model.QueryResultCases.test_description_set) Test QueryResult.description setter. ... ok test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases.test_description_set_no_seqrecord) Test QueryResult.description setter, without HSP SeqRecords. ... ok test_fragments (test_SearchIO_model.QueryResultCases.test_fragments) Test QueryResult.fragments. ... ok test_getitem_alt_ok (test_SearchIO_model.QueryResultCases.test_getitem_alt_ok) Test QueryResult.__getitem__, single item with alternative ID. ... ok test_getitem_default_ok (test_SearchIO_model.QueryResultCases.test_getitem_default_ok) Test QueryResult.__getitem__. ... ok test_getitem_int_ok (test_SearchIO_model.QueryResultCases.test_getitem_int_ok) Test QueryResult.__getitem__, with integer. ... ok test_getitem_slice_ok (test_SearchIO_model.QueryResultCases.test_getitem_slice_ok) Test QueryResult.__getitem__, with slice. ... ok test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases.test_getitm_slice_alt_ok) Test QueryResult.__getitem__, with slice and alt IDs. ... ok test_hit_filter (test_SearchIO_model.QueryResultCases.test_hit_filter) Test QueryResult.hit_filter. ... ok test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hit_filter_no_filtered) Test QueryResult.hit_filter, all hits filtered out. ... ok test_hit_filter_no_func (test_SearchIO_model.QueryResultCases.test_hit_filter_no_func) Test QueryResult.hit_filter, without arguments. ... ok test_hit_keys (test_SearchIO_model.QueryResultCases.test_hit_keys) Test QueryResult.hit_keys. ... ok test_hit_map (test_SearchIO_model.QueryResultCases.test_hit_map) Test QueryResult.hit_map. ... ok test_hit_map_no_func (test_SearchIO_model.QueryResultCases.test_hit_map_no_func) Test QueryResult.hit_map, without arguments. ... ok test_hits (test_SearchIO_model.QueryResultCases.test_hits) Test QueryResult.hits. ... ok test_hsp_filter (test_SearchIO_model.QueryResultCases.test_hsp_filter) Test QueryResult.hsp_filter. ... ok test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_filtered) Test QueryResult.hsp_filter, all hits filtered out. ... ok test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases.test_hsp_filter_no_func) Test QueryResult.hsp_filter, no arguments. ... ok test_hsp_map (test_SearchIO_model.QueryResultCases.test_hsp_map) Test QueryResult.hsp_map. ... ok test_hsp_map_no_func (test_SearchIO_model.QueryResultCases.test_hsp_map_no_func) Test QueryResult.hsp_map, without arguments. ... ok test_hsps (test_SearchIO_model.QueryResultCases.test_hsps) Test QueryResult.hsps. ... ok test_id_set (test_SearchIO_model.QueryResultCases.test_id_set) Test QueryResult.id setter. ... ok test_index (test_SearchIO_model.QueryResultCases.test_index) Test QueryResult.index. ... ok test_index_alt (test_SearchIO_model.QueryResultCases.test_index_alt) Test QueryResult.index, with alt ID. ... ok test_index_not_present (test_SearchIO_model.QueryResultCases.test_index_not_present) Test QueryResult.index, when index is not present. ... ok test_init_hits_only (test_SearchIO_model.QueryResultCases.test_init_hits_only) Test QueryResult.__init__, with hits only. ... ok test_init_id_only (test_SearchIO_model.QueryResultCases.test_init_id_only) Test QueryResult.__init__, with ID only. ... ok test_init_none (test_SearchIO_model.QueryResultCases.test_init_none) Test QueryResult.__init__, no arguments. ... ok test_items (test_SearchIO_model.QueryResultCases.test_items) Test QueryResult.items. ... ok test_iter (test_SearchIO_model.QueryResultCases.test_iter) Test QueryResult.__iter__. ... ok test_len (test_SearchIO_model.QueryResultCases.test_len) Test QueryResult.__len__. ... ok test_order (test_SearchIO_model.QueryResultCases.test_order) ... ok test_pickle (test_SearchIO_model.QueryResultCases.test_pickle) Test pickling and unpickling of QueryResult. ... ok test_pop_int_index_ok (test_SearchIO_model.QueryResultCases.test_pop_int_index_ok) Test QueryResult.pop, with integer index. ... ok test_pop_nonexistent_key (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_key) Test QueryResult.pop with default for nonexistent key. ... ok test_pop_nonexistent_with_default (test_SearchIO_model.QueryResultCases.test_pop_nonexistent_with_default) Test QueryResult.pop with default for nonexistent key. ... ok test_pop_ok (test_SearchIO_model.QueryResultCases.test_pop_ok) Test QueryResult.pop. ... ok test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases.test_pop_string_alt_ok) Test QueryResult.pop, with alternative ID. ... ok test_pop_string_index_ok (test_SearchIO_model.QueryResultCases.test_pop_string_index_ok) Test QueryResult.pop, with string index. ... ok test_repr (test_SearchIO_model.QueryResultCases.test_repr) Test QueryResult.__repr__. ... ok test_setitem_from_empty (test_SearchIO_model.QueryResultCases.test_setitem_from_empty) Test QueryResult.__setitem__, from empty container. ... ok test_setitem_ok (test_SearchIO_model.QueryResultCases.test_setitem_ok) Test QueryResult.__setitem__. ... ok test_setitem_ok_alt (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt) Test QueryResult.__setitem__, checking alt hit IDs. ... ok test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_existing) Test QueryResult.__setitem__, existing key. ... ok test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases.test_setitem_ok_alt_ok_promote) Test QueryResult.__setitem__, previously alt ID. ... ok test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_key_type) Test QueryResult.__setitem__, wrong key type. ... ok test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases.test_setitem_wrong_query_id) Test QueryResult.__setitem__, wrong query ID. ... ok test_setitem_wrong_type (test_SearchIO_model.QueryResultCases.test_setitem_wrong_type) Test QueryResult.__setitem__, wrong type. ... ok test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_key_not_in_place_ok) Test QueryResult.sort, with custom key, not in place. ... ok test_sort_key_ok (test_SearchIO_model.QueryResultCases.test_sort_key_ok) Test QueryResult.sort, with custom key. ... ok test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_not_in_place_ok) Test QueryResult.sort, not in place. ... ok test_sort_ok (test_SearchIO_model.QueryResultCases.test_sort_ok) Test QueryResult.sort. ... ok test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_not_in_place_ok) Test QueryResult.sort, reverse, not in place. ... ok test_sort_reverse_ok (test_SearchIO_model.QueryResultCases.test_sort_reverse_ok) Test QueryResult.sort, reverse. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py test_SearchIO_write ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SearchIO/_legacy/__init__.py:12: BiopythonDeprecationWarning: The 'Bio.SearchIO._legacy' module for parsing BLAST plain text output is deprecated and will be removed in a future release of Biopython. Consider generating your BLAST output for parsing as XML or tabular format instead. warnings.warn( ok test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt). ... ok test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt). ... ok test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases.test_write_multiple_from_blasttabc_allfields) Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt). ... ok test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttab) Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt). ... ok test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases.test_write_single_from_blasttabc) Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt). ... ok test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_multiple_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml). ... ok test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases.test_write_single_from_blastxml) Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml). ... ok test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpsl) Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl). ... ok test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_multiple_from_blatpslx) Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx). ... ok test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl) Test blat-psl writing from blat-psl, single query (psl_34_004.psl). ... ok test_write_single_from_blatpsl_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpsl_protein_query) Test blat-psl writing from blat-psl, single query (psl_35_002.psl). ... ok test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx) Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx). ... ok test_write_single_from_blatpslx_protein_query (test_SearchIO_write.BlatPslWriteCases.test_write_single_from_blatpslx_protein_query) Test blat-pslx writing from blat-pslx, single query (pslx_35_002.pslx). ... ok test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_multiple_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmscandomtab) Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases.test_write_single_from_hmmsearchdomtab) Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_multiple_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out). ... ok test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases.test_write_single_from_hmmertab) Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.225 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqFeature.py test_SeqFeature ... ok test_eq_identical (test_SeqFeature.TestCompoundLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestCompoundLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_reference_in_compound_location_record (test_SeqFeature.TestExtract.test_reference_in_compound_location_record) Test compound location with reference to another record. ... ok test_reference_in_compound_location_sequence (test_SeqFeature.TestExtract.test_reference_in_compound_location_sequence) Test compound location with reference to another sequence. ... ok test_reference_in_location_record (test_SeqFeature.TestExtract.test_reference_in_location_record) Test location with reference to another record. ... ok test_reference_in_location_sequence (test_SeqFeature.TestExtract.test_reference_in_location_sequence) Test location with reference to another sequence. ... ok test_fuzzy (test_SeqFeature.TestLocations.test_fuzzy) Test fuzzy representations. ... ok test_pickle (test_SeqFeature.TestPositions.test_pickle) Test pickle behaviour of position instances. ... ok test_eq_identical (test_SeqFeature.TestReference.test_eq_identical) Test two identical references eq() to True. ... ok test_eq_identical (test_SeqFeature.TestSeqFeature.test_eq_identical) ... ok test_translation_checks_cds (test_SeqFeature.TestSeqFeature.test_translation_checks_cds) Test that a CDS feature is subject to respective checks. ... ok test_eq_identical (test_SeqFeature.TestSimpleLocation.test_eq_identical) Test two identical locations are equal. ... ok test_eq_not_identical (test_SeqFeature.TestSimpleLocation.test_eq_not_identical) Test two different locations are not equal. ... ok test_offsets (test_SeqFeature.TestSimpleLocation.test_offsets) Test adding and subtracting integer offsets. ... ok test_start_before_end (test_SeqFeature.TestSimpleLocation.test_start_before_end) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.074 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py C test_SeqIO ... ok test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type) Convert Clustal to NEXUS with molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type) Convert Clustal to NEXUS without molecule type. ... ok test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok test_embl13 (test_SeqIO.TestSeqIO.test_embl13) Test parsing embl file with wrapped locations and unspecified type. ... ok test_embl14 (test_SeqIO.TestSeqIO.test_embl14) Test parsing file with features over-indented for EMBL. ... ok test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok test_empty_file (test_SeqIO.TestSeqIO.test_empty_file) Check parsers can cope with an empty file. ... ok test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type) Convert FASTA to SeqXML with molecule type. ... ok test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type) Convert FASTA to SeqXML without molecule type. ... ok test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16) Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20) Test parsing GenPept file with nasty bond locations. ... ok test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22) Test that genbank format write doesn't destroy db_source in annotations. ... ok test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23) Test that peptide genbank files can be written with long names. ... ok test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok test_ig3 (test_SeqIO.TestSeqIO.test_ig3) Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1) Test parsing file with features over-indented for EMBL. ... ok test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta) Testing FASTA with gzip. ... ok test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq) Testing FASTQ with gzip. ... ok test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank) Testing GenBank with gzip. ... ok ---------------------------------------------------------------------- Ran 1 test in 14.980 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py test_SeqIO_AbiIO ... ok test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type) Test if filetype is ABIF. ... ok test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1) Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok test_raw (test_SeqIO_AbiIO.TestAbi.test_raw) Test access to raw ABIF tags. ... ok test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord) Test if the extracted seqrecords data are equal to expected values. ... ok test_trim (test_SeqIO_AbiIO.TestAbi.test_trim) Test if trim works. ... ok test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type) Test if error is raised if filetype is not ABIF. ... ok test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag) Test that we can handle non-ascii tags. ... ok test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode) Test if exception is raised if file is not opened in 'rb' mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.297 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py test_SeqIO_FastaIO ... ok test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser) Test FastaTwoLineParser edge-cases. ... ok test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser) Test SimpleFastaParser edge-cases. ... ok test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser) Test FastaTwoLineParser exceptions. ... ok test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser) Test regular FastaTwoLineParser cases. ... ok test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser) Test regular SimpleFastaParser cases. ... ok test_multi_dna_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_dna_files) Test Fasta files containing multiple nucleotide sequences. ... ok test_multi_protein_files (test_SeqIO_FastaIO.TitleFunctions.test_multi_protein_files) Test Fasta files containing multiple protein sequences. ... ok test_no_name (test_SeqIO_FastaIO.TitleFunctions.test_no_name) Test FASTA record with no identifier. ... ok test_single_nucleic_files (test_SeqIO_FastaIO.TitleFunctions.test_single_nucleic_files) Test Fasta files containing a single nucleotide sequence. ... ok test_single_proteino_files (test_SeqIO_FastaIO.TitleFunctions.test_single_proteino_files) Test Fasta files containing a single protein sequence. ... ok test_fails (test_SeqIO_FastaIO.Wrapping.test_fails) Test case which should fail. ... ok test_passes (test_SeqIO_FastaIO.Wrapping.test_passes) Test case which should pass. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py test_SeqIO_Gck ... ok test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths) Read a file with incorrect length. ... ok test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read) Read an artificial sample file. ... ok test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read) Read a file with an incomplete header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/GenBank/Scanner.py:303: BiopythonParserWarning: Non-standard feature line wrapping (didn't break on comma)? warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) ok test_conversion (test_SeqIO_Insdc.ConvertTestsInsdc.test_conversion) Test format conversion by SeqIO.write/SeqIO.parse and SeqIO.convert. ... ok test_annotation1 (test_SeqIO_Insdc.TestEmbl.test_annotation1) Check parsing of annotation from EMBL files (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmbl.test_annotation2) Check parsing of annotation from EMBL files (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmbl.test_annotation3) Check parsing of annotation from EMBL files (3). ... ok test_annotation4 (test_SeqIO_Insdc.TestEmbl.test_annotation4) Check parsing of annotation from EMBL files (4). ... ok test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl.test_writing_empty_qualifiers) ... ok test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation1) Check writing-and-parsing EMBL file (1). ... ok test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation2) Check writing-and-parsing EMBL file (2). ... ok test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite.test_annotation3) Check writing-and-parsing EMBL file (3). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py test_SeqIO_NibIO ... ok test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.072 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py test_SeqIO_PdbIO ... ok test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader) Read a single-chain CIF without a header by ATOM entries. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader) Parse a PDB with no HEADER line. ... ok test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader) Read a single-chain PDB without a header by ATOM entries. ... ok test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion) Read a PDB with residue insertion code. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.979 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py test_SeqIO_QualityIO ... ok test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger) Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa) Mapping check for function phred_quality_from_solexa. ... ok test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina) Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa) Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred) Mapping check for function solexa_quality_from_phred. ... ok test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger) Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta) Check FASTQ parsing matches FASTA parsing. ... ok test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out) Check FASTQ to FASTA output. ... ok test_paired (test_SeqIO_QualityIO.TestQual.test_paired) Check FASTQ parsing matches FASTA+QUAL parsing. ... ok test_qual (test_SeqIO_QualityIO.TestQual.test_qual) Check FASTQ parsing matches QUAL parsing. ... ok test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative) Check QUAL negative scores mapped to PHRED zero. ... ok test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out) Check FASTQ to QUAL output. ... ok test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000) Read and write back simple example with mixed case 1000bp read. ... ok test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000) Read and write back simple example with upper case 2000bp read. ... ok test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna) Read and write back simple example with ambiguous DNA. ... ok test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna) Read and write back simple example with ambiguous RNA. ... ok test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end) Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start) Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle) Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end) Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start) Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest) Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original) Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02) Write and read back E3MFGYR02_random_10_reads.sff. ... ok test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end) Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start) Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle) Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start) Write and read back E3MFGYR02_index_at_start.sff. ... ok test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle) Write and read back E3MFGYR02_index_in_middle.sff. ... ok test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest) Write and read back E3MFGYR02_no_manifest.sff. ... ok test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed) Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta) Write and read back example.fasta. ... ok test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq) Write and read back example.fastq. ... ok test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual) Write and read back example.qual. ... ok test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated) Write and read back odd SeqRecord objects. ... ok test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff) Write and read back greek.sff. ... ok test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked) Write and read back illumina_faked.fastq. ... ok test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff) Write and read back paired.sff. ... ok test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93) Write and read back sanger_93.fastq. ... ok test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked) Write and read back sanger_faked.fastq. ... ok test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example) Write and read back solexa_example.fastq. ... ok test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked) Write and read back solexa_faked.fastq. ... ok test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky) Write and read back tricky.fastq. ... ok test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.357 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py test_SeqIO_SeqXML ... ok test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref) Read multiple cross references to a single source. ... ok test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property) Read property with multiple values. ... ok test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description) Check empty description. ... ok test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read) Read full characters set for each type. ... ok test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species) Check global species. ... ok test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition) Check local source. ... ok test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species) Check local species. ... ok test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required) Check minimal record. ... ok test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc) Read special XML characters in description. ... ok test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc) Test special unicode characters in the description. ... ok test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna) Read and write DNA. ... ok test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies) Read and write global species. ... ok test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein) Read and write protein. ... ok test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna) Read and write RNA. ... ok test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species) Test writing species from annotation tags. ... ok test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors) Handling of corrupt files. ... ok test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header) Check if the header information is parsed. ... ok test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header) Check if the header information is parsed. ... ok test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header) Check if the header information is parsed. ... ok test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header) Check if the header information is parsed. ... ok test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO) Files readable using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py test_SeqIO_SnapGene ... ok test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna) Read a file with supernumerary DNA packet. ... ok test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie) Read a file with missing or invalid cookie packet. ... ok test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna) Read a file without a DNA packet. ... ok test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet) Read a file with incomplete packet. ... ok test_read (test_SeqIO_SnapGene.TestSnapGene.test_read) Read sample files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_TwoBitIO.py test_SeqIO_TwoBitIO ... ok test_bigendian (test_SeqIO_TwoBitIO.Parsing.test_bigendian) ... ok test_littleendian (test_SeqIO_TwoBitIO.Parsing.test_littleendian) ... ok test_sequence_long (test_SeqIO_TwoBitIO.Parsing.test_sequence_long) ... ok test_add (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_add) ... ok test_bytes (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_bytes) ... ok test_contains (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_contains) ... ok test_count (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_count) ... ok test_defined (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_defined) ... ok test_endswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_endswith) ... ok test_find (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_find) ... ok test_getitem (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_getitem) ... ok test_hash (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_hash) ... ok test_index (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_index) ... ok test_islower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_islower) ... ok test_isupper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_isupper) ... ok test_lower (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lower) ... ok test_lstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_lstrip) ... ok test_mul (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_mul) ... ok test_radd (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_radd) ... ok test_replace (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_replace) ... ok test_repr (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_repr) ... ok test_rfind (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rfind) ... ok test_rindex (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rindex) ... ok test_rsplit (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_rstrip) ... ok test_split (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_split) ... ok test_startswith (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_startswith) ... ok test_str (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_str) ... ok test_strip (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_strip) ... ok test_translate (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_translate) ... ok test_upper (test_SeqIO_TwoBitIO.TestBaseClassMethods.test_upper) ... ok test_eq (test_SeqIO_TwoBitIO.TestComparisons.test_eq) ... ok test_ge (test_SeqIO_TwoBitIO.TestComparisons.test_ge) ... ok test_gt (test_SeqIO_TwoBitIO.TestComparisons.test_gt) ... ok test_le (test_SeqIO_TwoBitIO.TestComparisons.test_le) ... ok test_lt (test_SeqIO_TwoBitIO.TestComparisons.test_lt) ... ok test_ne (test_SeqIO_TwoBitIO.TestComparisons.test_ne) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.726 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py test_SeqIO_Xdna ... ok test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length) Read a file with incorrect length. ... ok test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type) Read a file with an unknown sequence type. ... ok test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features) Read a file with an incorrect number of features. ... ok test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version) Read a file with unexpected version number. ... ok test_read (test_SeqIO_Xdna.TestXdna.test_read) Read sample files. ... ok test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss) Emit warnings when dropping data on write. ... ok test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type) Write correct sequence type. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:1254: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/SeqIO/InsdcIO.py:550: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( ok test_after (test_SeqIO_features.FeatureWriting.test_after) Features: write/read simple after locations. ... ok test_before (test_SeqIO_features.FeatureWriting.test_before) Features: write/read simple before locations. ... ok test_between (test_SeqIO_features.FeatureWriting.test_between) GenBank/EMBL write/read simple between locations. ... ok test_exact (test_SeqIO_features.FeatureWriting.test_exact) GenBank/EMBL write/read simple exact locations. ... ok test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join) Features: write/read fuzzy join locations. ... ok test_join (test_SeqIO_features.FeatureWriting.test_join) GenBank/EMBL write/read simple join locations. ... ok test_oneof (test_SeqIO_features.FeatureWriting.test_oneof) Features: write/read simple one-of locations. ... ok test_unknown (test_SeqIO_features.FeatureWriting.test_unknown) GenBank/EMBL write/read with unknown end points. ... ok test_within (test_SeqIO_features.FeatureWriting.test_within) Features: write/read simple within locations. ... ok test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok test_CDS (test_SeqIO_features.NC_000932.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_CDS (test_SeqIO_features.NC_005816.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_Features (test_SeqIO_features.NC_005816.test_Features) Checking GenBank features sequences vs FASTA ffn file. ... ok test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok test_Genome (test_SeqIO_features.NC_005816.test_Genome) Checking GenBank sequence vs FASTA fna file. ... ok test_Translations (test_SeqIO_features.NC_005816.test_Translations) Checking translation of FASTA features (faa vs ffn). ... ok test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers) Pass in qualifiers to SeqFeatures. ... ok test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join) Feature on DNA (join, mixed strand). ... ok test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join) Feature on DNA (multi-join, mixed strand). ... ok test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between) Feature on protein (between location, zero length). ... ok test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join) Feature on protein (join). ... ok test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy) Feature on protein (fuzzy join). ... ok test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join) Feature on protein (multi-join). ... ok test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof) Feature on protein (one-of positions). ... ok test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple) Feature on protein (simple). ... ok test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna) Feature on DNA (simple, default strand). ... ok test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join) Feature on DNA (join, strand +1). ... ok test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after) Feature on DNA (join, strand -1, after position). ... ok test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before) Feature on DNA (join, strand -1, before position). ... ok test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus) Feature on DNA (join, strand -1). ... ok test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0) Feature on DNA (simple, strand 0). ... ok test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1) Feature on DNA (simple, strand +1). ... ok test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus) Feature on DNA (simple, strand -1). ... ok test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none) Feature on DNA (simple, strand None). ... ok test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna) Feature on RNA (simple, default strand). ... ok test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna) Feature on DNA (single letter, default strand). ... ok test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna) Feature on DNA (between location, zero length, default strand). ... ok test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end) Feature on DNA (between location at end, zero length, default strand). ... ok test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323) Write and read back AAA03323.embl. ... ok test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046) Write and read back AE017046.embl. ... ok test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited) Write and read back DD231055_edited.embl. ... ok test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs) Write and read back Human_contigs.embl. ... ok test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932) Write and read back NC_000932.gb. ... ok test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816) Write and read back NC_005816.gb. ... ok test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265) Write and read back NT_019265.gb. ... ok test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5) Write and read back SC10H5.embl. ... ok test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361) Write and read back TRBG361.embl. ... ok test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107) Write and read back U87107.embl. ... ok test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1) Write and read back arab1.gb. ... ok test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq) Write and read back blank_seq.gb. ... ok test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6) Write and read back cor6_6.gb. ... ok test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap) Write and read back dbsource_wrap.gb. ... ok test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords) Write and read back extra_keywords.gb. ... ok test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start) Write and read back gbvrl1_start.seq. ... ok test_noref (test_SeqIO_features.TestWriteRead.test_noref) Write and read back noref.gb. ... ok test_one_of (test_SeqIO_features.TestWriteRead.test_one_of) Write and read back of_one.gb. ... ok test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line) Write and read back origin_line.gb. ... ok test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1) Write and read back pri1.gb. ... ok test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq) Write and read back protein_refseq.gb. ... ok test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2) Write and read back protein_refseq2.gb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.459 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py test_SeqIO_index ... ok test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails) Reject alphabet argument in Bio.SeqIO.index(). ... ok test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db) Reject alphabet argument in Bio.SeqIO.index_db(). ... ok test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index) Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db) Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict) Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok test_raw_checks (test_SeqIO_index.IndexDictTests.test_raw_checks) ... ok test_simple_checks (test_SeqIO_index.IndexDictTests.test_simple_checks) ... ok test_order_index_db (test_SeqIO_index.IndexOrderingManyFiles.test_order_index_db) Check index_db preserves order in multiple indexed files. ... ok test_order_index (test_SeqIO_index.IndexOrderingSingleFile.test_order_index) Check index preserves order in indexed file. ... ok test_order_index_db (test_SeqIO_index.IndexOrderingSingleFile.test_order_index_db) Check index_db preserves ordering indexed file. ... ok test_order_to_dict (test_SeqIO_index.IndexOrderingSingleFile.test_order_to_dict) Check to_dict preserves order in indexed file. ... ok test_child_folder_rel (test_SeqIO_index.NewIndexTest.test_child_folder_rel) Check relative links to child folder. ... ok test_same_folder (test_SeqIO_index.NewIndexTest.test_same_folder) Check relative links in same folder. ... ok test_some_abs (test_SeqIO_index.NewIndexTest.test_some_abs) Check absolute filenames in index. ... ok test_old (test_SeqIO_index.OldIndexTest.test_old) Load existing index with no options (from parent directory). ... ok test_old_check_same_thread (test_SeqIO_index.OldIndexTest.test_old_check_same_thread) Setting check_same_thread to False doesn't raise an exception. ... ok test_old_contents (test_SeqIO_index.OldIndexTest.test_old_contents) Check actual filenames in existing indexes. ... ok test_old_files (test_SeqIO_index.OldIndexTest.test_old_files) Load existing index with correct files (from parent directory). ... ok test_old_files_same_dir (test_SeqIO_index.OldIndexTest.test_old_files_same_dir) Load existing index with correct files (from same directory). ... ok test_old_files_wrong (test_SeqIO_index.OldIndexTest.test_old_files_wrong) Load existing index with wrong files. ... ok test_old_files_wrong2 (test_SeqIO_index.OldIndexTest.test_old_files_wrong2) Load existing index with wrong number of files. ... ok test_old_format (test_SeqIO_index.OldIndexTest.test_old_format) Load existing index with correct format. ... ok test_old_format_wrong (test_SeqIO_index.OldIndexTest.test_old_format_wrong) Load existing index with wrong format. ... ok test_old_rel (test_SeqIO_index.OldIndexTest.test_old_rel) Load existing index (with relative paths) with no options (from parent directory). ... ok test_old_same_dir (test_SeqIO_index.OldIndexTest.test_old_same_dir) Load existing index with no options (from same directory). ... ok test_old_same_dir_rel (test_SeqIO_index.OldIndexTest.test_old_same_dir_rel) Load existing index (with relative paths) with no options (from same directory). ... ok ---------------------------------------------------------------------- Ran 1 test in 6.302 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_online.py test_SeqIO_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py C test_SeqIO_write ... ok test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py test_SeqRecord ... ok test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations) Pass in annotations to SeqRecords. ... ok test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations) Pass in letter annotations to SeqRecords. ... ok test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq) Replacing .seq if .letter_annotation present. ... ok test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq) Simple addition of Seq or string. ... ok test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left) Simple left addition of Seq or string. ... ok test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord) Simple left addition of SeqRecord from genbank file. ... ok test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple) Simple addition. ... ok test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift) Simple slice and add to shift. ... ok test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple) Simple slice and add. ... ok test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple) Simple slice. ... ok test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants) Simple slices using different start/end values. ... ok test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero) Zero slice. ... ok test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.123 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py test_SeqUtils ... ok test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok test_codon_adaptation_index (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index) ... ok test_codon_adaptation_index_calculation (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_calculation) Test Codon Adaptation Index (CAI) calculation for an mRNA. ... ok test_codon_adaptation_index_initialization (test_SeqUtils.SeqUtilsTests.test_codon_adaptation_index_initialization) Test Codon Adaptation Index (CAI) initialization from sequences. ... ok test_codon_usage_custom_old (test_SeqUtils.SeqUtilsTests.test_codon_usage_custom_old) Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests.test_codon_usage_ecoli) Test Codon Adaptation Index (CAI) using default E. coli data. ... ok test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests.test_crc_checksum_collision) ... ok test_gc_fraction (test_SeqUtils.SeqUtilsTests.test_gc_fraction) Tests gc_fraction function. ... ok test_lcc_mult (test_SeqUtils.SeqUtilsTests.test_lcc_mult) ... ok test_lcc_simp (test_SeqUtils.SeqUtilsTests.test_lcc_simp) ... ok test_seq1_seq3 (test_SeqUtils.SeqUtilsTests.test_seq1_seq3) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.154 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py test_Seq_objs ... ok test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok test_le (test_Seq_objs.ComparisonTests.test_le) ... ok test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq) Test if feature extraction works properly for unknown sequences. ... ok test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend) Check extending a MutableSeq object. ... ok test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error) Check MutableSeq __init__ raises the appropriate exceptions. ... ok test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem) Check setting sequence contents of a MutableSeq object. ... ok test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error) Check Seq __init__ raises the appropriate exceptions. ... ok test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap) Check count_overlap exception matches python string count method. ... ok test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG) Check our count_overlap method using GG with variable ends and starts. ... ok test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN) Check our count_overlap method using NN with variable ends and starts. ... ok test_equality (test_Seq_objs.StringMethodTests.test_equality) Test equality when mixing types. ... ok test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq) Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed) Check MutableSeq objects can be joined. ... ok test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file) Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq) Checks if Seq join correctly concatenates sequence with the spacer. ... ok test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file) Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok test_join_UnknownSeq (test_Seq_objs.StringMethodTests.test_join_UnknownSeq) Checks if UnknownSeq join correctly concatenates sequence with the spacer. ... ok test_join_UnknownSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_UnknownSeq_with_file (test_Seq_objs.StringMethodTests.test_join_UnknownSeq_with_file) Checks if UnknownSeq join correctly concatenates sequence from a file with the spacer. ... ok test_str_comparison (test_Seq_objs.StringMethodTests.test_str_comparison) ... ok test_str_count (test_Seq_objs.StringMethodTests.test_str_count) Check matches the python string count method. ... ok test_str_count_overlap_GG (test_Seq_objs.StringMethodTests.test_str_count_overlap_GG) Check our count_overlap method using GG. ... ok test_str_count_overlap_NN (test_Seq_objs.StringMethodTests.test_str_count_overlap_NN) Check our count_overlap method using NN. ... ok test_str_encode (test_Seq_objs.StringMethodTests.test_str_encode) Check matches the python string encode method. ... ok test_str_endswith (test_Seq_objs.StringMethodTests.test_str_endswith) Check matches the python string endswith method. ... ok test_str_find (test_Seq_objs.StringMethodTests.test_str_find) Check matches the python string find method. ... ok test_str_getitem (test_Seq_objs.StringMethodTests.test_str_getitem) Check slicing and indexing works like a string. ... ok test_str_hash (test_Seq_objs.StringMethodTests.test_str_hash) ... ok test_str_index (test_Seq_objs.StringMethodTests.test_str_index) Check matches the python string index method. ... ok test_str_islower (test_Seq_objs.StringMethodTests.test_str_islower) Check matches the python string islower method. ... ok test_str_isupper (test_Seq_objs.StringMethodTests.test_str_isupper) Check matches the python string isupper method. ... ok test_str_length (test_Seq_objs.StringMethodTests.test_str_length) Check matches the python string __len__ method. ... ok test_str_lower (test_Seq_objs.StringMethodTests.test_str_lower) Check matches the python string lower method. ... ok test_str_lstrip (test_Seq_objs.StringMethodTests.test_str_lstrip) Check matches the python string lstrip method. ... ok test_str_replace (test_Seq_objs.StringMethodTests.test_str_replace) Check matches the python string replace method. ... ok test_str_rfind (test_Seq_objs.StringMethodTests.test_str_rfind) Check matches the python string rfind method. ... ok test_str_rindex (test_Seq_objs.StringMethodTests.test_str_rindex) Check matches the python string rindex method. ... ok test_str_rsplit (test_Seq_objs.StringMethodTests.test_str_rsplit) Check matches the python string rsplit method. ... ok test_str_rstrip (test_Seq_objs.StringMethodTests.test_str_rstrip) Check matches the python string rstrip method. ... ok test_str_split (test_Seq_objs.StringMethodTests.test_str_split) Check matches the python string split method. ... ok test_str_startswith (test_Seq_objs.StringMethodTests.test_str_startswith) Check matches the python string startswith method. ... ok test_str_strip (test_Seq_objs.StringMethodTests.test_str_strip) Check matches the python string strip method. ... ok test_str_upper (test_Seq_objs.StringMethodTests.test_str_upper) Check matches the python string upper method. ... ok test_the_back_transcription (test_Seq_objs.StringMethodTests.test_the_back_transcription) Check obj.back_transcribe() method. ... ok test_the_complement (test_Seq_objs.StringMethodTests.test_the_complement) Check obj.complement() method. ... ok test_the_reverse_complement (test_Seq_objs.StringMethodTests.test_the_reverse_complement) Check obj.reverse_complement() method. ... ok test_the_transcription (test_Seq_objs.StringMethodTests.test_the_transcription) Check obj.transcribe() method. ... ok test_the_translate (test_Seq_objs.StringMethodTests.test_the_translate) Check obj.translate() method. ... ok test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_ambig_codons) Check obj.translate() method with ambiguous codons. ... ok test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests.test_the_translation_of_invalid_codons) Check obj.translate() method with invalid codons. ... ok test_the_translation_of_stops (test_Seq_objs.StringMethodTests.test_the_translation_of_stops) Check obj.translate() method with stop codons. ... ok test_tomutable (test_Seq_objs.StringMethodTests.test_tomutable) Check creating a MutableSeq object. ... ok test_toseq (test_Seq_objs.StringMethodTests.test_toseq) Check creating a Seq object. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.815 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SffIO.py test_SffIO ... ok test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok test_empty (test_SffIO.TestErrors.test_empty) ... ok test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok test_no_index (test_SffIO.TestErrors.test_no_index) ... ok test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok test_manifest (test_SffIO.TestIndex.test_manifest) ... ok test_index (test_SffIO.TestSelf.test_index) ... ok test_read (test_SffIO.TestSelf.test_read) ... ok test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok test_write (test_SffIO.TestSelf.test_write) ... ok test_coords (test_SffIO.TestUAN.test_coords) ... ok test_region (test_SffIO.TestUAN.test_region) ... ok test_time (test_SffIO.TestUAN.test_time) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py test_SwissProt ... ok test_O23729 (test_SwissProt.TestSwissProt.test_O23729) Parsing SwissProt file O23729.txt. ... ok test_O95832 (test_SwissProt.TestSwissProt.test_O95832) Parsing SwissProt file O95832.txt. ... ok test_P04439 (test_SwissProt.TestSwissProt.test_P04439) Parsing SwissProt file P04439.txt. ... ok test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186) Parsing SwissProt file P0A186.txt. ... ok test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95) Parsing SwissProt file P0CK95.txt. ... ok test_P16235 (test_SwissProt.TestSwissProt.test_P16235) Parsing SwissProt file P16235.txt. ... ok test_P39896 (test_SwissProt.TestSwissProt.test_P39896) Parsing SwissProt file P39896.txt. ... ok test_P60137 (test_SwissProt.TestSwissProt.test_P60137) Parsing SwissProt file P60137.txt. ... ok test_P60904 (test_SwissProt.TestSwissProt.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P62258 (test_SwissProt.TestSwissProt.test_P62258) Parsing SwissProt file P62258. ... ok test_P68308 (test_SwissProt.TestSwissProt.test_P68308) Parsing SwissProt file P68308.txt. ... ok test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454) Parsing SwissProt file Q13454.txt. ... ok test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639) Parsing SwissProt file Q13639. ... ok test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739) Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok test_ft_line (test_SwissProt.TestSwissProt.test_ft_line) Parsing SwissProt file O23729, which has a new-style FT line. ... ok test_sp012 (test_SwissProt.TestSwissProt.test_sp012) Parsing SwissProt file sp012. ... ok test_sp013 (test_SwissProt.TestSwissProt.test_sp013) Parsing SwissProt file sp013. ... ok test_sp015 (test_SwissProt.TestSwissProt.test_sp015) Parsing SwissProt file sp015. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.171 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py test_TogoWS ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.069 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py test_TreeConstruction ... ok test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.261 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniGene.py test_UniGene ... ok test_parse (test_UniGene.TestUniGene.test_parse) ... ok test_read (test_UniGene.TestUniGene.test_read) ... ok test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.026 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniProt_GOA.py test_UniProt_GOA ... ok test_gaf_iterator (test_UniProt_GOA.GoaTests.test_gaf_iterator) Test GOA GAF file iterator. ... ok test_gpa_iterator (test_UniProt_GOA.GoaTests.test_gpa_iterator) Test GOA GPA file iterator. ... ok test_gpi_iterator (test_UniProt_GOA.GoaTests.test_gpi_iterator) Test GOA GPI file iterator, gpi-version: 1.1. ... ok test_gpi_iterator_one_two (test_UniProt_GOA.GoaTests.test_gpi_iterator_one_two) Test GOA GPI file iterator, gpi-version: 1.2. ... ok test_selection_writing (test_UniProt_GOA.GoaTests.test_selection_writing) Test record_has, and writerec. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.029 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py test_Uniprot ... ok test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6) Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8) Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok test_P60904 (test_Uniprot.TestUniprot.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P84001 (test_Uniprot.TestUniprot.test_P84001) Parse mass spec structured comment with unknown loc. ... ok test_Q13639 (test_Uniprot.TestUniprot.test_Q13639) Compare SwissProt text and uniprot XML versions of Q13639. ... ok test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex) Compare SwissProt text and uniprot XML versions of several examples. ... ok test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index) Index SwissProt text and uniprot XML versions of several examples. ... ok test_sp016 (test_Uniprot.TestUniprot.test_sp016) Parsing SwissProt file sp016. ... ok test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed) Checks if parser supports new XML Element (submittedName). ... ok test_uni001 (test_Uniprot.TestUniprot.test_uni001) Parsing Uniprot file uni001. ... ok test_uni003 (test_Uniprot.TestUniprot.test_uni003) Parsing Uniprot file uni003. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.160 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` C + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Wise.py test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise. ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align.py test_align ... ok test_basic_alignment (test_align.TestBasics.test_basic_alignment) Basic tests on a simple alignment of three sequences. ... ok test_empty_alignment (test_align.TestBasics.test_empty_alignment) Very simple tests on an empty alignment. ... ok test_format_conversion (test_align.TestReading.test_format_conversion) Parse the alignment file and get an alignment object. ... ok test_read_clustal1 (test_align.TestReading.test_read_clustal1) Parse an alignment file and get an alignment object. ... ok test_read_clustal2 (test_align.TestReading.test_read_clustal2) Parse an alignment file and get an alignment object. ... ok test_read_fasta (test_align.TestReading.test_read_fasta) ... ok test_read_write_clustal (test_align.TestReading.test_read_write_clustal) Test the base alignment stuff. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_align_substitution_matrices.py test_align_substitution_matrices ... ok test_basics_matrix (test_align_substitution_matrices.TestBasics.test_basics_matrix) Test basic matrix operations. ... ok test_basics_vector (test_align_substitution_matrices.TestBasics.test_basics_vector) Test basic vector operations. ... ok test_nucleotide_freq (test_align_substitution_matrices.TestBasics.test_nucleotide_freq) Test nucleotide frequency calculations. ... ok test_pickling (test_align_substitution_matrices.TestBasics.test_pickling) Test pickling a substitution matrix. ... ok test_protein_freq (test_align_substitution_matrices.TestBasics.test_protein_freq) Test amino acid frequency calculations. ... ok test_read_write (test_align_substitution_matrices.TestBasics.test_read_write) Test reading and writing substitution matrices. ... ok test_loading (test_align_substitution_matrices.TestLoading.test_loading) Confirm that all provided substitution matrices can be loaded. ... ok test1_observed_frequencies (test_align_substitution_matrices.TestScoringMatrices.test1_observed_frequencies) Test calculating substitution frequencies. ... ok test2_observed_probabilities (test_align_substitution_matrices.TestScoringMatrices.test2_observed_probabilities) Test calculating substitution probabilities. ... ok test3_observed_symmetric_probabilities (test_align_substitution_matrices.TestScoringMatrices.test3_observed_symmetric_probabilities) Test symmetrizing substitution probabilities. ... ok test4_aminoacid_probabilities (test_align_substitution_matrices.TestScoringMatrices.test4_aminoacid_probabilities) Test calculating expected amino acid probabilities. ... ok test5_expected_probabilities (test_align_substitution_matrices.TestScoringMatrices.test5_expected_probabilities) Test calculating expected amino acid substitution probabilities. ... ok test6_scores (test_align_substitution_matrices.TestScoringMatrices.test6_scores) Test calculating amino acid substitution log-ratios. ... ok test_ident (test_align_substitution_matrices.TestScoringMatrices.test_ident) Test calculating the +6/-1 matrix as an approximation of BLOSUM62. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.362 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_cellosaurus.py test_cellosaurus ... ok test__str__ (test_cellosaurus.TestCellosaurus.test__str__) Test string function. ... ok test_parse (test_cellosaurus.TestCellosaurus.test_parse) Test parsing function. ... ok test_read (test_cellosaurus.TestCellosaurus.test_read) Test read function. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_codonalign.py test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/codonalignment.py:113: BiopythonWarning: Please make sure the two CodonAlignment objects are sharing the same codon table. This is not checked by Biopython. warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/Seq.py:3457: BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be translated as amino acid. warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:612: BiopythonWarning: start codon of pro1 (S 0) does not correspond to pro1 (TCA) warnings.warn( /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/codonalign/__init__.py:678: BiopythonWarning: start codon of pro2(S 0) does not correspond to pro2(TCA) warnings.warn( ok test_TypeError (test_codonalign.TestAddition.test_TypeError) Check that TypeError is thrown for non CodonAlignment/MultipleSequenceAlignment objects. ... ok test_ValueError (test_codonalign.TestAddition.test_ValueError) Check that ValueError is thrown for Alignments of different lengths. ... ok test_addition_CodonAlignment (test_codonalign.TestAddition.test_addition_CodonAlignment) Check addition of CodonAlignment and CodonAlignment. ... ok test_addition_MultipleSeqAlignment (test_codonalign.TestAddition.test_addition_MultipleSeqAlignment) Check addition of CodonAlignment and MultipleSeqAlignment. ... ok test_IO (test_codonalign.TestBuildAndIO.test_IO) ... ok test_align (test_codonalign.TestCodonAlignment.test_align) ... ok test_seq (test_codonalign.TestCodonSeq.test_seq) ... ok test_mk (test_codonalign.Test_MK.test_mk) ... ok test_build (test_codonalign.Test_build.test_build) ... ok test_dn_ds (test_codonalign.Test_dn_ds.test_dn_ds) ... ok test_dn_ds_matrix (test_codonalign.Test_dn_ds.test_dn_ds_matrix) ... ok ---------------------------------------------------------------------- Ran 1 test in 3.821 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_geo.py test_geo ... ok test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok test_record_str (test_geo.TestGeo.test_record_str) ... ok test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.057 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_kNN.py test_kNN ... ok test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok test_classify (test_kNN.TestKNN.test_classify) ... ok test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf.py test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.061 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.059 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs.py test_motifs ... ok test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok test_simple (test_motifs.MotifTestPWM.test_simple) Test if Bio.motifs PWM scoring works. ... ok test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char) Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case) Test if Bio.motifs PWM scoring works with mixed case. ... ok test_TFoutput (test_motifs.MotifTestsBasic.test_TFoutput) Ensure that we can write proper TransFac output files. ... ok test_alignace_parsing (test_motifs.MotifTestsBasic.test_alignace_parsing) Test if Bio.motifs can parse AlignAce output files. ... ok test_clusterbuster_parsing_and_output (test_motifs.MotifTestsBasic.test_clusterbuster_parsing_and_output) Test if Bio.motifs can parse and output Cluster Buster PFM files. ... ok test_format (test_motifs.MotifTestsBasic.test_format) ... ok test_pfm_four_columns_parsing (test_motifs.MotifTestsBasic.test_pfm_four_columns_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 columns). ... ok test_pfm_four_rows_parsing (test_motifs.MotifTestsBasic.test_pfm_four_rows_parsing) Test if Bio.motifs.pfm can parse motifs in position frequency matrix format (4 rows). ... ok test_pfm_parsing (test_motifs.MotifTestsBasic.test_pfm_parsing) Test if Bio.motifs can parse JASPAR-style pfm files. ... ok test_reverse_complement (test_motifs.MotifTestsBasic.test_reverse_complement) Test if motifs can be reverse-complemented. ... ok test_sites_parsing (test_motifs.MotifTestsBasic.test_sites_parsing) Test if Bio.motifs can parse JASPAR-style sites files. ... ok test_xms_parsing (test_motifs.MotifTestsBasic.test_xms_parsing) Test if Bio.motifs can parse and output xms PFM files. ... ok test_mast_parser_1 (test_motifs.TestMAST.test_mast_parser_1) Parse motifs/mast.crp0.de.oops.txt.xml file. ... ok test_mast_parser_2 (test_motifs.TestMAST.test_mast_parser_2) Parse motifs/mast.adh.de.oops.html.xml file. ... ok test_mast_parser_3 (test_motifs.TestMAST.test_mast_parser_3) Parse motifs/mast.Klf1-200.cd.oops.xml.xml file. ... ok test_meme_parser_1 (test_motifs.TestMEME.test_meme_parser_1) Parse motifs/meme.INO_up800.classic.oops.xml file. ... ok test_meme_parser_2 (test_motifs.TestMEME.test_meme_parser_2) Parsing motifs/meme.adh.classic.oops.xml file. ... ok test_meme_parser_3 (test_motifs.TestMEME.test_meme_parser_3) Parse motifs/meme.farntrans5.classic.anr.xml file. ... ok test_meme_parser_rna (test_motifs.TestMEME.test_meme_parser_rna) Test if Bio.motifs can parse MEME output files using RNA. ... ok test_minimal_meme_parser (test_motifs.TestMEME.test_minimal_meme_parser) Parse motifs/minimal_test.meme file. ... ok test_permissive_transfac_parser (test_motifs.TestTransfac.test_permissive_transfac_parser) Parse the TRANSFAC-like file motifs/MA0056.1.transfac. ... ok test_transfac_parser (test_motifs.TestTransfac.test_transfac_parser) Parse motifs/transfac.dat file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages C + /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py test_motifs_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.052 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.088 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux C + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.084 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py test_pairwise_alignment_map ... ok test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok test_internal (test_pairwise_alignment_map.TestSimple.test_internal) ... ok test_left_overhang (test_pairwise_alignment_map.TestSimple.test_left_overhang) ... ok test_reverse_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_sequence) ... ok test_reverse_transcript (test_pairwise_alignment_map.TestSimple.test_reverse_transcript) ... ok test_reverse_transcript_sequence (test_pairwise_alignment_map.TestSimple.test_reverse_transcript_sequence) ... ok test_right_overhang (test_pairwise_alignment_map.TestSimple.test_right_overhang) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype.py test_phenotype ... ok test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator) Test basic functionalities of CsvIterator file parser. ... ok test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator) Test basic functionalities of JsonIterator file parser. ... ok test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord) Test basic functionalities of PlateRecord objects. ... ok test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors) Test bad arguments with PlateRecord objects. ... ok test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord) Test basic functionalities of WellRecord objects. ... ok test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args) Test error handling of the fit method. ... ok test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO) Test basic functionalities of phenotype IO methods. ... ok test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors) Test bad arguments to phenotype IO methods. ... ok ---------------------------------------------------------------------- Ran 1 test in 6.940 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prodoc.py test_prodoc ... ok test_parse_pdoc (test_prodoc.TestProdocParse.test_parse_pdoc) Parsing an excerpt of prosite.doc. ... ok test_read_pdoc00100 (test_prodoc.TestProdocRead.test_read_pdoc00100) Reading Prodoc record PDOC00100. ... ok test_read_pdoc00113 (test_prodoc.TestProdocRead.test_read_pdoc00113) Reading Prodoc record PDOC00113. ... ok test_read_pdoc00144 (test_prodoc.TestProdocRead.test_read_pdoc00144) Reading Prodoc record PDOC00144. ... ok test_read_pdoc00149 (test_prodoc.TestProdocRead.test_read_pdoc00149) Reading Prodoc record PDOC00149. ... ok test_read_pdoc00340 (test_prodoc.TestProdocRead.test_read_pdoc00340) Reading Prodoc record PDOC00340. ... ok test_read_pdoc00424 (test_prodoc.TestProdocRead.test_read_pdoc00424) Reading Prodoc record PDOC00424. ... ok test_read_pdoc00472 (test_prodoc.TestProdocRead.test_read_pdoc00472) Reading Prodoc record PDOC00472. ... ok test_read_pdoc00640 (test_prodoc.TestProdocRead.test_read_pdoc00640) Reading Prodoc record PDOC00640. ... ok test_read_pdoc00787 (test_prodoc.TestProdocRead.test_read_pdoc00787) Reading Prodoc record PDOC00787. ... ok test_read_pdoc0933 (test_prodoc.TestProdocRead.test_read_pdoc0933) Reading Prodoc record PDOC00933. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prosite.py test_prosite ... ok test_read1 (test_prosite.TestPrositeRead.test_read1) Parsing Prosite record ps00107.txt. ... ok test_read2 (test_prosite.TestPrositeRead.test_read2) Parsing Prosite record ps00159.txt. ... ok test_read3 (test_prosite.TestPrositeRead.test_read3) Parsing Prosite record ps00165.txt. ... ok test_read4 (test_prosite.TestPrositeRead.test_read4) Parsing Prosite record ps00432.txt. ... ok test_read5 (test_prosite.TestPrositeRead.test_read5) Parsing Prosite record ps00488.txt. ... ok test_read6 (test_prosite.TestPrositeRead.test_read6) Parsing Prosite record ps00546.txt. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_seq.py test_seq ... ok test_ambiguous_values (test_seq.TestAmbiguousComplements.test_ambiguous_values) Test that other tests do not introduce characters to our values. ... ok test_mutable_seq (test_seq.TestAttributes.test_mutable_seq) ... ok test_seq (test_seq.TestAttributes.test_seq) ... ok test_complement_ambiguous_dna_values (test_seq.TestComplement.test_complement_ambiguous_dna_values) ... ok test_complement_ambiguous_rna_values (test_seq.TestComplement.test_complement_ambiguous_rna_values) ... ok test_complement_incompatible_letters (test_seq.TestComplement.test_complement_incompatible_letters) ... ok test_complement_of_dna (test_seq.TestComplement.test_complement_of_dna) ... ok test_complement_of_mixed_dna_rna (test_seq.TestComplement.test_complement_of_mixed_dna_rna) ... ok test_complement_of_rna (test_seq.TestComplement.test_complement_of_rna) ... ok test_immutable (test_seq.TestComplement.test_immutable) ... ok test_reverse_complements (test_seq.TestDoubleReverseComplement.test_reverse_complements) Test double reverse complement preserves the sequence. ... ok test_add_method (test_seq.TestMutableSeq.test_add_method) Test adding wrong type to MutableSeq. ... ok test_appending (test_seq.TestMutableSeq.test_appending) ... ok test_as_string (test_seq.TestMutableSeq.test_as_string) ... ok test_complement (test_seq.TestMutableSeq.test_complement) ... ok test_complement_dna_string (test_seq.TestMutableSeq.test_complement_dna_string) ... ok test_complement_mixed_aphabets (test_seq.TestMutableSeq.test_complement_mixed_aphabets) ... ok test_complement_old (test_seq.TestMutableSeq.test_complement_old) ... ok test_complement_rna (test_seq.TestMutableSeq.test_complement_rna) ... ok test_complement_rna_string (test_seq.TestMutableSeq.test_complement_rna_string) ... ok test_contains_method (test_seq.TestMutableSeq.test_contains_method) ... ok test_converting_to_immutable (test_seq.TestMutableSeq.test_converting_to_immutable) ... ok test_count (test_seq.TestMutableSeq.test_count) ... ok test_delete_stride_slice (test_seq.TestMutableSeq.test_delete_stride_slice) ... ok test_deleting_item (test_seq.TestMutableSeq.test_deleting_item) ... ok test_deleting_slice (test_seq.TestMutableSeq.test_deleting_slice) ... ok test_endswith (test_seq.TestMutableSeq.test_endswith) ... ok test_equal_comparison (test_seq.TestMutableSeq.test_equal_comparison) Test __eq__ comparison method. ... ok test_extend_method (test_seq.TestMutableSeq.test_extend_method) ... ok test_extend_with_mutable_seq (test_seq.TestMutableSeq.test_extend_with_mutable_seq) ... ok test_extract_third_nucleotide (test_seq.TestMutableSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestMutableSeq.test_first_nucleotide) ... ok test_greater_than_comparison (test_seq.TestMutableSeq.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_comparison_of_incompatible_types) ... ok test_greater_than_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_comparison_with_str) ... ok test_greater_than_or_equal_comparison (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_of_incompatible_types) ... ok test_greater_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_greater_than_or_equal_comparison_with_str) ... ok test_index (test_seq.TestMutableSeq.test_index) ... ok test_inserting (test_seq.TestMutableSeq.test_inserting) ... ok test_length (test_seq.TestMutableSeq.test_length) ... ok test_less_than_comparison (test_seq.TestMutableSeq.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_comparison_of_incompatible_types) ... ok test_less_than_comparison_with_str (test_seq.TestMutableSeq.test_less_than_comparison_with_str) ... ok test_less_than_or_equal_comparison (test_seq.TestMutableSeq.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_of_incompatible_types) ... ok test_less_than_or_equal_comparison_with_str (test_seq.TestMutableSeq.test_less_than_or_equal_comparison_with_str) ... ok test_mutableseq_construction (test_seq.TestMutableSeq.test_mutableseq_construction) Test MutableSeq object initialization. ... ok test_not_equal_comparison (test_seq.TestMutableSeq.test_not_equal_comparison) Test __ne__ comparison method. ... ok test_popping_last_item (test_seq.TestMutableSeq.test_popping_last_item) ... ok test_radd_method_wrong_type (test_seq.TestMutableSeq.test_radd_method_wrong_type) ... ok test_remove_items (test_seq.TestMutableSeq.test_remove_items) ... ok test_repr (test_seq.TestMutableSeq.test_repr) ... ok test_reverse (test_seq.TestMutableSeq.test_reverse) Test using reverse method. ... ok test_reverse_complement (test_seq.TestMutableSeq.test_reverse_complement) ... ok test_reverse_complement_old (test_seq.TestMutableSeq.test_reverse_complement_old) ... ok test_reverse_complement_rna (test_seq.TestMutableSeq.test_reverse_complement_rna) ... ok test_reverse_with_stride (test_seq.TestMutableSeq.test_reverse_with_stride) Test reverse using -1 stride. ... ok test_set_wobble_codon_to_n (test_seq.TestMutableSeq.test_set_wobble_codon_to_n) Test setting wobble codon to N (set slice with stride 3). ... ok test_setting_item (test_seq.TestMutableSeq.test_setting_item) ... ok test_setting_slices (test_seq.TestMutableSeq.test_setting_slices) ... ok test_startswith (test_seq.TestMutableSeq.test_startswith) ... ok test_transcribe (test_seq.TestMutableSeq.test_transcribe) ... ok test_truncated_repr (test_seq.TestMutableSeq.test_truncated_repr) ... ok test_immutable (test_seq.TestReverseComplement.test_immutable) ... ok test_reverse_complement (test_seq.TestReverseComplement.test_reverse_complement) ... ok test_reverse_complement_of_dna (test_seq.TestReverseComplement.test_reverse_complement_of_dna) ... ok test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement.test_reverse_complement_of_mixed_dna_rna) ... ok test_reverse_complement_of_rna (test_seq.TestReverseComplement.test_reverse_complement_of_rna) ... ok test_as_string (test_seq.TestSeq.test_as_string) Test converting Seq to string. ... ok test_cast_to_list (test_seq.TestSeq.test_cast_to_list) ... ok test_concatenation_of_seq (test_seq.TestSeq.test_concatenation_of_seq) ... ok test_extract_third_nucleotide (test_seq.TestSeq.test_extract_third_nucleotide) Test extracting every third nucleotide (slicing with stride 3). ... ok test_first_nucleotide (test_seq.TestSeq.test_first_nucleotide) Test getting first nucleotide of Seq. ... ok test_last_nucleotide (test_seq.TestSeq.test_last_nucleotide) Test getting last nucleotide of Seq. ... ok test_length (test_seq.TestSeq.test_length) Test len method on Seq object. ... ok test_replace (test_seq.TestSeq.test_replace) ... ok test_repr (test_seq.TestSeq.test_repr) Test representation of Seq object. ... ok test_reverse (test_seq.TestSeq.test_reverse) Test reverse using -1 stride. ... ok test_seq_construction (test_seq.TestSeq.test_seq_construction) Test Seq object initialization. ... ok test_slicing (test_seq.TestSeq.test_slicing) Test slicing of Seq. ... ok test_truncated_repr (test_seq.TestSeq.test_truncated_repr) ... ok test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides) ... ok test_adding_generic_nucleotide_with_other_nucleotides_inplace (test_seq.TestSeqAddition.test_adding_generic_nucleotide_with_other_nucleotides_inplace) ... ok test_adding_protein_with_nucleotides (test_seq.TestSeqAddition.test_adding_protein_with_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides) ... ok test_addition_dna_rna_with_generic_nucleotides_inplace (test_seq.TestSeqAddition.test_addition_dna_rna_with_generic_nucleotides_inplace) ... ok test_addition_dna_with_dna (test_seq.TestSeqAddition.test_addition_dna_with_dna) ... ok test_addition_dna_with_dna_inplace (test_seq.TestSeqAddition.test_addition_dna_with_dna_inplace) ... ok test_addition_dna_with_rna (test_seq.TestSeqAddition.test_addition_dna_with_rna) ... ok test_addition_proteins (test_seq.TestSeqAddition.test_addition_proteins) ... ok test_addition_proteins_inplace (test_seq.TestSeqAddition.test_addition_proteins_inplace) ... ok test_addition_rna_with_rna (test_seq.TestSeqAddition.test_addition_rna_with_rna) ... ok test_addition_rna_with_rna_inplace (test_seq.TestSeqAddition.test_addition_rna_with_rna_inplace) ... ok test_defined (test_seq.TestSeqDefined.test_defined) ... ok test_undefined (test_seq.TestSeqDefined.test_undefined) ... ok test_zero_length (test_seq.TestSeqDefined.test_zero_length) ... ok test_imul_method (test_seq.TestSeqMultiplication.test_imul_method) Test imul method; relies on addition and mull methods. ... ok test_imul_method_exceptions (test_seq.TestSeqMultiplication.test_imul_method_exceptions) Test imul method exceptions. ... ok test_mul_method (test_seq.TestSeqMultiplication.test_mul_method) Test mul method; relies on addition method. ... ok test_mul_method_exceptions (test_seq.TestSeqMultiplication.test_mul_method_exceptions) Test mul method exceptions. ... ok test_rmul_method (test_seq.TestSeqMultiplication.test_rmul_method) Test rmul method; relies on addition method. ... ok test_rmul_method_exceptions (test_seq.TestSeqMultiplication.test_rmul_method_exceptions) Test rmul method exceptions. ... ok test_add_method_using_wrong_object (test_seq.TestSeqStringMethods.test_add_method_using_wrong_object) ... ok test_append_nucleotides (test_seq.TestSeqStringMethods.test_append_nucleotides) ... ok test_append_proteins (test_seq.TestSeqStringMethods.test_append_proteins) ... ok test_contains_method (test_seq.TestSeqStringMethods.test_contains_method) ... ok test_counting_characters (test_seq.TestSeqStringMethods.test_counting_characters) ... ok test_endswith (test_seq.TestSeqStringMethods.test_endswith) ... ok test_finding_characters (test_seq.TestSeqStringMethods.test_finding_characters) ... ok test_greater_than_comparison (test_seq.TestSeqStringMethods.test_greater_than_comparison) Test __gt__ comparison method. ... ok test_greater_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_comparison_of_incompatible_types) Test incompatible types __gt__ comparison method. ... ok test_greater_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison) Test __ge__ comparison method. ... ok test_greater_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_greater_than_or_equal_comparison_of_incompatible_types) Test incompatible types __ge__ comparison method. ... ok test_hash (test_seq.TestSeqStringMethods.test_hash) ... ok test_less_than_comparison (test_seq.TestSeqStringMethods.test_less_than_comparison) Test __lt__ comparison method. ... ok test_less_than_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_comparison_of_incompatible_types) Test incompatible types __lt__ comparison method. ... ok test_less_than_or_equal_comparison (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison) Test __le__ comparison method. ... ok test_less_than_or_equal_comparison_of_incompatible_types (test_seq.TestSeqStringMethods.test_less_than_or_equal_comparison_of_incompatible_types) Test incompatible types __le__ comparison method. ... ok test_mutableseq_upper_lower (test_seq.TestSeqStringMethods.test_mutableseq_upper_lower) ... ok test_not_equal_comparsion (test_seq.TestSeqStringMethods.test_not_equal_comparsion) Test __ne__ comparison method. ... ok test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods.test_radd_method_using_wrong_object) ... ok test_splits (test_seq.TestSeqStringMethods.test_splits) ... ok test_startswith (test_seq.TestSeqStringMethods.test_startswith) ... ok test_string_methods (test_seq.TestSeqStringMethods.test_string_methods) ... ok test_stripping_characters (test_seq.TestSeqStringMethods.test_stripping_characters) ... ok test_stops (test_seq.TestStopCodons.test_stops) ... ok test_translation_of_stops (test_seq.TestStopCodons.test_translation_of_stops) ... ok test_back_transcribe_rna_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_into_dna) ... ok test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription.test_back_transcribe_rna_string_into_dna) ... ok test_seq_object_back_transcription_method (test_seq.TestTranscription.test_seq_object_back_transcription_method) ... ok test_seq_object_transcription_method (test_seq.TestTranscription.test_seq_object_transcription_method) ... ok test_transcription_dna_into_rna (test_seq.TestTranscription.test_transcription_dna_into_rna) ... ok test_transcription_dna_string_into_rna (test_seq.TestTranscription.test_transcription_dna_string_into_rna) ... ok test_gapped_seq_no_gap_char_given (test_seq.TestTranslating.test_gapped_seq_no_gap_char_given) ... ok test_gapped_seq_with_gap_char_given (test_seq.TestTranslating.test_gapped_seq_with_gap_char_given) ... ok test_translation (test_seq.TestTranslating.test_translation) ... ok test_translation_extra_stop_codon (test_seq.TestTranslating.test_translation_extra_stop_codon) ... ok test_translation_incomplete_codon (test_seq.TestTranslating.test_translation_incomplete_codon) ... ok test_translation_of_asparagine (test_seq.TestTranslating.test_translation_of_asparagine) ... ok test_translation_of_gapped_string_no_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_no_gap_char_given) ... ok test_translation_of_gapped_string_with_gap_char_given (test_seq.TestTranslating.test_translation_of_gapped_string_with_gap_char_given) ... ok test_translation_of_glutamine (test_seq.TestTranslating.test_translation_of_glutamine) ... ok test_translation_of_invalid_codon (test_seq.TestTranslating.test_translation_of_invalid_codon) ... ok test_translation_of_leucine (test_seq.TestTranslating.test_translation_of_leucine) ... ok test_translation_of_string (test_seq.TestTranslating.test_translation_of_string) ... ok test_translation_on_proteins (test_seq.TestTranslating.test_translation_on_proteins) Check translation fails on a protein. ... ok test_translation_to_stop (test_seq.TestTranslating.test_translation_to_stop) ... ok test_translation_using_cds (test_seq.TestTranslating.test_translation_using_cds) ... ok test_translation_using_tables_with_ambiguous_stop_codons (test_seq.TestTranslating.test_translation_using_tables_with_ambiguous_stop_codons) Check for error and warning messages. ... ok test_translation_with_bad_table_argument (test_seq.TestTranslating.test_translation_with_bad_table_argument) ... ok test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating.test_translation_with_codon_table_as_table_argument) ... ok test_translation_wrong_type (test_seq.TestTranslating.test_translation_wrong_type) Test translation table cannot be CodonTable. ... ok test_add_method (test_seq.TestUnknownSeq.test_add_method) ... ok test_back_transcribe (test_seq.TestUnknownSeq.test_back_transcribe) ... ok test_complement (test_seq.TestUnknownSeq.test_complement) ... ok test_count (test_seq.TestUnknownSeq.test_count) ... ok test_getitem_method (test_seq.TestUnknownSeq.test_getitem_method) ... ok test_length (test_seq.TestUnknownSeq.test_length) ... ok test_lower (test_seq.TestUnknownSeq.test_lower) ... ok test_repr (test_seq.TestUnknownSeq.test_repr) ... ok test_reverse_complement (test_seq.TestUnknownSeq.test_reverse_complement) ... ok test_transcribe (test_seq.TestUnknownSeq.test_transcribe) ... ok test_translation (test_seq.TestUnknownSeq.test_translation) ... ok test_ungap (test_seq.TestUnknownSeq.test_ungap) ... ok test_unknownseq_construction (test_seq.TestUnknownSeq.test_unknownseq_construction) ... ok test_upper (test_seq.TestUnknownSeq.test_upper) ... ok Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds + for test in `ls test_*.py | grep -v Nexus | grep -v Phylo | grep -v Tutorial | grep -v bgzf | grep -v SearchIO_blast | grep -v pairwise_aligner | grep -v SubsMat` + echo C C + export PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/lib64/python3.11/site-packages + /usr/bin/python3 run_tests.py --offline -v test_translate.py test_translate ... ok test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds Skipping any tests requiring internet access Python version: 3.11.1 (main, Dec 7 2022, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] Operating system: posix linux + popd ~/build/BUILD/python-biopython-1.80 + RPM_EC=0 ++ jobs -p Processing files: python3-biopython-1.80-1.fc38.x86_64 + exit 0 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.OTV43K + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.80 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + cp -pr python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.FPhs0I + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.80 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python3-biopython + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python3-biopython + cp -pr python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.80-1.fc38 python3-biopython = 1.80-1.fc38 python3-biopython(x86-64) = 1.80-1.fc38 python3.11-biopython = 1.80-1.fc38 python3.11dist(biopython) = 1.80 python3dist(biopython) = 1.80 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) python(abi) = 3.11 python3.11dist(numpy) rtld(GNU_HASH) Obsoletes: python-biopython < 1.80-1.fc38 Processing files: python-biopython-doc-1.80-1.fc38.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.w3bduK + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.80 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python-biopython-doc + cp -pr biopython-1.80/Doc /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/doc/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.3q5wTn + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.80 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python-biopython-doc + cp -pr biopython-1.80/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64/usr/share/licenses/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython-doc = 1.80-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-biopython-debugsource-1.80-1.fc38.x86_64 Provides: python-biopython-debugsource = 1.80-1.fc38 python-biopython-debugsource(x86-64) = 1.80-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.80-1.fc38.x86_64 Provides: debuginfo(build-id) = 2d086b89c6c8bb1ca24ff03a99f581fd10d73075 debuginfo(build-id) = 313e240576c4d5f214817843888fcdd87ce4bb66 debuginfo(build-id) = 321b5e0ebbc9ec44483912baacafcea038062c3f debuginfo(build-id) = 449a3e2a49a51b41b10c0cddc4595c20bfdd9bcb debuginfo(build-id) = 503278ed9e5154863c9e1a8427364f384a26e152 debuginfo(build-id) = 66ee61afac11b4075591839cc3d5da8833b4c768 debuginfo(build-id) = 9d7fdf1cd53a82329aa114d2a273df20671d7972 debuginfo(build-id) = c33a2b69cd5f5c5f47e56562e22f61ae23b1bc6d debuginfo(build-id) = e4100923fb8e639bee376916351a68b608b6074d python-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo = 1.80-1.fc38 python3-biopython-debuginfo(x86-64) = 1.80-1.fc38 python3.11-biopython-debuginfo = 1.80-1.fc38 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(x86-64) = 1.80-1.fc38 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 Wrote: /builddir/build/RPMS/python-biopython-doc-1.80-1.fc38.noarch.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.80-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.80-1.fc38.x86_64.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.80-1.fc38.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.fy8cfH + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.80 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.80-1.fc38.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.hX3Nqr + umask 022 + cd /builddir/build/BUILD + rm -rf python-biopython-1.80 python-biopython-1.80.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-biopython-1.80-1.fc38.src.rpm Finish: build phase for python-biopython-1.80-1.fc38.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1672135248.183296/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.80-1.fc38.src.rpm) Config(child) 3 minutes 7 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool