Warning: Permanently added '128.168.141.23' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6231540-fedora-rawhide-s390x --chroot fedora-rawhide-s390x Version: 0.68 PID: 11618 Logging PID: 11619 Task: {'appstream': False, 'background': True, 'build_id': 6231540, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-s390x', 'enable_net': False, 'fedora_review': False, 'git_hash': '5c48bea3567e991e208a8b2b5a736fd08f65d28f', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/python-biopython', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-biopython', 'package_version': '1.81-4', 'project_dirname': 'openblas-0.3.23', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-rawhide-s390x/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--psimovec', 'source_json': {}, 'source_type': None, 'submitter': 'psimovec', 'tags': [], 'task_id': '6231540-fedora-rawhide-s390x', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/python-biopython /var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/python-biopython', '/var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython'... Running: git checkout 5c48bea3567e991e208a8b2b5a736fd08f65d28f -- cmd: ['git', 'checkout', '5c48bea3567e991e208a8b2b5a736fd08f65d28f', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython rc: 0 stdout: stderr: Note: switching to '5c48bea3567e991e208a8b2b5a736fd08f65d28f'. 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 5c48bea automatic import of python-biopython Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/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-1.81.tar.gz INFO: Calling: curl -H Pragma: -o biopython-1.81.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23/python-biopython/biopython-1.81.tar.gz/md5/06cabd14f55d624db366ff75efb60ed2/biopython-1.81.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 18.4M 100 18.4M 0 0 6957k 0 0:00:02 0:00:02 --:--:-- 6958k INFO: Reading stdout from command: md5sum biopython-1.81.tar.gz Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython/python-biopython.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1691114939.268004 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 4.1 starting (python version = 3.11.3, NVR = mock-4.1-1.fc38)... 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-i1kicmfb/python-biopython/python-biopython.spec) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1691114939.268004/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: 4.1 INFO: Mock Version: 4.1 INFO: Package manager dnf detected and used (fallback) Start(bootstrap): installing dnf tooling 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 1.5 MB/s | 8.9 MB 00:05 Additional repo http_kojipkgs_fedoraproject_org 5.9 MB/s | 64 MB 00:10 fedora 9.3 MB/s | 63 MB 00:06 Last metadata expiration check: 0:00:02 ago on Fri Aug 4 02:09:46 2023. Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing: dnf-plugins-core noarch 4.4.2-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k python3-dnf noarch 4.16.2-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 546 k Installing dependencies: alternatives s390x 1.25-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k audit-libs s390x 3.1.1-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k basesystem noarch 11-18.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k bash s390x 5.2.15-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2-libs s390x 1.0.8-16.fc39 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noarch 2023c-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 433 k xz-libs s390x 5.4.4-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 114 k zchunk-libs s390x 1.3.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 51 k zlib s390x 1.2.13-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k Transaction Summary ======================================================================================================================================== Install 139 Packages Total download size: 56 M Installed size: 201 M Downloading Packages: (1/139): basesystem-11-18.fc39.noarch.rpm 7.9 kB/s | 7.2 kB 00:00 (2/139): alternatives-1.25-1.fc39.s390x.rpm 31 kB/s | 39 kB 00:01 (3/139): audit-libs-3.1.1-4.fc39.s390x.rpm 88 kB/s | 121 kB 00:01 (4/139): bzip2-libs-1.0.8-16.fc39.s390x.rpm 134 kB/s | 46 kB 00:00 (5/139): ca-certificates-2023.2.60_v7.0.306-2.f 1.2 MB/s | 837 kB 00:00 (6/139): bash-5.2.15-5.fc39.s390x.rpm 1.3 MB/s | 1.8 MB 00:01 (7/139): coreutils-9.3-2.fc39.s390x.rpm 1.3 MB/s | 1.2 MB 00:00 (8/139): crypto-policies-20230731-1.git5ed06e0. 197 kB/s | 68 kB 00:00 (9/139): coreutils-common-9.3-2.fc39.s390x.rpm 3.1 MB/s | 2.1 MB 00:00 (10/139): curl-8.2.1-1.fc39.s390x.rpm 993 kB/s | 344 kB 00:00 (11/139): cyrus-sasl-lib-2.1.28-11.fc39.s390x.r 2.3 MB/s | 819 kB 00:00 (12/139): dbus-libs-1.14.8-2.fc39.s390x.rpm 460 kB/s | 159 kB 00:00 (13/139): dnf-data-4.16.2-1.fc39.noarch.rpm 109 kB/s | 38 kB 00:00 (14/139): dnf-plugins-core-4.4.2-1.fc39.noarch. 110 kB/s | 38 kB 00:00 (15/139): elfutils-default-yama-scope-0.189-4.f 39 kB/s | 13 kB 00:00 (16/139): elfutils-libelf-0.189-4.fc39.s390x.rp 578 kB/s | 200 kB 00:00 (17/139): elfutils-libs-0.189-4.fc39.s390x.rpm 795 kB/s | 275 kB 00:00 (18/139): expat-2.5.0-3.fc39.s390x.rpm 330 kB/s | 114 kB 00:00 (19/139): fedora-gpg-keys-39-0.4.noarch.rpm 340 kB/s | 118 kB 00:00 (20/139): fedora-release-39-0.21.noarch.rpm 20 kB/s | 6.9 kB 00:00 (21/139): fedora-release-common-39-0.21.noarch. 49 kB/s | 17 kB 00:00 (22/139): fedora-release-identity-basic-39-0.21 22 kB/s | 7.6 kB 00:00 (23/139): fedora-repos-39-0.4.noarch.rpm 27 kB/s | 9.3 kB 00:00 (24/139): fedora-repos-rawhide-39-0.4.noarch.rp 26 kB/s | 8.9 kB 00:00 (25/139): file-libs-5.44-5.fc39.s390x.rpm 2.1 MB/s | 736 kB 00:00 (26/139): filesystem-3.18-6.fc39.s390x.rpm 3.1 MB/s | 1.1 MB 00:00 (27/139): findutils-4.9.0-5.fc39.s390x.rpm 1.4 MB/s | 488 kB 00:00 (28/139): fmt-10.0.0-3.fc39.s390x.rpm 379 kB/s | 132 kB 00:00 (29/139): gawk-5.2.2-2.fc39.s390x.rpm 3.1 MB/s | 1.1 MB 00:00 (30/139): gdbm-libs-1.23-4.fc39.s390x.rpm 169 kB/s | 58 kB 00:00 (31/139): glibc-common-2.37.9000-18.fc39.s390x. 1.0 MB/s | 359 kB 00:00 (32/139): glib2-2.77.1-1.fc39.s390x.rpm 4.0 MB/s | 2.8 MB 00:00 (33/139): glibc-2.37.9000-18.fc39.s390x.rpm 3.5 MB/s | 1.8 MB 00:00 (34/139): glibc-minimal-langpack-2.37.9000-18.f 186 kB/s | 64 kB 00:00 (35/139): gmp-6.2.1-5.fc39.s390x.rpm 944 kB/s | 325 kB 00:00 (36/139): gnupg2-2.4.3-2.fc39.s390x.rpm 5.1 MB/s | 2.7 MB 00:00 (37/139): gnutls-3.8.0-7.fc39.s390x.rpm 3.0 MB/s | 1.0 MB 00:00 (38/139): gpgme-1.20.0-5.fc39.s390x.rpm 642 kB/s | 222 kB 00:00 (39/139): grep-3.11-3.fc39.s390x.rpm 850 kB/s | 294 kB 00:00 (40/139): ima-evm-utils-1.5-2.fc39.s390x.rpm 183 kB/s | 63 kB 00:00 (41/139): json-c-0.16-5.fc39.s390x.rpm 121 kB/s | 42 kB 00:00 (42/139): keyutils-libs-1.6.1-7.fc39.s390x.rpm 90 kB/s | 31 kB 00:00 (43/139): krb5-libs-1.21-3.fc39.s390x.rpm 2.2 MB/s | 776 kB 00:00 (44/139): libacl-2.3.1-8.fc39.s390x.rpm 69 kB/s | 24 kB 00:00 (45/139): libarchive-3.7.1-1.fc39.s390x.rpm 1.2 MB/s | 441 kB 00:00 (46/139): libassuan-2.5.6-2.fc39.s390x.rpm 195 kB/s | 67 kB 00:00 (47/139): libattr-2.5.1-8.fc39.s390x.rpm 52 kB/s | 18 kB 00:00 (48/139): libb2-0.98.1-9.fc39.s390x.rpm 77 kB/s | 27 kB 00:00 (49/139): libblkid-2.39.1-3.fc39.s390x.rpm 351 kB/s | 120 kB 00:00 (50/139): libbrotli-1.0.9-13.fc39.s390x.rpm 985 kB/s | 343 kB 00:00 (51/139): libcap-2.48-7.fc39.s390x.rpm 199 kB/s | 69 kB 00:00 (52/139): libcap-ng-0.8.3-7.fc39.s390x.rpm 95 kB/s | 33 kB 00:00 (53/139): libcom_err-1.47.0-2.fc39.s390x.rpm 75 kB/s | 26 kB 00:00 (54/139): libcomps-0.1.19-3.fc39.s390x.rpm 225 kB/s | 79 kB 00:00 (55/139): libcurl-8.2.1-1.fc39.s390x.rpm 996 kB/s | 342 kB 00:00 (56/139): libdnf-0.70.2-1.fc39.s390x.rpm 1.8 MB/s | 646 kB 00:00 (57/139): libdnf5-5.1.0-2.fc39.s390x.rpm 2.4 MB/s | 876 kB 00:00 (58/139): libeconf-0.4.0-6.fc39.s390x.rpm 83 kB/s | 28 kB 00:00 (59/139): libevent-2.1.12-9.fc39.s390x.rpm 749 kB/s | 260 kB 00:00 (60/139): libffi-3.4.4-4.fc39.s390x.rpm 103 kB/s | 36 kB 00:00 (61/139): libfsverity-1.4-10.fc39.s390x.rpm 55 kB/s | 19 kB 00:00 (62/139): libgcc-13.2.1-1.fc39.s390x.rpm 237 kB/s | 82 kB 00:00 (63/139): libgcrypt-1.10.2-2.fc39.s390x.rpm 1.4 MB/s | 489 kB 00:00 (64/139): libgomp-13.2.1-1.fc39.s390x.rpm 940 kB/s | 323 kB 00:00 (65/139): libgpg-error-1.47-2.fc39.s390x.rpm 652 kB/s | 227 kB 00:00 (66/139): libidn2-2.3.4-3.fc39.s390x.rpm 322 kB/s | 111 kB 00:00 (67/139): libksba-1.6.4-2.fc39.s390x.rpm 469 kB/s | 162 kB 00:00 (68/139): libmodulemd-2.15.0-5.fc39.s390x.rpm 615 kB/s | 217 kB 00:00 (69/139): libmount-2.39.1-3.fc39.s390x.rpm 456 kB/s | 158 kB 00:00 (70/139): libnghttp2-1.55.1-2.fc39.s390x.rpm 227 kB/s | 78 kB 00:00 (71/139): libnsl2-2.0.0-6.fc39.s390x.rpm 86 kB/s | 30 kB 00:00 (72/139): libpsl-0.21.2-4.fc39.s390x.rpm 183 kB/s | 63 kB 00:00 (73/139): librepo-1.15.2-1.fc39.s390x.rpm 276 kB/s | 95 kB 00:00 (74/139): libreport-filesystem-2.17.11-3.fc39.n 41 kB/s | 14 kB 00:00 (75/139): libselinux-3.5-5.fc39.s390x.rpm 264 kB/s | 91 kB 00:00 (76/139): libsemanage-3.5-4.fc39.s390x.rpm 356 kB/s | 122 kB 00:00 (77/139): libsepol-3.5-2.fc39.s390x.rpm 953 kB/s | 330 kB 00:00 (78/139): libsigsegv-2.14-5.fc39.s390x.rpm 77 kB/s | 27 kB 00:00 (79/139): libsmartcols-2.39.1-3.fc39.s390x.rpm 203 kB/s | 70 kB 00:00 (80/139): libsolv-0.7.24-8.fc39.s390x.rpm 1.3 MB/s | 458 kB 00:00 (81/139): libssh-0.10.5-2.fc39.s390x.rpm 604 kB/s | 209 kB 00:00 (82/139): libssh-config-0.10.5-2.fc39.noarch.rp 27 kB/s | 9.2 kB 00:00 (83/139): libstdc++-13.2.1-1.fc39.s390x.rpm 2.7 MB/s | 949 kB 00:00 (84/139): libtasn1-4.19.0-3.fc39.s390x.rpm 225 kB/s | 77 kB 00:00 (85/139): libtirpc-1.3.3-1.rc1.fc39.1.s390x.rpm 277 kB/s | 96 kB 00:00 (86/139): libunistring-1.1-4.fc39.s390x.rpm 1.6 MB/s | 557 kB 00:00 (87/139): libuuid-2.39.1-3.fc39.s390x.rpm 82 kB/s | 28 kB 00:00 (88/139): libverto-0.3.2-6.fc39.s390x.rpm 61 kB/s | 21 kB 00:00 (89/139): libxcrypt-4.4.36-2.fc39.s390x.rpm 360 kB/s | 124 kB 00:00 (90/139): libxml2-2.10.4-3.fc39.s390x.rpm 2.0 MB/s | 712 kB 00:00 (91/139): libyaml-0.2.5-12.fc39.s390x.rpm 179 kB/s | 62 kB 00:00 (92/139): libzstd-1.5.5-4.fc39.s390x.rpm 997 kB/s | 342 kB 00:00 (93/139): lua-libs-5.4.6-3.fc39.s390x.rpm 409 kB/s | 142 kB 00:00 (94/139): lz4-libs-1.9.4-4.fc39.s390x.rpm 237 kB/s | 81 kB 00:00 (95/139): mpdecimal-2.5.1-7.fc39.s390x.rpm 287 kB/s | 100 kB 00:00 (96/139): mpfr-4.2.0-3.fc39.s390x.rpm 866 kB/s | 298 kB 00:00 (97/139): ncurses-base-6.4-6.20230520.fc39.noar 182 kB/s | 63 kB 00:00 (98/139): ncurses-libs-6.4-6.20230520.fc39.s390 1.0 MB/s | 361 kB 00:00 (99/139): nettle-3.9.1-2.fc39.s390x.rpm 1.3 MB/s | 456 kB 00:00 (100/139): npth-1.6-14.fc39.s390x.rpm 70 kB/s | 24 kB 00:00 (101/139): openldap-2.6.6-1.fc39.s390x.rpm 758 kB/s | 262 kB 00:00 (102/139): p11-kit-0.25.0-2.fc39.s390x.rpm 1.4 MB/s | 493 kB 00:00 (103/139): openssl-libs-3.1.1-1.fc39.s390x.rpm 3.6 MB/s | 1.9 MB 00:00 (104/139): pcre2-10.42-1.fc39.2.s390x.rpm 721 kB/s | 250 kB 00:00 (105/139): pcre2-syntax-10.42-1.fc39.2.noarch.r 417 kB/s | 143 kB 00:00 (106/139): p11-kit-trust-0.25.0-2.fc39.s390x.rp 164 kB/s | 141 kB 00:00 (107/139): popt-1.19-3.fc39.s390x.rpm 180 kB/s | 62 kB 00:00 (108/139): publicsuffix-list-dafsa-20230614-2.f 167 kB/s | 57 kB 00:00 (109/139): python-pip-wheel-23.1.2-5.fc39.noarc 4.1 MB/s | 1.4 MB 00:00 (110/139): python3-3.12.0~b4-2.fc39.s390x.rpm 75 kB/s | 26 kB 00:00 (111/139): python3-dbus-1.3.2-4.fc39.s390x.rpm 421 kB/s | 147 kB 00:00 (112/139): python3-distro-1.8.0-6.fc39.noarch.r 130 kB/s | 44 kB 00:00 (113/139): python3-dateutil-2.8.2-10.fc39.noarc 499 kB/s | 344 kB 00:00 (114/139): python3-dnf-4.16.2-1.fc39.noarch.rpm 1.5 MB/s | 546 kB 00:00 (115/139): python3-dnf-plugins-core-4.4.2-1.fc3 810 kB/s | 278 kB 00:00 (116/139): python3-gpg-1.20.0-5.fc39.s390x.rpm 815 kB/s | 284 kB 00:00 (117/139): python3-hawkey-0.70.2-1.fc39.s390x.r 288 kB/s | 100 kB 00:00 (118/139): python3-libcomps-0.1.19-3.fc39.s390x 143 kB/s | 49 kB 00:00 (119/139): python3-libdnf-0.70.2-1.fc39.s390x.r 1.5 MB/s | 799 kB 00:00 (120/139): python3-rpm-4.18.92-1.fc39.s390x.rpm 200 kB/s | 69 kB 00:00 (121/139): python3-six-1.16.0-12.fc39.noarch.rp 119 kB/s | 41 kB 00:00 (122/139): python3-systemd-235-5.fc39.s390x.rpm 287 kB/s | 100 kB 00:00 (123/139): readline-8.2-4.fc39.s390x.rpm 660 kB/s | 229 kB 00:00 (124/139): python3-libs-3.12.0~b4-2.fc39.s390x. 8.4 MB/s | 8.8 MB 00:01 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101 kB 00:00 -------------------------------------------------------------------------------- Total 3.0 MB/s | 56 MB 00:18 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.s390x 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-1.fc39.s390x 1/139 Running scriptlet: libgcc-13.2.1-1.fc39.s390x 1/139 Installing : tzdata-2023c-2.fc39.noarch 2/139 Installing : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 3/139 Running scriptlet: crypto-policies-20230731-1.git5ed06e0.fc39.noarc 3/139 Installing : fedora-release-identity-basic-39-0.21.noarch 4/139 Installing : fedora-repos-rawhide-39-0.4.noarch 5/139 Installing : fedora-gpg-keys-39-0.4.noarch 6/139 Installing : fedora-repos-39-0.4.noarch 7/139 Installing : fedora-release-common-39-0.21.noarch 8/139 Installing : fedora-release-39-0.21.noarch 9/139 Installing : setup-2.14.4-1.fc39.noarch 10/139 Running scriptlet: setup-2.14.4-1.fc39.noarch 10/139 Installing : filesystem-3.18-6.fc39.s390x 11/139 Installing : basesystem-11-18.fc39.noarch 12/139 Installing : publicsuffix-list-dafsa-20230614-2.fc39.noarch 13/139 Installing : 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nettle-3.9.1-2.fc39.s390x 71/139 Installing : file-libs-5.44-5.fc39.s390x 72/139 Installing : elfutils-default-yama-scope-0.189-4.fc39.noarch 73/139 Running scriptlet: elfutils-default-yama-scope-0.189-4.fc39.noarch 73/139 Installing : elfutils-libs-0.189-4.fc39.s390x 74/139 Installing : alternatives-1.25-1.fc39.s390x 75/139 Installing : p11-kit-trust-0.25.0-2.fc39.s390x 76/139 Running scriptlet: p11-kit-trust-0.25.0-2.fc39.s390x 76/139 Installing : gnutls-3.8.0-7.fc39.s390x 77/139 Installing : glib2-2.77.1-1.fc39.s390x 78/139 Installing : libbrotli-1.0.9-13.fc39.s390x 79/139 Installing : libcap-ng-0.8.3-7.fc39.s390x 80/139 Installing : audit-libs-3.1.1-4.fc39.s390x 81/139 Installing : libsemanage-3.5-4.fc39.s390x 82/139 Installing : libeconf-0.4.0-6.fc39.s390x 83/139 Installing : shadow-utils-2:4.13-8.fc39.s390x 84/139 Installing : libnghttp2-1.55.1-2.fc39.s390x 85/139 Installing : libsigsegv-2.14-5.fc39.s390x 86/139 Installing : gawk-5.2.2-2.fc39.s390x 87/139 Installing : libverto-0.3.2-6.fc39.s390x 88/139 Installing : libyaml-0.2.5-12.fc39.s390x 89/139 Installing : mpdecimal-2.5.1-7.fc39.s390x 90/139 Installing : npth-1.6-14.fc39.s390x 91/139 Installing : libssh-config-0.10.5-2.fc39.noarch 92/139 Installing : libreport-filesystem-2.17.11-3.fc39.noarch 93/139 Installing : coreutils-common-9.3-2.fc39.s390x 94/139 Installing : openssl-libs-1:3.1.1-1.fc39.s390x 95/139 Installing : coreutils-9.3-2.fc39.s390x 96/139 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 97/139 Installing : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 97/139 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 97/139 Installing : krb5-libs-1.21-3.fc39.s390x 98/139 Installing : libtirpc-1.3.3-1.rc1.fc39.1.s390x 99/139 Installing : zchunk-libs-1.3.1-2.fc39.s390x 100/139 Installing : libnsl2-2.0.0-6.fc39.s390x 101/139 Installing : libssh-0.10.5-2.fc39.s390x 102/139 Installing : python-pip-wheel-23.1.2-5.fc39.noarch 103/139 Installing : python3-3.12.0~b4-2.fc39.s390x 104/139 Installing : python3-libs-3.12.0~b4-2.fc39.s390x 105/139 Installing : python3-libcomps-0.1.19-3.fc39.s390x 106/139 Installing : python3-dbus-1.3.2-4.fc39.s390x 107/139 Installing : python3-distro-1.8.0-6.fc39.noarch 108/139 Installing : python3-six-1.16.0-12.fc39.noarch 109/139 Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 110/139 Installing : python3-systemd-235-5.fc39.s390x 111/139 Installing : libarchive-3.7.1-1.fc39.s390x 112/139 Installing : libevent-2.1.12-9.fc39.s390x 113/139 Installing : openldap-2.6.6-1.fc39.s390x 114/139 Installing : libcurl-8.2.1-1.fc39.s390x 115/139 Running scriptlet: tpm2-tss-4.0.1-4.fc39.s390x 116/139 useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Installing : tpm2-tss-4.0.1-4.fc39.s390x 116/139 Installing : gnupg2-2.4.3-2.fc39.s390x 117/139 Installing : gpgme-1.20.0-5.fc39.s390x 118/139 Installing : librepo-1.15.2-1.fc39.s390x 119/139 Installing : python3-gpg-1.20.0-5.fc39.s390x 120/139 Installing : ima-evm-utils-1.5-2.fc39.s390x 121/139 Installing : curl-8.2.1-1.fc39.s390x 122/139 Installing : libfsverity-1.4-10.fc39.s390x 123/139 Installing : rpm-sequoia-1.4.1-2.fc39.s390x 124/139 Installing : rpm-libs-4.18.92-1.fc39.s390x 125/139 Installing : libmodulemd-2.15.0-5.fc39.s390x 126/139 Installing : libsolv-0.7.24-8.fc39.s390x 127/139 Installing : libdnf-0.70.2-1.fc39.s390x 128/139 Installing : python3-libdnf-0.70.2-1.fc39.s390x 129/139 Installing : python3-hawkey-0.70.2-1.fc39.s390x 130/139 Installing : libdnf5-5.1.0-2.fc39.s390x 131/139 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : dnf-data-4.16.2-1.fc39.noarch 132/139 Installing : rpm-build-libs-4.18.92-1.fc39.s390x 133/139 Installing : rpm-sign-libs-4.18.92-1.fc39.s390x 134/139 Installing : python3-rpm-4.18.92-1.fc39.s390x 135/139 Installing : python3-dnf-4.16.2-1.fc39.noarch 136/139 Installing : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 137/139 Installing : dnf-plugins-core-4.4.2-1.fc39.noarch 138/139 Running scriptlet: rpm-4.18.92-1.fc39.s390x 139/139 Installing : rpm-4.18.92-1.fc39.s390x 139/139 Running scriptlet: filesystem-3.18-6.fc39.s390x 139/139 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 139/139 Running scriptlet: rpm-4.18.92-1.fc39.s390x 139/139 Verifying : alternatives-1.25-1.fc39.s390x 1/139 Verifying : audit-libs-3.1.1-4.fc39.s390x 2/139 Verifying : basesystem-11-18.fc39.noarch 3/139 Verifying : bash-5.2.15-5.fc39.s390x 4/139 Verifying : bzip2-libs-1.0.8-16.fc39.s390x 5/139 Verifying : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 6/139 Verifying : coreutils-9.3-2.fc39.s390x 7/139 Verifying : coreutils-common-9.3-2.fc39.s390x 8/139 Verifying : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 9/139 Verifying : curl-8.2.1-1.fc39.s390x 10/139 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.s390x 11/139 Verifying : dbus-libs-1:1.14.8-2.fc39.s390x 12/139 Verifying : dnf-data-4.16.2-1.fc39.noarch 13/139 Verifying : dnf-plugins-core-4.4.2-1.fc39.noarch 14/139 Verifying : elfutils-default-yama-scope-0.189-4.fc39.noarch 15/139 Verifying : elfutils-libelf-0.189-4.fc39.s390x 16/139 Verifying : elfutils-libs-0.189-4.fc39.s390x 17/139 Verifying : expat-2.5.0-3.fc39.s390x 18/139 Verifying : fedora-gpg-keys-39-0.4.noarch 19/139 Verifying : fedora-release-39-0.21.noarch 20/139 Verifying : fedora-release-common-39-0.21.noarch 21/139 Verifying : fedora-release-identity-basic-39-0.21.noarch 22/139 Verifying : fedora-repos-39-0.4.noarch 23/139 Verifying : fedora-repos-rawhide-39-0.4.noarch 24/139 Verifying : file-libs-5.44-5.fc39.s390x 25/139 Verifying : filesystem-3.18-6.fc39.s390x 26/139 Verifying : findutils-1:4.9.0-5.fc39.s390x 27/139 Verifying : fmt-10.0.0-3.fc39.s390x 28/139 Verifying : gawk-5.2.2-2.fc39.s390x 29/139 Verifying : gdbm-libs-1:1.23-4.fc39.s390x 30/139 Verifying : glib2-2.77.1-1.fc39.s390x 31/139 Verifying : glibc-2.37.9000-18.fc39.s390x 32/139 Verifying : glibc-common-2.37.9000-18.fc39.s390x 33/139 Verifying : glibc-minimal-langpack-2.37.9000-18.fc39.s390x 34/139 Verifying : gmp-1:6.2.1-5.fc39.s390x 35/139 Verifying : gnupg2-2.4.3-2.fc39.s390x 36/139 Verifying : gnutls-3.8.0-7.fc39.s390x 37/139 Verifying : gpgme-1.20.0-5.fc39.s390x 38/139 Verifying : grep-3.11-3.fc39.s390x 39/139 Verifying : ima-evm-utils-1.5-2.fc39.s390x 40/139 Verifying : json-c-0.16-5.fc39.s390x 41/139 Verifying : keyutils-libs-1.6.1-7.fc39.s390x 42/139 Verifying : krb5-libs-1.21-3.fc39.s390x 43/139 Verifying : libacl-2.3.1-8.fc39.s390x 44/139 Verifying : libarchive-3.7.1-1.fc39.s390x 45/139 Verifying : libassuan-2.5.6-2.fc39.s390x 46/139 Verifying : libattr-2.5.1-8.fc39.s390x 47/139 Verifying : libb2-0.98.1-9.fc39.s390x 48/139 Verifying : libblkid-2.39.1-3.fc39.s390x 49/139 Verifying : libbrotli-1.0.9-13.fc39.s390x 50/139 Verifying : libcap-2.48-7.fc39.s390x 51/139 Verifying : libcap-ng-0.8.3-7.fc39.s390x 52/139 Verifying : libcom_err-1.47.0-2.fc39.s390x 53/139 Verifying : libcomps-0.1.19-3.fc39.s390x 54/139 Verifying : libcurl-8.2.1-1.fc39.s390x 55/139 Verifying : libdnf-0.70.2-1.fc39.s390x 56/139 Verifying : libdnf5-5.1.0-2.fc39.s390x 57/139 Verifying : libeconf-0.4.0-6.fc39.s390x 58/139 Verifying : libevent-2.1.12-9.fc39.s390x 59/139 Verifying : libffi-3.4.4-4.fc39.s390x 60/139 Verifying : libfsverity-1.4-10.fc39.s390x 61/139 Verifying : libgcc-13.2.1-1.fc39.s390x 62/139 Verifying : libgcrypt-1.10.2-2.fc39.s390x 63/139 Verifying : libgomp-13.2.1-1.fc39.s390x 64/139 Verifying : libgpg-error-1.47-2.fc39.s390x 65/139 Verifying : libidn2-2.3.4-3.fc39.s390x 66/139 Verifying : libksba-1.6.4-2.fc39.s390x 67/139 Verifying : libmodulemd-2.15.0-5.fc39.s390x 68/139 Verifying : libmount-2.39.1-3.fc39.s390x 69/139 Verifying : libnghttp2-1.55.1-2.fc39.s390x 70/139 Verifying : libnsl2-2.0.0-6.fc39.s390x 71/139 Verifying : libpsl-0.21.2-4.fc39.s390x 72/139 Verifying : librepo-1.15.2-1.fc39.s390x 73/139 Verifying : libreport-filesystem-2.17.11-3.fc39.noarch 74/139 Verifying : libselinux-3.5-5.fc39.s390x 75/139 Verifying : libsemanage-3.5-4.fc39.s390x 76/139 Verifying : libsepol-3.5-2.fc39.s390x 77/139 Verifying : libsigsegv-2.14-5.fc39.s390x 78/139 Verifying : libsmartcols-2.39.1-3.fc39.s390x 79/139 Verifying : libsolv-0.7.24-8.fc39.s390x 80/139 Verifying : libssh-0.10.5-2.fc39.s390x 81/139 Verifying : libssh-config-0.10.5-2.fc39.noarch 82/139 Verifying : libstdc++-13.2.1-1.fc39.s390x 83/139 Verifying : libtasn1-4.19.0-3.fc39.s390x 84/139 Verifying : libtirpc-1.3.3-1.rc1.fc39.1.s390x 85/139 Verifying : libunistring-1.1-4.fc39.s390x 86/139 Verifying : libuuid-2.39.1-3.fc39.s390x 87/139 Verifying : libverto-0.3.2-6.fc39.s390x 88/139 Verifying : libxcrypt-4.4.36-2.fc39.s390x 89/139 Verifying : libxml2-2.10.4-3.fc39.s390x 90/139 Verifying : libyaml-0.2.5-12.fc39.s390x 91/139 Verifying : libzstd-1.5.5-4.fc39.s390x 92/139 Verifying : lua-libs-5.4.6-3.fc39.s390x 93/139 Verifying : lz4-libs-1.9.4-4.fc39.s390x 94/139 Verifying : mpdecimal-2.5.1-7.fc39.s390x 95/139 Verifying : mpfr-4.2.0-3.fc39.s390x 96/139 Verifying : ncurses-base-6.4-6.20230520.fc39.noarch 97/139 Verifying : ncurses-libs-6.4-6.20230520.fc39.s390x 98/139 Verifying : nettle-3.9.1-2.fc39.s390x 99/139 Verifying : npth-1.6-14.fc39.s390x 100/139 Verifying : openldap-2.6.6-1.fc39.s390x 101/139 Verifying : openssl-libs-1:3.1.1-1.fc39.s390x 102/139 Verifying : p11-kit-0.25.0-2.fc39.s390x 103/139 Verifying : p11-kit-trust-0.25.0-2.fc39.s390x 104/139 Verifying : pcre2-10.42-1.fc39.2.s390x 105/139 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 106/139 Verifying : popt-1.19-3.fc39.s390x 107/139 Verifying : publicsuffix-list-dafsa-20230614-2.fc39.noarch 108/139 Verifying : python-pip-wheel-23.1.2-5.fc39.noarch 109/139 Verifying : python3-3.12.0~b4-2.fc39.s390x 110/139 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 111/139 Verifying : python3-dbus-1.3.2-4.fc39.s390x 112/139 Verifying : python3-distro-1.8.0-6.fc39.noarch 113/139 Verifying : python3-dnf-4.16.2-1.fc39.noarch 114/139 Verifying : python3-dnf-plugins-core-4.4.2-1.fc39.noarch 115/139 Verifying : python3-gpg-1.20.0-5.fc39.s390x 116/139 Verifying : python3-hawkey-0.70.2-1.fc39.s390x 117/139 Verifying : python3-libcomps-0.1.19-3.fc39.s390x 118/139 Verifying : python3-libdnf-0.70.2-1.fc39.s390x 119/139 Verifying : python3-libs-3.12.0~b4-2.fc39.s390x 120/139 Verifying : python3-rpm-4.18.92-1.fc39.s390x 121/139 Verifying : python3-six-1.16.0-12.fc39.noarch 122/139 Verifying : python3-systemd-235-5.fc39.s390x 123/139 Verifying : readline-8.2-4.fc39.s390x 124/139 Verifying : rpm-4.18.92-1.fc39.s390x 125/139 Verifying : rpm-build-libs-4.18.92-1.fc39.s390x 126/139 Verifying : rpm-libs-4.18.92-1.fc39.s390x 127/139 Verifying : rpm-sequoia-1.4.1-2.fc39.s390x 128/139 Verifying : rpm-sign-libs-4.18.92-1.fc39.s390x 129/139 Verifying : sed-4.8-14.fc39.s390x 130/139 Verifying : setup-2.14.4-1.fc39.noarch 131/139 Verifying : shadow-utils-2:4.13-8.fc39.s390x 132/139 Verifying : sqlite-libs-3.42.0-7.fc39.s390x 133/139 Verifying : systemd-libs-254-1.fc39.s390x 134/139 Verifying : tpm2-tss-4.0.1-4.fc39.s390x 135/139 Verifying : tzdata-2023c-2.fc39.noarch 136/139 Verifying : xz-libs-5.4.4-1.fc39.s390x 137/139 Verifying : zchunk-libs-1.3.1-2.fc39.s390x 138/139 Verifying : zlib-1.2.13-4.fc39.s390x 139/139 Installed products updated. Installed: alternatives-1.25-1.fc39.s390x audit-libs-3.1.1-4.fc39.s390x basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.s390x bzip2-libs-1.0.8-16.fc39.s390x ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-2.fc39.s390x coreutils-common-9.3-2.fc39.s390x crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.2.1-1.fc39.s390x cyrus-sasl-lib-2.1.28-11.fc39.s390x dbus-libs-1:1.14.8-2.fc39.s390x dnf-data-4.16.2-1.fc39.noarch dnf-plugins-core-4.4.2-1.fc39.noarch elfutils-default-yama-scope-0.189-4.fc39.noarch elfutils-libelf-0.189-4.fc39.s390x elfutils-libs-0.189-4.fc39.s390x expat-2.5.0-3.fc39.s390x fedora-gpg-keys-39-0.4.noarch fedora-release-39-0.21.noarch fedora-release-common-39-0.21.noarch fedora-release-identity-basic-39-0.21.noarch fedora-repos-39-0.4.noarch fedora-repos-rawhide-39-0.4.noarch file-libs-5.44-5.fc39.s390x filesystem-3.18-6.fc39.s390x findutils-1:4.9.0-5.fc39.s390x fmt-10.0.0-3.fc39.s390x gawk-5.2.2-2.fc39.s390x gdbm-libs-1:1.23-4.fc39.s390x glib2-2.77.1-1.fc39.s390x glibc-2.37.9000-18.fc39.s390x glibc-common-2.37.9000-18.fc39.s390x glibc-minimal-langpack-2.37.9000-18.fc39.s390x gmp-1:6.2.1-5.fc39.s390x gnupg2-2.4.3-2.fc39.s390x gnutls-3.8.0-7.fc39.s390x gpgme-1.20.0-5.fc39.s390x grep-3.11-3.fc39.s390x ima-evm-utils-1.5-2.fc39.s390x json-c-0.16-5.fc39.s390x keyutils-libs-1.6.1-7.fc39.s390x krb5-libs-1.21-3.fc39.s390x libacl-2.3.1-8.fc39.s390x libarchive-3.7.1-1.fc39.s390x libassuan-2.5.6-2.fc39.s390x libattr-2.5.1-8.fc39.s390x libb2-0.98.1-9.fc39.s390x libblkid-2.39.1-3.fc39.s390x libbrotli-1.0.9-13.fc39.s390x libcap-2.48-7.fc39.s390x libcap-ng-0.8.3-7.fc39.s390x libcom_err-1.47.0-2.fc39.s390x libcomps-0.1.19-3.fc39.s390x libcurl-8.2.1-1.fc39.s390x libdnf-0.70.2-1.fc39.s390x libdnf5-5.1.0-2.fc39.s390x libeconf-0.4.0-6.fc39.s390x libevent-2.1.12-9.fc39.s390x libffi-3.4.4-4.fc39.s390x libfsverity-1.4-10.fc39.s390x libgcc-13.2.1-1.fc39.s390x libgcrypt-1.10.2-2.fc39.s390x libgomp-13.2.1-1.fc39.s390x libgpg-error-1.47-2.fc39.s390x libidn2-2.3.4-3.fc39.s390x libksba-1.6.4-2.fc39.s390x libmodulemd-2.15.0-5.fc39.s390x libmount-2.39.1-3.fc39.s390x libnghttp2-1.55.1-2.fc39.s390x libnsl2-2.0.0-6.fc39.s390x libpsl-0.21.2-4.fc39.s390x librepo-1.15.2-1.fc39.s390x libreport-filesystem-2.17.11-3.fc39.noarch libselinux-3.5-5.fc39.s390x libsemanage-3.5-4.fc39.s390x libsepol-3.5-2.fc39.s390x libsigsegv-2.14-5.fc39.s390x libsmartcols-2.39.1-3.fc39.s390x libsolv-0.7.24-8.fc39.s390x libssh-0.10.5-2.fc39.s390x libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc39.s390x libtasn1-4.19.0-3.fc39.s390x libtirpc-1.3.3-1.rc1.fc39.1.s390x libunistring-1.1-4.fc39.s390x libuuid-2.39.1-3.fc39.s390x libverto-0.3.2-6.fc39.s390x libxcrypt-4.4.36-2.fc39.s390x libxml2-2.10.4-3.fc39.s390x libyaml-0.2.5-12.fc39.s390x libzstd-1.5.5-4.fc39.s390x lua-libs-5.4.6-3.fc39.s390x lz4-libs-1.9.4-4.fc39.s390x mpdecimal-2.5.1-7.fc39.s390x mpfr-4.2.0-3.fc39.s390x ncurses-base-6.4-6.20230520.fc39.noarch ncurses-libs-6.4-6.20230520.fc39.s390x nettle-3.9.1-2.fc39.s390x npth-1.6-14.fc39.s390x openldap-2.6.6-1.fc39.s390x openssl-libs-1:3.1.1-1.fc39.s390x p11-kit-0.25.0-2.fc39.s390x p11-kit-trust-0.25.0-2.fc39.s390x pcre2-10.42-1.fc39.2.s390x pcre2-syntax-10.42-1.fc39.2.noarch popt-1.19-3.fc39.s390x publicsuffix-list-dafsa-20230614-2.fc39.noarch python-pip-wheel-23.1.2-5.fc39.noarch python3-3.12.0~b4-2.fc39.s390x python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.s390x python3-distro-1.8.0-6.fc39.noarch python3-dnf-4.16.2-1.fc39.noarch python3-dnf-plugins-core-4.4.2-1.fc39.noarch python3-gpg-1.20.0-5.fc39.s390x python3-hawkey-0.70.2-1.fc39.s390x python3-libcomps-0.1.19-3.fc39.s390x python3-libdnf-0.70.2-1.fc39.s390x python3-libs-3.12.0~b4-2.fc39.s390x python3-rpm-4.18.92-1.fc39.s390x python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.s390x readline-8.2-4.fc39.s390x rpm-4.18.92-1.fc39.s390x rpm-build-libs-4.18.92-1.fc39.s390x rpm-libs-4.18.92-1.fc39.s390x rpm-sequoia-1.4.1-2.fc39.s390x rpm-sign-libs-4.18.92-1.fc39.s390x sed-4.8-14.fc39.s390x setup-2.14.4-1.fc39.noarch shadow-utils-2:4.13-8.fc39.s390x sqlite-libs-3.42.0-7.fc39.s390x systemd-libs-254-1.fc39.s390x tpm2-tss-4.0.1-4.fc39.s390x tzdata-2023c-2.fc39.noarch xz-libs-5.4.4-1.fc39.s390x zchunk-libs-1.3.1-2.fc39.s390x zlib-1.2.13-4.fc39.s390x Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/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: 4.1 INFO: Mock Version: 4.1 INFO: Package manager dnf detected and used (direct choice) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 3.0 kB/s | 1.5 kB 00:00 Copr repository 13 MB/s | 8.9 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 4.4 kB/s | 3.8 kB 00:00 fedora 4.8 kB/s | 4.4 kB 00:00 Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash s390x 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 142 k lua-srpm-macros noarch 1-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.6 k lz4-libs s390x 1.9.4-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 81 k mpfr s390x 4.2.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 298 k ncurses-base noarch 6.4-6.20230520.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 63 k ncurses-libs s390x 6.4-6.20230520.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 361 k ocaml-srpm-macros noarch 8-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k openblas-srpm-macros noarch 2-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.5 k openldap s390x 2.6.6-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262 k openssl-libs s390x 1:3.1.1-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.9 M p11-kit s390x 0.25.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 493 k p11-kit-trust s390x 0.25.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 141 k package-notes-srpm-macros noarch 0.5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k pam s390x 1.5.3-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 521 k pam-libs s390x 1.5.3-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 59 k pcre2 s390x 10.42-1.fc39.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 250 k pcre2-syntax noarch 10.42-1.fc39.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 143 k perl-srpm-macros noarch 1-51.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.0 k pkgconf s390x 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k pkgconf-m4 noarch 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k pkgconf-pkg-config s390x 1.9.5-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.6 k popt s390x 1.19-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 62 k publicsuffix-list-dafsa noarch 20230614-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 57 k pyproject-srpm-macros noarch 1.9.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k python-srpm-macros noarch 3.12-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k qt5-srpm-macros noarch 5.15.10-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.3 k qt6-srpm-macros noarch 6.5.2-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.2 k readline s390x 8.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 229 k rpm s390x 4.18.92-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 510 k rpm-build-libs s390x 4.18.92-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 97 k rpm-libs s390x 4.18.92-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 323 k rpm-sequoia s390x 1.4.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 986 k rpmautospec-rpm-macros noarch 0.3.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.8 k rust-srpm-macros noarch 24-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k setup noarch 2.14.4-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 148 k sqlite-libs s390x 3.42.0-7.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 728 k systemd-libs s390x 254-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 693 k tzdata noarch 2023c-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 433 k util-linux-core s390x 2.39.1-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482 k xxhash-libs s390x 0.8.2-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k xz-libs s390x 5.4.4-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 114 k zip s390x 3.0-38.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 283 k zlib s390x 1.2.13-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k zstd s390x 1.5.5-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 506 k Installing Groups: Buildsystem building group Transaction Summary ======================================================================================================================================== Install 153 Packages Total size: 52 M Installed size: 180 M Downloading Packages: [SKIPPED] gdb-minimal-13.2-6.fc39.s390x.rpm: Already downloaded [SKIPPED] alternatives-1.25-1.fc39.s390x.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.1.1-4.fc39.s390x.rpm: Already downloaded [SKIPPED] authselect-1.4.2-3.fc39.s390x.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.2-3.fc39.s390x.rpm: Already downloaded [SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.15-5.fc39.s390x.rpm: Already downloaded [SKIPPED] binutils-2.40-13.fc39.s390x.rpm: Already downloaded [SKIPPED] binutils-gold-2.40-13.fc39.s390x.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-16.fc39.s390x.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-16.fc39.s390x.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.3-2.fc39.s390x.rpm: Already downloaded [SKIPPED] coreutils-common-9.3-2.fc39.s390x.rpm: Already downloaded [SKIPPED] cpio-2.14-4.fc39.s390x.rpm: Already downloaded [SKIPPED] cracklib-2.9.11-2.fc39.s390x.rpm: Already downloaded [SKIPPED] crypto-policies-20230731-1.git5ed06e0.fc39.noarch.rpm: Already downloaded [SKIPPED] curl-8.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-11.fc39.s390x.rpm: Already downloaded [SKIPPED] debugedit-5.0-10.fc39.s390x.rpm: Already downloaded [SKIPPED] diffutils-3.10-3.fc39.s390x.rpm: Already downloaded [SKIPPED] dwz-0.15-3.fc39.s390x.rpm: Already downloaded [SKIPPED] ed-1.19-4.fc39.s390x.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-9.fc39.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.189-4.fc39.s390x.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.189-4.fc39.s390x.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.189-4.fc39.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.189-4.fc39.s390x.rpm: Already downloaded [SKIPPED] elfutils-libs-0.189-4.fc39.s390x.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-39-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-release-39-0.21.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-39-0.21.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-39-0.21.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-39-0.4.noarch.rpm: Already downloaded [SKIPPED] fedora-repos-rawhide-39-0.4.noarch.rpm: Already downloaded [SKIPPED] file-5.44-5.fc39.s390x.rpm: Already downloaded [SKIPPED] file-libs-5.44-5.fc39.s390x.rpm: Already downloaded [SKIPPED] filesystem-3.18-6.fc39.s390x.rpm: Already downloaded [SKIPPED] findutils-4.9.0-5.fc39.s390x.rpm: Already downloaded [SKIPPED] fonts-srpm-macros-2.0.5-12.fc39.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-8.fc39.noarch.rpm: Already downloaded [SKIPPED] gawk-5.2.2-2.fc39.s390x.rpm: Already downloaded [SKIPPED] gdbm-libs-1.23-4.fc39.s390x.rpm: Already downloaded [SKIPPED] ghc-srpm-macros-1.6.1-2.fc39.noarch.rpm: Already downloaded [SKIPPED] glibc-2.37.9000-18.fc39.s390x.rpm: Already downloaded [SKIPPED] glibc-common-2.37.9000-18.fc39.s390x.rpm: Already downloaded [SKIPPED] glibc-gconv-extra-2.37.9000-18.fc39.s390x.rpm: Already downloaded [SKIPPED] glibc-minimal-langpack-2.37.9000-18.fc39.s390x.rpm: Already downloaded [SKIPPED] gmp-6.2.1-5.fc39.s390x.rpm: Already downloaded [SKIPPED] gnat-srpm-macros-6-3.fc39.noarch.rpm: Already downloaded [SKIPPED] go-srpm-macros-3.2.0-6.fc39.noarch.rpm: Already downloaded [SKIPPED] grep-3.11-3.fc39.s390x.rpm: Already downloaded [SKIPPED] gzip-1.12-6.fc39.s390x.rpm: Already downloaded [SKIPPED] info-7.0.3-3.fc39.s390x.rpm: Already downloaded [SKIPPED] jansson-2.13.1-7.fc39.s390x.rpm: Already downloaded [SKIPPED] kernel-srpm-macros-1.0-20.fc39.noarch.rpm: Already downloaded [SKIPPED] keyutils-libs-1.6.1-7.fc39.s390x.rpm: Already downloaded [SKIPPED] krb5-libs-1.21-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libacl-2.3.1-8.fc39.s390x.rpm: Already downloaded [SKIPPED] libarchive-3.7.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libattr-2.5.1-8.fc39.s390x.rpm: Already downloaded [SKIPPED] libblkid-2.39.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libbrotli-1.0.9-13.fc39.s390x.rpm: Already downloaded [SKIPPED] libcap-2.48-7.fc39.s390x.rpm: Already downloaded [SKIPPED] libcap-ng-0.8.3-7.fc39.s390x.rpm: Already downloaded [SKIPPED] libcom_err-1.47.0-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libcurl-8.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libdb-5.3.28-56.fc39.s390x.rpm: Already downloaded [SKIPPED] libeconf-0.4.0-6.fc39.s390x.rpm: Already downloaded [SKIPPED] libevent-2.1.12-9.fc39.s390x.rpm: Already downloaded [SKIPPED] libfdisk-2.39.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libffi-3.4.4-4.fc39.s390x.rpm: Already downloaded [SKIPPED] libgcc-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libgomp-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libidn2-2.3.4-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libmount-2.39.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libnghttp2-1.55.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libnsl2-2.0.0-6.fc39.s390x.rpm: Already downloaded [SKIPPED] libpkgconf-1.9.5-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libpsl-0.21.2-4.fc39.s390x.rpm: Already downloaded [SKIPPED] libpwquality-1.4.5-6.fc39.s390x.rpm: Already downloaded 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unzip-6.0-62.fc39.s390x.rpm: Already downloaded [SKIPPED] util-linux-2.39.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] util-linux-core-2.39.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] which-2.21-40.fc39.s390x.rpm: Already downloaded [SKIPPED] xxhash-libs-0.8.2-1.fc39.s390x.rpm: Already downloaded [SKIPPED] xz-5.4.4-1.fc39.s390x.rpm: Already downloaded [SKIPPED] xz-libs-5.4.4-1.fc39.s390x.rpm: Already downloaded [SKIPPED] zip-3.0-38.fc39.s390x.rpm: Already downloaded [SKIPPED] zlib-1.2.13-4.fc39.s390x.rpm: Already downloaded [SKIPPED] zstd-1.5.5-4.fc39.s390x.rpm: Already downloaded Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.s390x 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-1.fc39.s390x 1/153 Running scriptlet: libgcc-13.2.1-1.fc39.s390x 1/153 Installing : crypto-policies-20230731-1.git5ed06e0.fc39.noarc 2/153 Running scriptlet: crypto-policies-20230731-1.git5ed06e0.fc39.noarc 2/153 Installing : tzdata-2023c-2.fc39.noarch 3/153 Installing : fedora-release-identity-basic-39-0.21.noarch 4/153 Installing : fedora-repos-rawhide-39-0.4.noarch 5/153 Installing : fedora-gpg-keys-39-0.4.noarch 6/153 Installing : fedora-repos-39-0.4.noarch 7/153 Installing : fedora-release-common-39-0.21.noarch 8/153 Installing : fedora-release-39-0.21.noarch 9/153 Installing : setup-2.14.4-1.fc39.noarch 10/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.4-1.fc39.noarch 10/153 Installing : filesystem-3.18-6.fc39.s390x 11/153 Installing : basesystem-11-18.fc39.noarch 12/153 Installing : rust-srpm-macros-24-3.fc39.noarch 13/153 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Installing : info-7.0.3-3.fc39.s390x 153/153 Running scriptlet: filesystem-3.18-6.fc39.s390x 153/153 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 153/153 Running scriptlet: authselect-libs-1.4.2-3.fc39.s390x 153/153 Running scriptlet: rpm-4.18.92-1.fc39.s390x 153/153 Running scriptlet: info-7.0.3-3.fc39.s390x 153/153 Verifying : gdb-minimal-13.2-6.fc39.s390x 1/153 Verifying : alternatives-1.25-1.fc39.s390x 2/153 Verifying : ansible-srpm-macros-1-11.fc39.noarch 3/153 Verifying : audit-libs-3.1.1-4.fc39.s390x 4/153 Verifying : authselect-1.4.2-3.fc39.s390x 5/153 Verifying : authselect-libs-1.4.2-3.fc39.s390x 6/153 Verifying : basesystem-11-18.fc39.noarch 7/153 Verifying : bash-5.2.15-5.fc39.s390x 8/153 Verifying : binutils-2.40-13.fc39.s390x 9/153 Verifying : binutils-gold-2.40-13.fc39.s390x 10/153 Verifying : bzip2-1.0.8-16.fc39.s390x 11/153 Verifying : bzip2-libs-1.0.8-16.fc39.s390x 12/153 Verifying : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 13/153 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pam-1.5.3-2.fc39.s390x 113/153 Verifying : pam-libs-1.5.3-2.fc39.s390x 114/153 Verifying : patch-2.7.6-22.fc39.s390x 115/153 Verifying : pcre2-10.42-1.fc39.2.s390x 116/153 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 117/153 Verifying : perl-srpm-macros-1-51.fc39.noarch 118/153 Verifying : pkgconf-1.9.5-2.fc39.s390x 119/153 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 120/153 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.s390x 121/153 Verifying : popt-1.19-3.fc39.s390x 122/153 Verifying : publicsuffix-list-dafsa-20230614-2.fc39.noarch 123/153 Verifying : pyproject-srpm-macros-1.9.0-2.fc39.noarch 124/153 Verifying : python-srpm-macros-3.12-2.fc39.noarch 125/153 Verifying : qt5-srpm-macros-5.15.10-2.fc39.noarch 126/153 Verifying : qt6-srpm-macros-6.5.2-2.fc39.noarch 127/153 Verifying : readline-8.2-4.fc39.s390x 128/153 Verifying : redhat-rpm-config-261-1.fc39.noarch 129/153 Verifying : rpm-4.18.92-1.fc39.s390x 130/153 Verifying : rpm-build-4.18.92-1.fc39.s390x 131/153 Verifying : rpm-build-libs-4.18.92-1.fc39.s390x 132/153 Verifying : rpm-libs-4.18.92-1.fc39.s390x 133/153 Verifying : rpm-sequoia-1.4.1-2.fc39.s390x 134/153 Verifying : rpmautospec-rpm-macros-0.3.5-4.fc39.noarch 135/153 Verifying : rust-srpm-macros-24-3.fc39.noarch 136/153 Verifying : sed-4.8-14.fc39.s390x 137/153 Verifying : setup-2.14.4-1.fc39.noarch 138/153 Verifying : shadow-utils-2:4.13-8.fc39.s390x 139/153 Verifying : sqlite-libs-3.42.0-7.fc39.s390x 140/153 Verifying : systemd-libs-254-1.fc39.s390x 141/153 Verifying : tar-2:1.35-1.fc39.s390x 142/153 Verifying : tzdata-2023c-2.fc39.noarch 143/153 Verifying : unzip-6.0-62.fc39.s390x 144/153 Verifying : util-linux-2.39.1-3.fc39.s390x 145/153 Verifying : util-linux-core-2.39.1-3.fc39.s390x 146/153 Verifying : which-2.21-40.fc39.s390x 147/153 Verifying : xxhash-libs-0.8.2-1.fc39.s390x 148/153 Verifying : xz-5.4.4-1.fc39.s390x 149/153 Verifying : xz-libs-5.4.4-1.fc39.s390x 150/153 Verifying : zip-3.0-38.fc39.s390x 151/153 Verifying : zlib-1.2.13-4.fc39.s390x 152/153 Verifying : zstd-1.5.5-4.fc39.s390x 153/153 Installed: alternatives-1.25-1.fc39.s390x ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.1-4.fc39.s390x authselect-1.4.2-3.fc39.s390x authselect-libs-1.4.2-3.fc39.s390x basesystem-11-18.fc39.noarch bash-5.2.15-5.fc39.s390x binutils-2.40-13.fc39.s390x binutils-gold-2.40-13.fc39.s390x bzip2-1.0.8-16.fc39.s390x bzip2-libs-1.0.8-16.fc39.s390x ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-2.fc39.s390x coreutils-common-9.3-2.fc39.s390x cpio-2.14-4.fc39.s390x cracklib-2.9.11-2.fc39.s390x crypto-policies-20230731-1.git5ed06e0.fc39.noarch curl-8.2.1-1.fc39.s390x cyrus-sasl-lib-2.1.28-11.fc39.s390x debugedit-5.0-10.fc39.s390x diffutils-3.10-3.fc39.s390x dwz-0.15-3.fc39.s390x ed-1.19-4.fc39.s390x efi-srpm-macros-5-9.fc39.noarch elfutils-0.189-4.fc39.s390x elfutils-debuginfod-client-0.189-4.fc39.s390x elfutils-default-yama-scope-0.189-4.fc39.noarch elfutils-libelf-0.189-4.fc39.s390x elfutils-libs-0.189-4.fc39.s390x fedora-gpg-keys-39-0.4.noarch fedora-release-39-0.21.noarch fedora-release-common-39-0.21.noarch fedora-release-identity-basic-39-0.21.noarch fedora-repos-39-0.4.noarch fedora-repos-rawhide-39-0.4.noarch file-5.44-5.fc39.s390x file-libs-5.44-5.fc39.s390x filesystem-3.18-6.fc39.s390x findutils-1:4.9.0-5.fc39.s390x fonts-srpm-macros-1:2.0.5-12.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.s390x gdb-minimal-13.2-6.fc39.s390x gdbm-libs-1:1.23-4.fc39.s390x ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.37.9000-18.fc39.s390x glibc-common-2.37.9000-18.fc39.s390x glibc-gconv-extra-2.37.9000-18.fc39.s390x glibc-minimal-langpack-2.37.9000-18.fc39.s390x gmp-1:6.2.1-5.fc39.s390x gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.2.0-6.fc39.noarch grep-3.11-3.fc39.s390x gzip-1.12-6.fc39.s390x info-7.0.3-3.fc39.s390x jansson-2.13.1-7.fc39.s390x kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.s390x krb5-libs-1.21-3.fc39.s390x libacl-2.3.1-8.fc39.s390x libarchive-3.7.1-1.fc39.s390x libattr-2.5.1-8.fc39.s390x libblkid-2.39.1-3.fc39.s390x libbrotli-1.0.9-13.fc39.s390x libcap-2.48-7.fc39.s390x libcap-ng-0.8.3-7.fc39.s390x libcom_err-1.47.0-2.fc39.s390x libcurl-8.2.1-1.fc39.s390x libdb-5.3.28-56.fc39.s390x libeconf-0.4.0-6.fc39.s390x libevent-2.1.12-9.fc39.s390x libfdisk-2.39.1-3.fc39.s390x libffi-3.4.4-4.fc39.s390x libgcc-13.2.1-1.fc39.s390x libgomp-13.2.1-1.fc39.s390x libidn2-2.3.4-3.fc39.s390x libmount-2.39.1-3.fc39.s390x libnghttp2-1.55.1-2.fc39.s390x libnsl2-2.0.0-6.fc39.s390x libpkgconf-1.9.5-2.fc39.s390x libpsl-0.21.2-4.fc39.s390x libpwquality-1.4.5-6.fc39.s390x libselinux-3.5-5.fc39.s390x libsemanage-3.5-4.fc39.s390x libsepol-3.5-2.fc39.s390x libsigsegv-2.14-5.fc39.s390x libsmartcols-2.39.1-3.fc39.s390x libssh-0.10.5-2.fc39.s390x libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-1.fc39.s390x libtasn1-4.19.0-3.fc39.s390x libtirpc-1.3.3-1.rc1.fc39.1.s390x libunistring-1.1-4.fc39.s390x libutempter-1.2.1-10.fc39.s390x libuuid-2.39.1-3.fc39.s390x libverto-0.3.2-6.fc39.s390x libxcrypt-4.4.36-2.fc39.s390x libxml2-2.10.4-3.fc39.s390x libzstd-1.5.5-4.fc39.s390x lua-libs-5.4.6-3.fc39.s390x lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.s390x mpfr-4.2.0-3.fc39.s390x ncurses-base-6.4-6.20230520.fc39.noarch ncurses-libs-6.4-6.20230520.fc39.s390x ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.s390x openssl-libs-1:3.1.1-1.fc39.s390x p11-kit-0.25.0-2.fc39.s390x p11-kit-trust-0.25.0-2.fc39.s390x package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-2.fc39.s390x pam-libs-1.5.3-2.fc39.s390x patch-2.7.6-22.fc39.s390x pcre2-10.42-1.fc39.2.s390x pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.s390x pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.s390x popt-1.19-3.fc39.s390x publicsuffix-list-dafsa-20230614-2.fc39.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch python-srpm-macros-3.12-2.fc39.noarch qt5-srpm-macros-5.15.10-2.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch readline-8.2-4.fc39.s390x redhat-rpm-config-261-1.fc39.noarch rpm-4.18.92-1.fc39.s390x rpm-build-4.18.92-1.fc39.s390x rpm-build-libs-4.18.92-1.fc39.s390x rpm-libs-4.18.92-1.fc39.s390x rpm-sequoia-1.4.1-2.fc39.s390x rpmautospec-rpm-macros-0.3.5-4.fc39.noarch rust-srpm-macros-24-3.fc39.noarch sed-4.8-14.fc39.s390x setup-2.14.4-1.fc39.noarch shadow-utils-2:4.13-8.fc39.s390x sqlite-libs-3.42.0-7.fc39.s390x systemd-libs-254-1.fc39.s390x tar-2:1.35-1.fc39.s390x tzdata-2023c-2.fc39.noarch unzip-6.0-62.fc39.s390x util-linux-2.39.1-3.fc39.s390x util-linux-core-2.39.1-3.fc39.s390x which-2.21-40.fc39.s390x xxhash-libs-0.8.2-1.fc39.s390x xz-5.4.4-1.fc39.s390x xz-libs-5.4.4-1.fc39.s390x zip-3.0-38.fc39.s390x zlib-1.2.13-4.fc39.s390x zstd-1.5.5-4.fc39.s390x Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: libpsl-0.21.2-4.fc39.s390x libcap-2.48-7.fc39.s390x systemd-libs-254-1.fc39.s390x rpm-libs-4.18.92-1.fc39.s390x bzip2-libs-1.0.8-16.fc39.s390x ghc-srpm-macros-1.6.1-2.fc39.noarch setup-2.14.4-1.fc39.noarch qt6-srpm-macros-6.5.2-2.fc39.noarch libnghttp2-1.55.1-2.fc39.s390x publicsuffix-list-dafsa-20230614-2.fc39.noarch libxcrypt-4.4.36-2.fc39.s390x krb5-libs-1.21-3.fc39.s390x libpwquality-1.4.5-6.fc39.s390x filesystem-3.18-6.fc39.s390x file-5.44-5.fc39.s390x libsigsegv-2.14-5.fc39.s390x libunistring-1.1-4.fc39.s390x tzdata-2023c-2.fc39.noarch lz4-libs-1.9.4-4.fc39.s390x libmount-2.39.1-3.fc39.s390x libnsl2-2.0.0-6.fc39.s390x rust-srpm-macros-24-3.fc39.noarch mpfr-4.2.0-3.fc39.s390x pcre2-10.42-1.fc39.2.s390x python-srpm-macros-3.12-2.fc39.noarch gnat-srpm-macros-6-3.fc39.noarch openldap-2.6.6-1.fc39.s390x libselinux-3.5-5.fc39.s390x fonts-srpm-macros-2.0.5-12.fc39.noarch p11-kit-0.25.0-2.fc39.s390x pkgconf-pkg-config-1.9.5-2.fc39.s390x zip-3.0-38.fc39.s390x grep-3.11-3.fc39.s390x ed-1.19-4.fc39.s390x patch-2.7.6-22.fc39.s390x pam-1.5.3-2.fc39.s390x elfutils-default-yama-scope-0.189-4.fc39.noarch libstdc++-13.2.1-1.fc39.s390x gmp-6.2.1-5.fc39.s390x coreutils-9.3-2.fc39.s390x gdb-minimal-13.2-6.fc39.s390x fedora-release-identity-basic-39-0.21.noarch libutempter-1.2.1-10.fc39.s390x jansson-2.13.1-7.fc39.s390x unzip-6.0-62.fc39.s390x elfutils-libelf-0.189-4.fc39.s390x crypto-policies-20230731-1.git5ed06e0.fc39.noarch pcre2-syntax-10.42-1.fc39.2.noarch shadow-utils-4.13-8.fc39.s390x gawk-5.2.2-2.fc39.s390x libssh-config-0.10.5-2.fc39.noarch fedora-repos-rawhide-39-0.4.noarch cpio-2.14-4.fc39.s390x cyrus-sasl-lib-2.1.28-11.fc39.s390x pam-libs-1.5.3-2.fc39.s390x glibc-minimal-langpack-2.37.9000-18.fc39.s390x libdb-5.3.28-56.fc39.s390x fedora-gpg-keys-39-0.4.noarch rpm-4.18.92-1.fc39.s390x pkgconf-1.9.5-2.fc39.s390x libssh-0.10.5-2.fc39.s390x authselect-1.4.2-3.fc39.s390x util-linux-core-2.39.1-3.fc39.s390x glibc-gconv-extra-2.37.9000-18.fc39.s390x libgomp-13.2.1-1.fc39.s390x p11-kit-trust-0.25.0-2.fc39.s390x package-notes-srpm-macros-0.5-9.fc39.noarch ncurses-libs-6.4-6.20230520.fc39.s390x libverto-0.3.2-6.fc39.s390x fedora-repos-39-0.4.noarch libsemanage-3.5-4.fc39.s390x libcom_err-1.47.0-2.fc39.s390x basesystem-11-18.fc39.noarch libcap-ng-0.8.3-7.fc39.s390x cracklib-2.9.11-2.fc39.s390x libgcc-13.2.1-1.fc39.s390x libarchive-3.7.1-1.fc39.s390x libpkgconf-1.9.5-2.fc39.s390x libcurl-8.2.1-1.fc39.s390x rpm-sequoia-1.4.1-2.fc39.s390x alternatives-1.25-1.fc39.s390x libfdisk-2.39.1-3.fc39.s390x rpmautospec-rpm-macros-0.3.5-4.fc39.noarch libeconf-0.4.0-6.fc39.s390x ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch pyproject-srpm-macros-1.9.0-2.fc39.noarch keyutils-libs-1.6.1-7.fc39.s390x qt5-srpm-macros-5.15.10-2.fc39.noarch popt-1.19-3.fc39.s390x authselect-libs-1.4.2-3.fc39.s390x coreutils-common-9.3-2.fc39.s390x util-linux-2.39.1-3.fc39.s390x fedora-release-common-39-0.21.noarch binutils-2.40-13.fc39.s390x zstd-1.5.5-4.fc39.s390x openssl-libs-3.1.1-1.fc39.s390x sed-4.8-14.fc39.s390x dwz-0.15-3.fc39.s390x glibc-2.37.9000-18.fc39.s390x zlib-1.2.13-4.fc39.s390x go-srpm-macros-3.2.0-6.fc39.noarch findutils-4.9.0-5.fc39.s390x libzstd-1.5.5-4.fc39.s390x libsmartcols-2.39.1-3.fc39.s390x info-7.0.3-3.fc39.s390x xz-5.4.4-1.fc39.s390x lua-libs-5.4.6-3.fc39.s390x elfutils-0.189-4.fc39.s390x libevent-2.1.12-9.fc39.s390x glibc-common-2.37.9000-18.fc39.s390x libffi-3.4.4-4.fc39.s390x readline-8.2-4.fc39.s390x ocaml-srpm-macros-8-2.fc39.noarch debugedit-5.0-10.fc39.s390x fpc-srpm-macros-1.3-8.fc39.noarch audit-libs-3.1.1-4.fc39.s390x perl-srpm-macros-1-51.fc39.noarch libuuid-2.39.1-3.fc39.s390x libsepol-3.5-2.fc39.s390x file-libs-5.44-5.fc39.s390x gdbm-libs-1.23-4.fc39.s390x redhat-rpm-config-261-1.fc39.noarch rpm-build-4.18.92-1.fc39.s390x pkgconf-m4-1.9.5-2.fc39.noarch fedora-release-39-0.21.noarch libblkid-2.39.1-3.fc39.s390x binutils-gold-2.40-13.fc39.s390x which-2.21-40.fc39.s390x kernel-srpm-macros-1.0-20.fc39.noarch libbrotli-1.0.9-13.fc39.s390x ansible-srpm-macros-1-11.fc39.noarch gzip-1.12-6.fc39.s390x libxml2-2.10.4-3.fc39.s390x libidn2-2.3.4-3.fc39.s390x lua-srpm-macros-1-9.fc39.noarch diffutils-3.10-3.fc39.s390x openblas-srpm-macros-2-14.fc39.noarch xz-libs-5.4.4-1.fc39.s390x libacl-2.3.1-8.fc39.s390x elfutils-libs-0.189-4.fc39.s390x libtirpc-1.3.3-1.rc1.fc39.1.s390x libattr-2.5.1-8.fc39.s390x tar-1.35-1.fc39.s390x libtasn1-4.19.0-3.fc39.s390x rpm-build-libs-4.18.92-1.fc39.s390x ncurses-base-6.4-6.20230520.fc39.noarch bash-5.2.15-5.fc39.s390x curl-8.2.1-1.fc39.s390x xxhash-libs-0.8.2-1.fc39.s390x efi-srpm-macros-5-9.fc39.noarch elfutils-debuginfod-client-0.189-4.fc39.s390x sqlite-libs-3.42.0-7.fc39.s390x bzip2-1.0.8-16.fc39.s390x Start: buildsrpm Start: rpmbuild -bs Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689897600 Wrote: /builddir/build/SRPMS/python-biopython-1.81-4.fc39.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-i1kicmfb/python-biopython/python-biopython.spec) Config(child) 2 minutes 9 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=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/python-biopython-1.81-4.fc39.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1691114939.268004 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 4.1 starting (python version = 3.11.3, NVR = mock-4.1-1.fc38)... 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-1.81-4.fc39.src.rpm) Config(fedora-rawhide-s390x) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1691114939.268004/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1691114939.268004/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: 4.1 INFO: Mock Version: 4.1 INFO: Package manager dnf detected and used (fallback) Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/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: 4.1 INFO: Mock Version: 4.1 INFO: Package manager dnf detected and used (direct choice) Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 2.6 kB/s | 1.5 kB 00:00 Copr repository 13 MB/s | 8.9 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 4.4 kB/s | 3.8 kB 00:00 fedora 806 B/s | 4.4 kB 00:05 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for python-biopython-1.81-4.fc39.src.rpm Start: build setup for python-biopython-1.81-4.fc39.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689897600 Wrote: /builddir/build/SRPMS/python-biopython-1.81-4.fc39.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 259 B/s | 1.5 kB 00:06 Additional repo http_kojipkgs_fedoraproject_org 4.4 kB/s | 3.8 kB 00:00 fedora 4.9 kB/s | 4.4 kB 00:00 Dependencies resolved. ================================================================================================================================== Package Arch Version Repository Size ================================================================================================================================== Installing: gcc s390x 13.2.1-1.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 M mysql-connector-python3 noarch 8.0.21-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 538 k python3-devel s390x 3.12.0~b4-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 273 k python3-mysqlclient s390x 2.1.1-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96 k python3-numpy s390x 1:1.24.4-2.fc39 copr_base 7.3 M python3-psycopg2 s390x 2.9.6-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 201 k python3-rdflib noarch 6.2.0-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 882 k python3-reportlab noarch 4.0.4-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.2 M python3-setuptools noarch 67.7.2-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.4 M Installing dependencies: abattis-cantarell-vf-fonts noarch 0.301-10.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k annobin-docs noarch 12.23-1.fc39 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 14 k python3-six noarch 1.16.0-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k xml-common noarch 0.6.3-61.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k Transaction Summary ================================================================================================================================== Install 84 Packages Total size: 96 M Total download size: 6.7 M Installed size: 346 M Downloading Packages: [SKIPPED] flexiblas-3.3.1-5.fc39.s390x.rpm: Already downloaded [SKIPPED] flexiblas-netlib-3.3.1-5.fc39.s390x.rpm: Already downloaded [SKIPPED] flexiblas-openblas-openmp-3.3.1-5.fc39.s390x.rpm: Already downloaded [SKIPPED] graphite2-1.3.14-12.fc39.s390x.rpm: Already downloaded [SKIPPED] openblas-0.3.23-1.fc39.s390x.rpm: Already downloaded [SKIPPED] openblas-openmp-0.3.23-1.fc39.s390x.rpm: Already downloaded [SKIPPED] python3-numpy-1.24.4-2.fc39.s390x.rpm: Already downloaded [SKIPPED] abattis-cantarell-vf-fonts-0.301-10.fc39.noarch.rpm: Already downloaded [SKIPPED] annobin-docs-12.23-1.fc39.noarch.rpm: Already downloaded [SKIPPED] annobin-plugin-gcc-12.23-1.fc39.s390x.rpm: Already downloaded [SKIPPED] cairo-1.17.8-5.fc39.s390x.rpm: Already downloaded [SKIPPED] cpp-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] default-fonts-core-sans-4.0-6.fc39.noarch.rpm: Already downloaded [SKIPPED] dejavu-sans-fonts-2.37-20.fc38.noarch.rpm: Already downloaded [SKIPPED] expat-2.5.0-3.fc39.s390x.rpm: Already downloaded [SKIPPED] fontconfig-2.14.2-4.fc39.s390x.rpm: Already downloaded [SKIPPED] fonts-filesystem-2.0.5-12.fc39.noarch.rpm: Already downloaded [SKIPPED] freetype-2.13.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] fribidi-1.0.13-2.fc39.s390x.rpm: Already downloaded [SKIPPED] gc-8.2.2-4.fc39.s390x.rpm: Already downloaded [SKIPPED] gcc-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] glib2-2.77.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] glibc-devel-2.37.9000-18.fc39.s390x.rpm: Already downloaded [SKIPPED] glibc-headers-s390-2.37.9000-18.fc39.noarch.rpm: Already downloaded [SKIPPED] gnutls-3.8.0-7.fc39.s390x.rpm: Already downloaded [SKIPPED] google-noto-fonts-common-20230801-1.fc39.noarch.rpm: Already downloaded [SKIPPED] google-noto-sans-vf-fonts-20230801-1.fc39.noarch.rpm: Already downloaded [SKIPPED] guile22-2.2.7-9.fc39.s390x.rpm: Already downloaded [SKIPPED] harfbuzz-8.1.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] jbigkit-libs-2.1-26.fc39.s390x.rpm: Already downloaded [SKIPPED] kernel-headers-6.5.0-0.rc2.git0.1.fc39.s390x.rpm: Already downloaded [SKIPPED] lcms2-2.15-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libX11-1.8.6-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libX11-common-1.8.6-2.fc39.noarch.rpm: Already downloaded [SKIPPED] libXau-1.0.11-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libXext-1.3.5-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libXrender-0.9.11-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libasan-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libatomic-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libb2-0.98.1-9.fc39.s390x.rpm: Already downloaded [SKIPPED] libgfortran-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libimagequant-4.0.1-5.fc39.s390x.rpm: Already downloaded [SKIPPED] libjpeg-turbo-2.1.4-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libmpc-1.3.1-3.fc39.s390x.rpm: Already downloaded [SKIPPED] libpng-1.6.37-15.fc39.s390x.rpm: Already downloaded [SKIPPED] libraqm-0.8.0-5.fc39.s390x.rpm: Already downloaded [SKIPPED] libtiff-4.4.0-7.fc39.s390x.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.7-7.fc39.s390x.rpm: Already downloaded [SKIPPED] libubsan-13.2.1-1.fc39.s390x.rpm: Already downloaded [SKIPPED] libwebp-1.3.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] libxcb-1.13.1-12.fc39.s390x.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.4.36-2.fc39.s390x.rpm: Already downloaded [SKIPPED] make-4.4.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] mpdecimal-2.5.1-7.fc39.s390x.rpm: Already downloaded [SKIPPED] nettle-3.9.1-2.fc39.s390x.rpm: Already downloaded [SKIPPED] openjpeg2-2.5.0-4.fc39.s390x.rpm: Already downloaded [SKIPPED] pixman-0.42.2-2.fc39.s390x.rpm: Already downloaded [SKIPPED] pyproject-rpm-macros-1.9.0-2.fc39.noarch.rpm: Already downloaded [SKIPPED] python-pip-wheel-23.1.2-5.fc39.noarch.rpm: Already downloaded [SKIPPED] python-rpm-macros-3.12-2.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-3.12.0~b4-2.fc39.s390x.rpm: Already downloaded [SKIPPED] python3-devel-3.12.0~b4-2.fc39.s390x.rpm: Already downloaded [SKIPPED] python3-libs-3.12.0~b4-2.fc39.s390x.rpm: Already downloaded [SKIPPED] python3-olefile-0.46-21.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-packaging-23.1-4.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-pillow-10.0.0-2.fc39.s390x.rpm: Already downloaded [SKIPPED] python3-pyparsing-3.0.9-11.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-generators-14-7.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-macros-3.12-2.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-setuptools-67.7.2-5.fc39.noarch.rpm: Already downloaded [SKIPPED] python3-six-1.16.0-12.fc39.noarch.rpm: Already downloaded [SKIPPED] xml-common-0.6.3-61.fc39.noarch.rpm: Already downloaded (74/84): mariadb-connector-c-config-3.3.5-2.fc3 7.9 kB/s | 8.8 kB 00:01 (75/84): libpq-15.3-1.fc39.s390x.rpm 136 kB/s | 218 kB 00:01 (76/84): mariadb-connector-c-3.3.5-2.fc39.s390x 137 kB/s | 222 kB 00:01 (77/84): python3-isodate-0.6.1-9.fc39.noarch.rp 183 kB/s | 67 kB 00:00 (78/84): protobuf-3.19.6-6.fc39.s390x.rpm 1.4 MB/s | 1.0 MB 00:00 (79/84): mysql-connector-python3-8.0.21-10.fc39 444 kB/s | 538 kB 00:01 (80/84): python3-mysqlclient-2.1.1-5.fc39.s390x 276 kB/s | 96 kB 00:00 (81/84): python3-protobuf-3.19.6-6.fc39.s390x.r 1.1 MB/s | 390 kB 00:00 (82/84): python3-psycopg2-2.9.6-3.fc39.s390x.rp 385 kB/s | 201 kB 00:00 (83/84): python3-rdflib-6.2.0-4.fc39.noarch.rpm 1.6 MB/s | 882 kB 00:00 (84/84): python3-reportlab-4.0.4-3.fc39.noarch. 5.9 MB/s | 3.2 MB 00:00 -------------------------------------------------------------------------------- Total 2.1 MB/s | 6.7 MB 00:03 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : fonts-filesystem-1:2.0.5-12.fc39.noarch 1/84 Installing : python-rpm-macros-3.12-2.fc39.noarch 2/84 Installing : python3-rpm-macros-3.12-2.fc39.noarch 3/84 Installing : libwebp-1.3.1-2.fc39.s390x 4/84 Installing : libpng-2:1.6.37-15.fc39.s390x 5/84 Installing : libmpc-1.3.1-3.fc39.s390x 6/84 Installing : libjpeg-turbo-2.1.4-3.fc39.s390x 7/84 Installing : libgfortran-13.2.1-1.fc39.s390x 8/84 Installing : cpp-13.2.1-1.fc39.s390x 9/84 Installing : pyproject-rpm-macros-1.9.0-2.fc39.noarch 10/84 Installing : abattis-cantarell-vf-fonts-0.301-10.fc39.noarch 11/84 Installing : dejavu-sans-fonts-2.37-20.fc38.noarch 12/84 Running scriptlet: xml-common-0.6.3-61.fc39.noarch 13/84 Installing : xml-common-0.6.3-61.fc39.noarch 13/84 Installing : python-pip-wheel-23.1.2-5.fc39.noarch 14/84 Installing : protobuf-3.19.6-6.fc39.s390x 15/84 Installing : pixman-0.42.2-2.fc39.s390x 16/84 Installing : openjpeg2-2.5.0-4.fc39.s390x 17/84 Installing : nettle-3.9.1-2.fc39.s390x 18/84 Installing : gnutls-3.8.0-7.fc39.s390x 19/84 Installing : glib2-2.77.1-1.fc39.s390x 20/84 Installing : mpdecimal-2.5.1-7.fc39.s390x 21/84 Installing : mariadb-connector-c-config-3.3.5-2.fc39.noarch 22/84 Installing : mariadb-connector-c-3.3.5-2.fc39.s390x 23/84 Installing : libubsan-13.2.1-1.fc39.s390x 24/84 Installing : libtool-ltdl-2.4.7-7.fc39.s390x 25/84 Installing : libpq-15.3-1.fc39.s390x 26/84 Installing : libimagequant-4.0.1-5.fc39.s390x 27/84 Installing : libb2-0.98.1-9.fc39.s390x 28/84 Installing : libatomic-13.2.1-1.fc39.s390x 29/84 Installing : libasan-13.2.1-1.fc39.s390x 30/84 Installing : libXau-1.0.11-3.fc39.s390x 31/84 Installing : libxcb-1.13.1-12.fc39.s390x 32/84 Installing : libX11-common-1.8.6-2.fc39.noarch 33/84 Installing : libX11-1.8.6-2.fc39.s390x 34/84 Installing : libXext-1.3.5-3.fc39.s390x 35/84 Installing : libXrender-0.9.11-3.fc39.s390x 36/84 Installing : lcms2-2.15-2.fc39.s390x 37/84 Installing : kernel-headers-6.5.0-0.rc2.git0.1.fc39.s390x 38/84 Installing : jbigkit-libs-2.1-26.fc39.s390x 39/84 Installing : libtiff-4.4.0-7.fc39.s390x 40/84 Installing : google-noto-fonts-common-20230801-1.fc39.noarch 41/84 Installing : google-noto-sans-vf-fonts-20230801-1.fc39.noarch 42/84 Installing : default-fonts-core-sans-4.0-6.fc39.noarch 43/84 Installing : glibc-headers-s390-2.37.9000-18.fc39.noarch 44/84 Installing : libxcrypt-devel-4.4.36-2.fc39.s390x 45/84 Installing : glibc-devel-2.37.9000-18.fc39.s390x 46/84 Installing : gc-8.2.2-4.fc39.s390x 47/84 Installing : guile22-2.2.7-9.fc39.s390x 48/84 Installing : make-1:4.4.1-2.fc39.s390x 49/84 Installing : gcc-13.2.1-1.fc39.s390x 50/84 Running scriptlet: gcc-13.2.1-1.fc39.s390x 50/84 Installing : fribidi-1.0.13-2.fc39.s390x 51/84 Installing : expat-2.5.0-3.fc39.s390x 52/84 Installing : python3-3.12.0~b4-2.fc39.s390x 53/84 Installing : python3-libs-3.12.0~b4-2.fc39.s390x 54/84 Installing : python3-olefile-0.46-21.fc39.noarch 55/84 Installing : python3-packaging-23.1-4.fc39.noarch 56/84 Installing : python3-rpm-generators-14-7.fc39.noarch 57/84 Installing : python3-protobuf-3.19.6-6.fc39.s390x 58/84 Installing : python3-pyparsing-3.0.9-11.fc39.noarch 59/84 Installing : python3-setuptools-67.7.2-5.fc39.noarch 60/84 Installing : python3-six-1.16.0-12.fc39.noarch 61/84 Installing : python3-isodate-0.6.1-9.fc39.noarch 62/84 Installing : annobin-docs-12.23-1.fc39.noarch 63/84 Installing : openblas-0.3.23-1.fc39.s390x 64/84 Installing : openblas-openmp-0.3.23-1.fc39.s390x 65/84 Installing : flexiblas-netlib-3.3.1-5.fc39.s390x 66/84 Installing : flexiblas-openblas-openmp-3.3.1-5.fc39.s390x 67/84 Installing : flexiblas-3.3.1-5.fc39.s390x 68/84 Installing : graphite2-1.3.14-12.fc39.s390x 69/84 Installing : cairo-1.17.8-5.fc39.s390x 70/84 Installing : harfbuzz-8.1.1-1.fc39.s390x 71/84 Installing : freetype-2.13.1-2.fc39.s390x 72/84 Installing : fontconfig-2.14.2-4.fc39.s390x 73/84 Running scriptlet: fontconfig-2.14.2-4.fc39.s390x 73/84 Installing : libraqm-0.8.0-5.fc39.s390x 74/84 Installing : python3-pillow-10.0.0-2.fc39.s390x 75/84 Installing : python3-reportlab-4.0.4-3.fc39.noarch 76/84 Installing : python3-numpy-1:1.24.4-2.fc39.s390x 77/84 Installing : annobin-plugin-gcc-12.23-1.fc39.s390x 78/84 Running scriptlet: annobin-plugin-gcc-12.23-1.fc39.s390x 78/84 Installing : python3-rdflib-6.2.0-4.fc39.noarch 79/84 Installing : mysql-connector-python3-8.0.21-10.fc39.noarch 80/84 Installing : python3-devel-3.12.0~b4-2.fc39.s390x 81/84 Installing : python3-mysqlclient-2.1.1-5.fc39.s390x 82/84 Installing : python3-psycopg2-2.9.6-3.fc39.s390x 83/84 Installing : gcc-plugin-annobin-13.2.1-1.fc39.s390x 84/84 Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc39.s390x 84/84 Running scriptlet: fontconfig-2.14.2-4.fc39.s390x 84/84 Running scriptlet: gcc-plugin-annobin-13.2.1-1.fc39.s390x 84/84 Verifying : flexiblas-3.3.1-5.fc39.s390x 1/84 Verifying : flexiblas-netlib-3.3.1-5.fc39.s390x 2/84 Verifying : flexiblas-openblas-openmp-3.3.1-5.fc39.s390x 3/84 Verifying : graphite2-1.3.14-12.fc39.s390x 4/84 Verifying : openblas-0.3.23-1.fc39.s390x 5/84 Verifying : openblas-openmp-0.3.23-1.fc39.s390x 6/84 Verifying : python3-numpy-1:1.24.4-2.fc39.s390x 7/84 Verifying : abattis-cantarell-vf-fonts-0.301-10.fc39.noarch 8/84 Verifying : annobin-docs-12.23-1.fc39.noarch 9/84 Verifying : annobin-plugin-gcc-12.23-1.fc39.s390x 10/84 Verifying : cairo-1.17.8-5.fc39.s390x 11/84 Verifying : cpp-13.2.1-1.fc39.s390x 12/84 Verifying : default-fonts-core-sans-4.0-6.fc39.noarch 13/84 Verifying : dejavu-sans-fonts-2.37-20.fc38.noarch 14/84 Verifying : expat-2.5.0-3.fc39.s390x 15/84 Verifying : fontconfig-2.14.2-4.fc39.s390x 16/84 Verifying : fonts-filesystem-1:2.0.5-12.fc39.noarch 17/84 Verifying : freetype-2.13.1-2.fc39.s390x 18/84 Verifying : fribidi-1.0.13-2.fc39.s390x 19/84 Verifying : gc-8.2.2-4.fc39.s390x 20/84 Verifying : gcc-13.2.1-1.fc39.s390x 21/84 Verifying : gcc-plugin-annobin-13.2.1-1.fc39.s390x 22/84 Verifying : glib2-2.77.1-1.fc39.s390x 23/84 Verifying : glibc-devel-2.37.9000-18.fc39.s390x 24/84 Verifying : glibc-headers-s390-2.37.9000-18.fc39.noarch 25/84 Verifying : gnutls-3.8.0-7.fc39.s390x 26/84 Verifying : google-noto-fonts-common-20230801-1.fc39.noarch 27/84 Verifying : google-noto-sans-vf-fonts-20230801-1.fc39.noarch 28/84 Verifying : guile22-2.2.7-9.fc39.s390x 29/84 Verifying : harfbuzz-8.1.1-1.fc39.s390x 30/84 Verifying : jbigkit-libs-2.1-26.fc39.s390x 31/84 Verifying : kernel-headers-6.5.0-0.rc2.git0.1.fc39.s390x 32/84 Verifying : lcms2-2.15-2.fc39.s390x 33/84 Verifying : libX11-1.8.6-2.fc39.s390x 34/84 Verifying : libX11-common-1.8.6-2.fc39.noarch 35/84 Verifying : libXau-1.0.11-3.fc39.s390x 36/84 Verifying : libXext-1.3.5-3.fc39.s390x 37/84 Verifying : libXrender-0.9.11-3.fc39.s390x 38/84 Verifying : libasan-13.2.1-1.fc39.s390x 39/84 Verifying : libatomic-13.2.1-1.fc39.s390x 40/84 Verifying : libb2-0.98.1-9.fc39.s390x 41/84 Verifying : libgfortran-13.2.1-1.fc39.s390x 42/84 Verifying : libimagequant-4.0.1-5.fc39.s390x 43/84 Verifying : libjpeg-turbo-2.1.4-3.fc39.s390x 44/84 Verifying : libmpc-1.3.1-3.fc39.s390x 45/84 Verifying : libpng-2:1.6.37-15.fc39.s390x 46/84 Verifying : libpq-15.3-1.fc39.s390x 47/84 Verifying : libraqm-0.8.0-5.fc39.s390x 48/84 Verifying : libtiff-4.4.0-7.fc39.s390x 49/84 Verifying : libtool-ltdl-2.4.7-7.fc39.s390x 50/84 Verifying : libubsan-13.2.1-1.fc39.s390x 51/84 Verifying : libwebp-1.3.1-2.fc39.s390x 52/84 Verifying : libxcb-1.13.1-12.fc39.s390x 53/84 Verifying : libxcrypt-devel-4.4.36-2.fc39.s390x 54/84 Verifying : make-1:4.4.1-2.fc39.s390x 55/84 Verifying : mariadb-connector-c-3.3.5-2.fc39.s390x 56/84 Verifying : mariadb-connector-c-config-3.3.5-2.fc39.noarch 57/84 Verifying : mpdecimal-2.5.1-7.fc39.s390x 58/84 Verifying : mysql-connector-python3-8.0.21-10.fc39.noarch 59/84 Verifying : nettle-3.9.1-2.fc39.s390x 60/84 Verifying : openjpeg2-2.5.0-4.fc39.s390x 61/84 Verifying : pixman-0.42.2-2.fc39.s390x 62/84 Verifying : protobuf-3.19.6-6.fc39.s390x 63/84 Verifying : pyproject-rpm-macros-1.9.0-2.fc39.noarch 64/84 Verifying : python-pip-wheel-23.1.2-5.fc39.noarch 65/84 Verifying : python-rpm-macros-3.12-2.fc39.noarch 66/84 Verifying : python3-3.12.0~b4-2.fc39.s390x 67/84 Verifying : python3-devel-3.12.0~b4-2.fc39.s390x 68/84 Verifying : python3-isodate-0.6.1-9.fc39.noarch 69/84 Verifying : python3-libs-3.12.0~b4-2.fc39.s390x 70/84 Verifying : python3-mysqlclient-2.1.1-5.fc39.s390x 71/84 Verifying : python3-olefile-0.46-21.fc39.noarch 72/84 Verifying : python3-packaging-23.1-4.fc39.noarch 73/84 Verifying : python3-pillow-10.0.0-2.fc39.s390x 74/84 Verifying : python3-protobuf-3.19.6-6.fc39.s390x 75/84 Verifying : python3-psycopg2-2.9.6-3.fc39.s390x 76/84 Verifying : python3-pyparsing-3.0.9-11.fc39.noarch 77/84 Verifying : python3-rdflib-6.2.0-4.fc39.noarch 78/84 Verifying : python3-reportlab-4.0.4-3.fc39.noarch 79/84 Verifying : python3-rpm-generators-14-7.fc39.noarch 80/84 Verifying : python3-rpm-macros-3.12-2.fc39.noarch 81/84 Verifying : python3-setuptools-67.7.2-5.fc39.noarch 82/84 Verifying : python3-six-1.16.0-12.fc39.noarch 83/84 Verifying : xml-common-0.6.3-61.fc39.noarch 84/84 Installed: abattis-cantarell-vf-fonts-0.301-10.fc39.noarch annobin-docs-12.23-1.fc39.noarch annobin-plugin-gcc-12.23-1.fc39.s390x cairo-1.17.8-5.fc39.s390x cpp-13.2.1-1.fc39.s390x default-fonts-core-sans-4.0-6.fc39.noarch dejavu-sans-fonts-2.37-20.fc38.noarch expat-2.5.0-3.fc39.s390x flexiblas-3.3.1-5.fc39.s390x flexiblas-netlib-3.3.1-5.fc39.s390x flexiblas-openblas-openmp-3.3.1-5.fc39.s390x fontconfig-2.14.2-4.fc39.s390x fonts-filesystem-1:2.0.5-12.fc39.noarch freetype-2.13.1-2.fc39.s390x fribidi-1.0.13-2.fc39.s390x gc-8.2.2-4.fc39.s390x gcc-13.2.1-1.fc39.s390x gcc-plugin-annobin-13.2.1-1.fc39.s390x glib2-2.77.1-1.fc39.s390x glibc-devel-2.37.9000-18.fc39.s390x glibc-headers-s390-2.37.9000-18.fc39.noarch gnutls-3.8.0-7.fc39.s390x google-noto-fonts-common-20230801-1.fc39.noarch google-noto-sans-vf-fonts-20230801-1.fc39.noarch graphite2-1.3.14-12.fc39.s390x guile22-2.2.7-9.fc39.s390x harfbuzz-8.1.1-1.fc39.s390x jbigkit-libs-2.1-26.fc39.s390x kernel-headers-6.5.0-0.rc2.git0.1.fc39.s390x lcms2-2.15-2.fc39.s390x libX11-1.8.6-2.fc39.s390x libX11-common-1.8.6-2.fc39.noarch libXau-1.0.11-3.fc39.s390x libXext-1.3.5-3.fc39.s390x libXrender-0.9.11-3.fc39.s390x libasan-13.2.1-1.fc39.s390x libatomic-13.2.1-1.fc39.s390x libb2-0.98.1-9.fc39.s390x libgfortran-13.2.1-1.fc39.s390x libimagequant-4.0.1-5.fc39.s390x libjpeg-turbo-2.1.4-3.fc39.s390x libmpc-1.3.1-3.fc39.s390x libpng-2:1.6.37-15.fc39.s390x libpq-15.3-1.fc39.s390x libraqm-0.8.0-5.fc39.s390x libtiff-4.4.0-7.fc39.s390x libtool-ltdl-2.4.7-7.fc39.s390x libubsan-13.2.1-1.fc39.s390x libwebp-1.3.1-2.fc39.s390x libxcb-1.13.1-12.fc39.s390x libxcrypt-devel-4.4.36-2.fc39.s390x make-1:4.4.1-2.fc39.s390x mariadb-connector-c-3.3.5-2.fc39.s390x mariadb-connector-c-config-3.3.5-2.fc39.noarch mpdecimal-2.5.1-7.fc39.s390x mysql-connector-python3-8.0.21-10.fc39.noarch nettle-3.9.1-2.fc39.s390x openblas-0.3.23-1.fc39.s390x openblas-openmp-0.3.23-1.fc39.s390x openjpeg2-2.5.0-4.fc39.s390x pixman-0.42.2-2.fc39.s390x protobuf-3.19.6-6.fc39.s390x pyproject-rpm-macros-1.9.0-2.fc39.noarch python-pip-wheel-23.1.2-5.fc39.noarch python-rpm-macros-3.12-2.fc39.noarch python3-3.12.0~b4-2.fc39.s390x python3-devel-3.12.0~b4-2.fc39.s390x python3-isodate-0.6.1-9.fc39.noarch python3-libs-3.12.0~b4-2.fc39.s390x python3-mysqlclient-2.1.1-5.fc39.s390x python3-numpy-1:1.24.4-2.fc39.s390x python3-olefile-0.46-21.fc39.noarch python3-packaging-23.1-4.fc39.noarch python3-pillow-10.0.0-2.fc39.s390x python3-protobuf-3.19.6-6.fc39.s390x python3-psycopg2-2.9.6-3.fc39.s390x python3-pyparsing-3.0.9-11.fc39.noarch python3-rdflib-6.2.0-4.fc39.noarch python3-reportlab-4.0.4-3.fc39.noarch python3-rpm-generators-14-7.fc39.noarch python3-rpm-macros-3.12-2.fc39.noarch python3-setuptools-67.7.2-5.fc39.noarch python3-six-1.16.0-12.fc39.noarch xml-common-0.6.3-61.fc39.noarch Complete! Finish: build setup for python-biopython-1.81-4.fc39.src.rpm Start: rpmbuild python-biopython-1.81-4.fc39.src.rpm Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1689897600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.eA20Ba + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf python-biopython-1.81 + /usr/bin/mkdir -p python-biopython-1.81 + cd python-biopython-1.81 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/biopython-1.81.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/python-biopython-1.81-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/python-biopython-1.81-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd biopython-1.81 ~/build/BUILD/python-biopython-1.81/biopython-1.81 ~/build/BUILD/python-biopython-1.81 Patch #0 (python-biopython-fix_for_python312.patch): + echo 'Patch #0 (python-biopython-fix_for_python312.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file Tests/test_Entrez.py Patch #1 (python-biopython-fix_compatibility_with_reportlab4.patch): + echo 'Patch #1 (python-biopython-fix_compatibility_with_reportlab4.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file Tests/test_GraphicsBitmaps.py + 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-1.81 python3 ~/build/BUILD/python-biopython-1.81 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.biTtQN + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,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-1.81 + pushd python3 ~/build/BUILD/python-biopython-1.81/python3 ~/build/BUILD/python-biopython-1.81 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' running build running build_py creating build creating build/lib.linux-s390x-cpython-312 creating build/lib.linux-s390x-cpython-312/Bio copying Bio/File.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/LogisticRegression.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/MarkovModel.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/MaxEntropy.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/NaiveBayes.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/Seq.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/SeqFeature.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/SeqRecord.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/__init__.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/_utils.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/bgzf.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/kNN.py -> build/lib.linux-s390x-cpython-312/Bio copying Bio/pairwise2.py -> build/lib.linux-s390x-cpython-312/Bio creating build/lib.linux-s390x-cpython-312/Bio/Affy copying Bio/Affy/CelFile.py -> build/lib.linux-s390x-cpython-312/Bio/Affy copying Bio/Affy/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Affy creating build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/AlignInfo.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/a2m.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/bed.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/bigbed.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/bigmaf.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/bigpsl.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/clustal.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/emboss.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/exonerate.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/fasta.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/hhr.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/interfaces.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/maf.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/mauve.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/msf.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/nexus.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/phylip.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/psl.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/sam.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/stockholm.py -> build/lib.linux-s390x-cpython-312/Bio/Align copying Bio/Align/tabular.py -> build/lib.linux-s390x-cpython-312/Bio/Align creating build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Prank.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications copying Bio/Align/Applications/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Align/Applications creating build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices copying Bio/Align/substitution_matrices/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices creating build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/FastaIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/Interfaces.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/MafIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/MauveIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/MsfIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/NexusIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO copying Bio/AlignIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/AlignIO creating build/lib.linux-s390x-cpython-312/Bio/Alphabet copying Bio/Alphabet/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Alphabet creating build/lib.linux-s390x-cpython-312/Bio/Application copying Bio/Application/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Application creating build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/Applications.py -> build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/NCBIWWW.py -> build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/NCBIXML.py -> build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/Record.py -> build/lib.linux-s390x-cpython-312/Bio/Blast copying Bio/Blast/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Blast creating build/lib.linux-s390x-cpython-312/Bio/CAPS copying Bio/CAPS/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/CAPS creating build/lib.linux-s390x-cpython-312/Bio/Cluster copying Bio/Cluster/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Cluster creating build/lib.linux-s390x-cpython-312/Bio/codonalign copying Bio/codonalign/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/codonalign copying Bio/codonalign/codonalignment.py -> build/lib.linux-s390x-cpython-312/Bio/codonalign copying Bio/codonalign/codonseq.py -> build/lib.linux-s390x-cpython-312/Bio/codonalign creating build/lib.linux-s390x-cpython-312/Bio/Compass copying Bio/Compass/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Compass creating build/lib.linux-s390x-cpython-312/Bio/Data copying Bio/Data/CodonTable.py -> build/lib.linux-s390x-cpython-312/Bio/Data copying Bio/Data/IUPACData.py -> build/lib.linux-s390x-cpython-312/Bio/Data copying Bio/Data/PDBData.py -> build/lib.linux-s390x-cpython-312/Bio/Data copying Bio/Data/SCOPData.py -> build/lib.linux-s390x-cpython-312/Bio/Data copying Bio/Data/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Data creating build/lib.linux-s390x-cpython-312/Bio/Emboss copying Bio/Emboss/Applications.py -> build/lib.linux-s390x-cpython-312/Bio/Emboss copying Bio/Emboss/Primer3.py -> build/lib.linux-s390x-cpython-312/Bio/Emboss copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-s390x-cpython-312/Bio/Emboss copying Bio/Emboss/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Emboss creating build/lib.linux-s390x-cpython-312/Bio/Entrez copying Bio/Entrez/Parser.py -> build/lib.linux-s390x-cpython-312/Bio/Entrez copying Bio/Entrez/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Entrez creating build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/Enzyme.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prodoc.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/Prosite.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy copying Bio/ExPASy/cellosaurus.py -> build/lib.linux-s390x-cpython-312/Bio/ExPASy creating build/lib.linux-s390x-cpython-312/Bio/GenBank copying Bio/GenBank/Record.py -> build/lib.linux-s390x-cpython-312/Bio/GenBank copying Bio/GenBank/Scanner.py -> build/lib.linux-s390x-cpython-312/Bio/GenBank copying Bio/GenBank/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/GenBank copying Bio/GenBank/utils.py -> build/lib.linux-s390x-cpython-312/Bio/GenBank creating build/lib.linux-s390x-cpython-312/Bio/Geo copying Bio/Geo/Record.py -> build/lib.linux-s390x-cpython-312/Bio/Geo copying Bio/Geo/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Geo creating build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/Comparative.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/Distribution.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/KGML_vis.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics copying Bio/Graphics/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics creating build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram creating build/lib.linux-s390x-cpython-312/Bio/HMM copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-s390x-cpython-312/Bio/HMM copying Bio/HMM/MarkovModel.py -> build/lib.linux-s390x-cpython-312/Bio/HMM copying Bio/HMM/Trainer.py -> build/lib.linux-s390x-cpython-312/Bio/HMM copying Bio/HMM/Utilities.py -> build/lib.linux-s390x-cpython-312/Bio/HMM copying Bio/HMM/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/HMM creating build/lib.linux-s390x-cpython-312/Bio/KEGG copying Bio/KEGG/REST.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG copying Bio/KEGG/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG creating build/lib.linux-s390x-cpython-312/Bio/KEGG/Compound copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/Compound creating build/lib.linux-s390x-cpython-312/Bio/KEGG/Enzyme copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/Enzyme creating build/lib.linux-s390x-cpython-312/Bio/KEGG/Gene copying Bio/KEGG/Gene/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/Gene creating build/lib.linux-s390x-cpython-312/Bio/KEGG/Map copying Bio/KEGG/Map/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/Map creating build/lib.linux-s390x-cpython-312/Bio/PDB creating build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/DefaultParser.py -> build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf copying Bio/PDB/mmtf/mmtfio.py -> build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf creating build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML creating build/lib.linux-s390x-cpython-312/Bio/Medline copying Bio/Medline/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Medline creating build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/alignace.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/clusterbuster.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/mast.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/matrix.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/meme.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/minimal.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/pfm.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/thresholds.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/transfac.py -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/motifs/xms.py -> build/lib.linux-s390x-cpython-312/Bio/motifs creating build/lib.linux-s390x-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/motifs/applications copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-s390x-cpython-312/Bio/motifs/applications creating build/lib.linux-s390x-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/motifs/jaspar copying Bio/motifs/jaspar/db.py -> build/lib.linux-s390x-cpython-312/Bio/motifs/jaspar creating build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/Nexus/Nexus.py -> build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/Nexus/Nodes.py -> build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/Nexus/StandardData.py -> build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/Nexus/Trees.py -> build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/Nexus/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Nexus creating build/lib.linux-s390x-cpython-312/Bio/NMR copying Bio/NMR/NOEtools.py -> build/lib.linux-s390x-cpython-312/Bio/NMR copying Bio/NMR/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/NMR copying Bio/NMR/xpktools.py -> build/lib.linux-s390x-cpython-312/Bio/NMR creating build/lib.linux-s390x-cpython-312/Bio/Pathway copying Bio/Pathway/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Pathway creating build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Atom.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Chain.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/DSSP.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Dice.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Entity.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/FragmentMapper.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/HSExposure.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/MMCIFParser.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Model.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/NACCESS.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/NeighborSearch.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PDBExceptions.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PDBIO.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PDBList.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PDBParser.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PICIO.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/PSEA.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Polypeptide.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Residue.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/ResidueDepth.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/SASA.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/SCADIO.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Selection.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Structure.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/StructureAlignment.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/StructureBuilder.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/Superimposer.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/cealign.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/ic_data.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/ic_rebuild.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/internal_coords.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/mmcifio.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/qcprot.py -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/vectors.py -> build/lib.linux-s390x-cpython-312/Bio/PDB creating build/lib.linux-s390x-cpython-312/Bio/phenotype copying Bio/phenotype/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/phenotype copying Bio/phenotype/phen_micro.py -> build/lib.linux-s390x-cpython-312/Bio/phenotype copying Bio/phenotype/pm_fitting.py -> build/lib.linux-s390x-cpython-312/Bio/phenotype creating build/lib.linux-s390x-cpython-312/Bio/PopGen copying Bio/PopGen/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen creating build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/Controller.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop creating build/lib.linux-s390x-cpython-312/Bio/Restriction copying Bio/Restriction/PrintFormat.py -> build/lib.linux-s390x-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction.py -> build/lib.linux-s390x-cpython-312/Bio/Restriction copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-s390x-cpython-312/Bio/Restriction copying Bio/Restriction/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Restriction creating build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Cla.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Des.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Dom.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Hie.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Raf.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/Residues.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP copying Bio/SCOP/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SCOP creating build/lib.linux-s390x-cpython-312/Bio/SearchIO copying Bio/SearchIO/BlatIO.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO copying Bio/SearchIO/FastaIO.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO copying Bio/SearchIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO copying Bio/SearchIO/_index.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO copying Bio/SearchIO/_utils.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/NCBIStandalone.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/ParserSupport.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy copying Bio/SearchIO/_legacy/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/_base.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hit.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/hsp.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model copying Bio/SearchIO/_model/query.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HHsuiteIO copying Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HHsuiteIO creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO copying Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO creating build/lib.linux-s390x-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/InterproscanIO copying Bio/SearchIO/InterproscanIO/interproscan_xml.py -> build/lib.linux-s390x-cpython-312/Bio/SearchIO/InterproscanIO creating build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/AbiIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/AceIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/FastaIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/GckIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/IgIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/Interfaces.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/NibIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/PdbIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/PhdIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/PirIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/QualityIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/SffIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/SnapGeneIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/SwissIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/TabIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/TwoBitIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/XdnaIO.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/SeqIO/_index.py -> build/lib.linux-s390x-cpython-312/Bio/SeqIO creating build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils copying Bio/SeqUtils/lcc.py -> build/lib.linux-s390x-cpython-312/Bio/SeqUtils creating build/lib.linux-s390x-cpython-312/Bio/Sequencing copying Bio/Sequencing/Ace.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing copying Bio/Sequencing/Phd.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing copying Bio/Sequencing/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing creating build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_Novoalign.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications creating build/lib.linux-s390x-cpython-312/Bio/SVDSuperimposer copying Bio/SVDSuperimposer/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SVDSuperimposer creating build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer copying Bio/PDB/QCPSuperimposer/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer creating build/lib.linux-s390x-cpython-312/Bio/SwissProt copying Bio/SwissProt/KeyWList.py -> build/lib.linux-s390x-cpython-312/Bio/SwissProt copying Bio/SwissProt/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/SwissProt creating build/lib.linux-s390x-cpython-312/Bio/TogoWS copying Bio/TogoWS/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/TogoWS creating build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/BaseTree.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/CDAO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/CDAOIO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/Consensus.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/NeXML.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/Newick.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/NewickIO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/NexusIO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXML.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/_io.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo copying Bio/Phylo/_utils.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo creating build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/_Raxml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications creating build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_baseml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_codeml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/codeml.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML creating build/lib.linux-s390x-cpython-312/Bio/UniGene copying Bio/UniGene/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/UniGene creating build/lib.linux-s390x-cpython-312/Bio/UniProt copying Bio/UniProt/GOA.py -> build/lib.linux-s390x-cpython-312/Bio/UniProt copying Bio/UniProt/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/UniProt creating build/lib.linux-s390x-cpython-312/Bio/Wise copying Bio/Wise/__init__.py -> build/lib.linux-s390x-cpython-312/Bio/Wise copying Bio/Wise/dnal.py -> build/lib.linux-s390x-cpython-312/Bio/Wise copying Bio/Wise/psw.py -> build/lib.linux-s390x-cpython-312/Bio/Wise creating build/lib.linux-s390x-cpython-312/BioSQL copying BioSQL/__init__.py -> build/lib.linux-s390x-cpython-312/BioSQL copying BioSQL/Loader.py -> build/lib.linux-s390x-cpython-312/BioSQL copying BioSQL/DBUtils.py -> build/lib.linux-s390x-cpython-312/BioSQL copying BioSQL/BioSeqDatabase.py -> build/lib.linux-s390x-cpython-312/BioSQL copying BioSQL/BioSeq.py -> build/lib.linux-s390x-cpython-312/BioSQL running egg_info writing biopython.egg-info/PKG-INFO writing dependency_links to biopython.egg-info/dependency_links.txt writing requirements to biopython.egg-info/requires.txt writing top-level names to biopython.egg-info/top_level.txt reading manifest file 'biopython.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'Tests/Gck/DGVC_GCK.zip' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '*.py{}' found anywhere in distribution warning: no previously-included files matching '*.py-e' found anywhere in distribution warning: no previously-included files found matching 'Bio/Align/substitution_matrices/data/README.txt' adding license file 'LICENSE' adding license file 'LICENSE.rst' writing manifest file 'biopython.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Align.substitution_matrices.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Align.substitution_matrices.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Align.substitution_matrices.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Align.substitution_matrices.data' to be distributed and are already explicitly excluding 'Bio.Align.substitution_matrices.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.DTDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.DTDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.DTDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.DTDs' to be distributed and are already explicitly excluding 'Bio.Entrez.DTDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'Bio.Entrez.XSDs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'Bio.Entrez.XSDs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'Bio.Entrez.XSDs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'Bio.Entrez.XSDs' to be distributed and are already explicitly excluding 'Bio.Entrez.XSDs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying Bio/cpairwise2module.c -> build/lib.linux-s390x-cpython-312/Bio copying Bio/Align/_aligners.c -> build/lib.linux-s390x-cpython-312/Bio/Align creating build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER22 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER6 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BENNER74 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTN -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLASTP -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM45 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM50 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM62 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM80 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/BLOSUM90 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/DAYHOFF -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/FENG -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GENETIC -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/GONNET1992 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/HOXD70 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JOHNSON -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/JONES -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/LEVIN -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MCLACHLAN -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MDM78 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/MEGABLAST -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/NUC.4.4 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM250 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM30 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/PAM70 -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RAO -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/RISLER -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/SCHNEIDER -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/STR -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Align/substitution_matrices/data/TRANS -> build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data copying Bio/Cluster/cluster.c -> build/lib.linux-s390x-cpython-312/Bio/Cluster copying Bio/Cluster/cluster.h -> build/lib.linux-s390x-cpython-312/Bio/Cluster copying Bio/Cluster/clustermodule.c -> build/lib.linux-s390x-cpython-312/Bio/Cluster creating build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-embedded-index2.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/BITS-question-answer2.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/EMBL_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/GenBank_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/HomoloGene.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-chars1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-common1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-display1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-format1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-funding1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-link1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-list1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-math1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-modules1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-notat1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-para1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-phrase1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-references1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-related-object1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-section1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Systems.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NCBI_all.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/NSE.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/OMSSA.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PDB_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PIR_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/PRF_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/SP_General.mod.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/XHTMLtablesetup.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivearticle.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-classes.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-mixes.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/archivecustom-modules.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/articlemeta.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/backmatter.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_100301.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_110101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_120101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_130101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_140101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/bookdoc_150101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-classes.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/display.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eInfo_020511.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_090910.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eLink_101123.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/ePost_020511.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSearch_020511.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSpell.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/eSummary_041029.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/egquery.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/einfo.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/elink_020122.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/epost.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esearch.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary-v1.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/esummary_gene.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/format.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/htmltable.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsa.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsb.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsc.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsn.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamso.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isoamsr.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isobox.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr1.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isocyr2.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isodia.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk1.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk2.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk3.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat1.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isolat2.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomopf.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isomscr.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isonum.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isopub.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/isotech.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/journalmeta.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/link.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/math.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml-in-pubmed.mod -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml2.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3-qname1.mod -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathml3.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mathmlsetup.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlalias.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/mmlextra.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/modules.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_011101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmcommon_090101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_011101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedline_090101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmserials_100101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/notat.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/para.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/phrase.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pmc-1.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_020114.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_080101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_090101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_100301.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_110101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_120101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_130501.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_140101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_150101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_180601.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/pubmed_190101.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/references.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/section.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/taxon.dtd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xhtml-table-1.mod -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs copying Bio/Entrez/DTDs/xmlspecchars.ent -> build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs creating build/lib.linux-s390x-cpython-312/Bio/Entrez/XSDs copying Bio/Entrez/XSDs/IPGReportSet.xsd -> build/lib.linux-s390x-cpython-312/Bio/Entrez/XSDs copying Bio/motifs/_pwm.c -> build/lib.linux-s390x-cpython-312/Bio/motifs copying Bio/Nexus/cnexus.c -> build/lib.linux-s390x-cpython-312/Bio/Nexus copying Bio/PDB/ccealignmodule.c -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/PDB/kdtrees.c -> build/lib.linux-s390x-cpython-312/Bio/PDB copying Bio/SeqIO/_twoBitIO.c -> build/lib.linux-s390x-cpython-312/Bio/SeqIO copying Bio/PDB/QCPSuperimposer/qcprotmodule.c -> build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer running build_ext building 'Bio.Align._aligners' extension creating build/temp.linux-s390x-cpython-312 creating build/temp.linux-s390x-cpython-312/Bio creating build/temp.linux-s390x-cpython-312/Bio/Align gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/Align/_aligners.c -o build/temp.linux-s390x-cpython-312/Bio/Align/_aligners.o Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_global_align_compare’: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c: In function ‘Aligner_watermansmithbeyer_local_align_compare’: Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34: Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_global_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6872:34: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34: Bio/Align/_aligners.c:5737:16: warning: ‘Iy_row’ may be used uninitialized [-Wmaybe-uninitialized] 5737 | if (Iy_row) { \ | ^ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5406:14: note: ‘Iy_row’ was declared here 5406 | double** Iy_row; \ | ^~~~~~ In function ‘Aligner_watermansmithbeyer_local_align_matrix’, inlined from ‘Aligner_align’ at Bio/Align/_aligners.c:6878:34: Bio/Align/_aligners.c:5735:12: warning: ‘Ix_row’ may be used uninitialized [-Wmaybe-uninitialized] 5735 | if (Ix_row) { \ | ^ Bio/Align/_aligners.c: In function ‘Aligner_align’: Bio/Align/_aligners.c:5405:14: note: ‘Ix_row’ was declared here 5405 | double** Ix_row; \ | ^~~~~~ 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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/Align/_aligners.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/Align/_aligners.cpython-312-s390x-linux-gnu.so building 'Bio.cpairwise2' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/cpairwise2module.c -o build/temp.linux-s390x-cpython-312/Bio/cpairwise2module.o Bio/cpairwise2module.c: In function ‘_get_match_score’: Bio/cpairwise2module.c:60:5: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 60 | if(!(py_result = PyEval_CallObject(py_match_fn, py_arglist))) | ^~ In file included from /usr/include/python3.12/Python.h:95, from Bio/cpairwise2module.c:16: /usr/include/python3.12/ceval.h:27:43: note: declared here 27 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/cpairwise2module.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/cpairwise2.cpython-312-s390x-linux-gnu.so building 'Bio.Nexus.cnexus' extension creating build/temp.linux-s390x-cpython-312/Bio/Nexus gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/Nexus/cnexus.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/Nexus/cnexus.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/Nexus/cnexus.cpython-312-s390x-linux-gnu.so building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension creating build/temp.linux-s390x-cpython-312/Bio/PDB creating build/temp.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-312-s390x-linux-gnu.so building 'Bio.motifs._pwm' extension creating build/temp.linux-s390x-cpython-312/Bio/motifs gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/motifs/_pwm.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/motifs/_pwm.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/motifs/_pwm.cpython-312-s390x-linux-gnu.so building 'Bio.Cluster._cluster' extension creating build/temp.linux-s390x-cpython-312/Bio/Cluster gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/Cluster/cluster.c -o build/temp.linux-s390x-cpython-312/Bio/Cluster/cluster.o gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/Cluster/clustermodule.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/Cluster/cluster.o build/temp.linux-s390x-cpython-312/Bio/Cluster/clustermodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/Cluster/_cluster.cpython-312-s390x-linux-gnu.so building 'Bio.PDB.kdtrees' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/PDB/kdtrees.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/PDB/kdtrees.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/PDB/kdtrees.cpython-312-s390x-linux-gnu.so building 'Bio.PDB.ccealign' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/PDB/ccealignmodule.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/PDB/ccealignmodule.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/PDB/ccealign.cpython-312-s390x-linux-gnu.so building 'Bio.SeqIO._twoBitIO' extension creating build/temp.linux-s390x-cpython-312/Bio/SeqIO gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -fPIC -I/usr/include/python3.12 -c Bio/SeqIO/_twoBitIO.c -o build/temp.linux-s390x-cpython-312/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,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection build/temp.linux-s390x-cpython-312/Bio/SeqIO/_twoBitIO.o -L/usr/lib64 -o build/lib.linux-s390x-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-s390x-linux-gnu.so + popd ~/build/BUILD/python-biopython-1.81 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.NvJWIG + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x ++ dirname /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,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-1.81 + pushd python3 ~/build/BUILD/python-biopython-1.81/python3 ~/build/BUILD/python-biopython-1.81 + /usr/bin/python3 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x --install-data=/usr/share/python-biopython running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64 creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL copying build/lib.linux-s390x-cpython-312/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL copying build/lib.linux-s390x-cpython-312/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL copying build/lib.linux-s390x-cpython-312/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL copying build/lib.linux-s390x-cpython-312/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL copying build/lib.linux-s390x-cpython-312/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/cpairwise2.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/cpairwise2module.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise copying build/lib.linux-s390x-cpython-312/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise copying build/lib.linux-s390x-cpython-312/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise copying build/lib.linux-s390x-cpython-312/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniProt copying build/lib.linux-s390x-cpython-312/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniProt copying build/lib.linux-s390x-cpython-312/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniProt creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniGene copying build/lib.linux-s390x-cpython-312/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniGene creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications copying build/lib.linux-s390x-cpython-312/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo copying build/lib.linux-s390x-cpython-312/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/TogoWS copying build/lib.linux-s390x-cpython-312/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/TogoWS creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SwissProt copying build/lib.linux-s390x-cpython-312/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SwissProt copying build/lib.linux-s390x-cpython-312/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SwissProt creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SVDSuperimposer copying build/lib.linux-s390x-cpython-312/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SVDSuperimposer creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing copying build/lib.linux-s390x-cpython-312/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils copying build/lib.linux-s390x-cpython-312/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/_twoBitIO.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/_twoBitIO.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/XdnaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/TwoBitIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/SnapGeneIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/NibIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/GckIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO copying build/lib.linux-s390x-cpython-312/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/InterproscanIO/interproscan_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/InterproscanIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/HHsuiteIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_legacy/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO copying build/lib.linux-s390x-cpython-312/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP copying build/lib.linux-s390x-cpython-312/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction copying build/lib.linux-s390x-cpython-312/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction copying build/lib.linux-s390x-cpython-312/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction copying build/lib.linux-s390x-cpython-312/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction copying build/lib.linux-s390x-cpython-312/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop copying build/lib.linux-s390x-cpython-312/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype copying build/lib.linux-s390x-cpython-312/Bio/phenotype/pm_fitting.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype copying build/lib.linux-s390x-cpython-312/Bio/phenotype/phen_micro.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype copying build/lib.linux-s390x-cpython-312/Bio/phenotype/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-312/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep copying build/lib.linux-s390x-cpython-312/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR copying build/lib.linux-s390x-cpython-312/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR copying build/lib.linux-s390x-cpython-312/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR copying build/lib.linux-s390x-cpython-312/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/cnexus.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/cnexus.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/StandardData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus copying build/lib.linux-s390x-cpython-312/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/_pwm.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/_pwm.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar copying build/lib.linux-s390x-cpython-312/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar copying build/lib.linux-s390x-cpython-312/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-s390x-cpython-312/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-s390x-cpython-312/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/applications copying build/lib.linux-s390x-cpython-312/Bio/motifs/xms.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/pfm.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/minimal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/clusterbuster.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs copying build/lib.linux-s390x-cpython-312/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Medline copying build/lib.linux-s390x-cpython-312/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Medline creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/ccealign.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/kdtrees.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/kdtrees.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/ccealignmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer/qcprotmodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-s390x-cpython-312/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer copying build/lib.linux-s390x-cpython-312/Bio/PDB/vectors.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/qcprot.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/mmcifio.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/internal_coords.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/ic_rebuild.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/ic_data.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/cealign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/SCADIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/SASA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PICIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB copying build/lib.linux-s390x-cpython-312/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf/mmtfio.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf copying build/lib.linux-s390x-cpython-312/Bio/PDB/mmtf/DefaultParser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML copying build/lib.linux-s390x-cpython-312/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Map copying build/lib.linux-s390x-cpython-312/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Map creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Gene copying build/lib.linux-s390x-cpython-312/Bio/KEGG/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Gene creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Enzyme copying build/lib.linux-s390x-cpython-312/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Enzyme creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Compound copying build/lib.linux-s390x-cpython-312/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Compound copying build/lib.linux-s390x-cpython-312/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG copying build/lib.linux-s390x-cpython-312/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM copying build/lib.linux-s390x-cpython-312/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM copying build/lib.linux-s390x-cpython-312/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM copying build/lib.linux-s390x-cpython-312/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM copying build/lib.linux-s390x-cpython-312/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM copying build/lib.linux-s390x-cpython-312/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram copying build/lib.linux-s390x-cpython-312/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics copying build/lib.linux-s390x-cpython-312/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Geo copying build/lib.linux-s390x-cpython-312/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Geo copying build/lib.linux-s390x-cpython-312/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Geo creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank copying build/lib.linux-s390x-cpython-312/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank copying build/lib.linux-s390x-cpython-312/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank copying build/lib.linux-s390x-cpython-312/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank copying build/lib.linux-s390x-cpython-312/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/cellosaurus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy copying build/lib.linux-s390x-cpython-312/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/XSDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/XSDs/IPGReportSet.xsd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/XSDs creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/xhtml-table-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/xhtml-inlstyle-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_190101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_180601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_180101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathml3-qname1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/mathml-in-pubmed.mod -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/esummary_gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/epost.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/elink.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Systems.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-xmlspecchars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-section1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-related-object1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-references1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-phrase1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-para1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-notat1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-nlmcitation1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-mathml3-mathmlsetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-math1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-list1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-link1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-journalmeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-funding1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-format1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-display1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-default-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-default-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-common1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-common-atts1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-chars1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-backmatter1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-articlemeta1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-modules1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-models1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-mixes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-archivecustom-classes1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-archivearticle1-3-mathml3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-ali-namespace1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/JATS-XHTMLtablesetup1-3.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/BITS-question-answer2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/DTDs/BITS-embedded-index2.ent -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/DTDs copying build/lib.linux-s390x-cpython-312/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez copying build/lib.linux-s390x-cpython-312/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss copying build/lib.linux-s390x-cpython-312/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss copying build/lib.linux-s390x-cpython-312/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss copying build/lib.linux-s390x-cpython-312/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss copying build/lib.linux-s390x-cpython-312/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data copying build/lib.linux-s390x-cpython-312/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data copying build/lib.linux-s390x-cpython-312/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data copying build/lib.linux-s390x-cpython-312/Bio/Data/PDBData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data copying build/lib.linux-s390x-cpython-312/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data copying build/lib.linux-s390x-cpython-312/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Compass copying build/lib.linux-s390x-cpython-312/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Compass creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign copying build/lib.linux-s390x-cpython-312/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign copying build/lib.linux-s390x-cpython-312/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign copying build/lib.linux-s390x-cpython-312/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster copying build/lib.linux-s390x-cpython-312/Bio/Cluster/_cluster.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster copying build/lib.linux-s390x-cpython-312/Bio/Cluster/clustermodule.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster copying build/lib.linux-s390x-cpython-312/Bio/Cluster/cluster.h -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster copying build/lib.linux-s390x-cpython-312/Bio/Cluster/cluster.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster copying build/lib.linux-s390x-cpython-312/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/CAPS copying build/lib.linux-s390x-cpython-312/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/CAPS creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast copying build/lib.linux-s390x-cpython-312/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Application copying build/lib.linux-s390x-cpython-312/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Application creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Alphabet copying build/lib.linux-s390x-cpython-312/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Alphabet creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/MsfIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/MauveIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/MafIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO copying build/lib.linux-s390x-cpython-312/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/_aligners.cpython-312-s390x-linux-gnu.so -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/_aligners.c -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/TRANS -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/STR -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/SCHNEIDER -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/RISLER -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/RAO -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/PAM70 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/PAM30 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/PAM250 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/NUC.4.4 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/MEGABLAST -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/MDM78 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/MCLACHLAN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/LEVIN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/JONES -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/JOHNSON -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/HOXD70 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/GONNET1992 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/GENETIC -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/FENG -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/DAYHOFF -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM90 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM80 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM62 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM50 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLOSUM45 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLASTP -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BLASTN -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BENNER74 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BENNER6 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/data/BENNER22 -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/data copying build/lib.linux-s390x-cpython-312/Bio/Align/substitution_matrices/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications copying build/lib.linux-s390x-cpython-312/Bio/Align/tabular.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/stockholm.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/sam.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/psl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/phylip.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/msf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/mauve.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/maf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/hhr.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/fasta.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/exonerate.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/emboss.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/clustal.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/bigpsl.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/bigmaf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/bigbed.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/bed.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/a2m.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align copying build/lib.linux-s390x-cpython-312/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align creating /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Affy copying build/lib.linux-s390x-cpython-312/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Affy copying build/lib.linux-s390x-cpython-312/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Affy copying build/lib.linux-s390x-cpython-312/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio copying build/lib.linux-s390x-cpython-312/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL/BioSeq.py to BioSeq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL/BioSeqDatabase.py to BioSeqDatabase.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL/DBUtils.py to DBUtils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL/Loader.py to Loader.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/BioSQL/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise/psw.py to psw.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise/dnal.py to dnal.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Wise/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniProt/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniProt/GOA.py to GOA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/UniGene/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/yn00.py to yn00.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/codeml.py to codeml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/chi2.py to chi2.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/baseml.py to baseml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/_parse_yn00.py to _parse_yn00.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/_parse_codeml.py to _parse_codeml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/_parse_baseml.py to _parse_baseml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/_paml.py to _paml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PAML/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications/_Raxml.py to _Raxml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications/_Phyml.py to _Phyml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Applications/_Fasttree.py to _Fasttree.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/_io.py to _io.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/_cdao_owl.py to _cdao_owl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/TreeConstruction.py to TreeConstruction.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PhyloXMLIO.py to PhyloXMLIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/PhyloXML.py to PhyloXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/NexusIO.py to NexusIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/NewickIO.py to NewickIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Newick.py to Newick.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/NeXMLIO.py to NeXMLIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/NeXML.py to NeXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/Consensus.py to Consensus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/CDAOIO.py to CDAOIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/CDAO.py to CDAO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Phylo/BaseTree.py to BaseTree.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/TogoWS/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SwissProt/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SwissProt/KeyWList.py to KeyWList.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SVDSuperimposer/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications/_samtools.py to _samtools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications/_bwa.py to _bwa.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Applications/_Novoalign.py to _Novoalign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Phd.py to Phd.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Sequencing/Ace.py to Ace.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/lcc.py to lcc.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/ProtParamData.py to ProtParamData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/ProtParam.py to ProtParam.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/MeltingTemp.py to MeltingTemp.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/IsoelectricPoint.py to IsoelectricPoint.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/CodonUsageIndices.py to CodonUsageIndices.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/CodonUsage.py to CodonUsage.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqUtils/CheckSum.py to CheckSum.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/_index.py to _index.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/XdnaIO.py to XdnaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/UniprotIO.py to UniprotIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/TwoBitIO.py to TwoBitIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/TabIO.py to TabIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/SwissIO.py to SwissIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/SnapGeneIO.py to SnapGeneIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/SffIO.py to SffIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/SeqXmlIO.py to SeqXmlIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/QualityIO.py to QualityIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/PirIO.py to PirIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/PhdIO.py to PhdIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/PdbIO.py to PdbIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/NibIO.py to NibIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/Interfaces.py to Interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py to InsdcIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/IgIO.py to IgIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/GckIO.py to GckIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/AceIO.py to AceIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/AbiIO.py to AbiIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO/interproscan_xml.py to interproscan_xml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/InterproscanIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO/hhsuite2_text.py to hhsuite2_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/HHsuiteIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model/query.py to query.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model/hsp.py to hsp.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model/hit.py to hit.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model/_base.py to _base.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_model/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy/ParserSupport.py to ParserSupport.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_legacy/NCBIStandalone.py to NCBIStandalone.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/_index.py to _index.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Residues.py to Residues.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Raf.py to Raf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Hie.py to Hie.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Dom.py to Dom.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Des.py to Des.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SCOP/Cla.py to Cla.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction/Restriction.py to Restriction.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop/LargeFileParser.py to LargeFileParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop/FileParser.py to FileParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop/EasyController.py to EasyController.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/GenePop/Controller.py to Controller.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PopGen/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype/pm_fitting.py to pm_fitting.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype/phen_micro.py to phen_micro.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/phenotype/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep/MultiGraph.py to MultiGraph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/Rep/Graph.py to Graph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Pathway/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR/xpktools.py to xpktools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NMR/NOEtools.py to NOEtools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus/Trees.py to Trees.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus/StandardData.py to StandardData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus/Nodes.py to Nodes.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Nexus/Nexus.py to Nexus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar/db.py to db.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/jaspar/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/applications/_xxmotif.py to _xxmotif.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/xms.py to xms.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/transfac.py to transfac.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/thresholds.py to thresholds.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/pfm.py to pfm.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/minimal.py to minimal.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/meme.py to meme.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/matrix.py to matrix.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/mast.py to mast.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/clusterbuster.py to clusterbuster.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/alignace.py to alignace.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/motifs/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Medline/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/QCPSuperimposer/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/vectors.py to vectors.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/qcprot.py to qcprot.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/parse_pdb_header.py to parse_pdb_header.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmcifio.py to mmcifio.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/internal_coords.py to internal_coords.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/ic_rebuild.py to ic_rebuild.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/ic_data.py to ic_data.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/cealign.py to cealign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Superimposer.py to Superimposer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/StructureBuilder.py to StructureBuilder.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/StructureAlignment.py to StructureAlignment.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Structure.py to Structure.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Selection.py to Selection.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/SCADIO.py to SCADIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/SASA.py to SASA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/ResidueDepth.py to ResidueDepth.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Residue.py to Residue.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Polypeptide.py to Polypeptide.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PSEA.py to PSEA.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PICIO.py to PICIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PDBParser.py to PDBParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PDBList.py to PDBList.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PDBIO.py to PDBIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/PDBExceptions.py to PDBExceptions.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/NeighborSearch.py to NeighborSearch.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/NACCESS.py to NACCESS.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Model.py to Model.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/MMCIFParser.py to MMCIFParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/MMCIF2Dict.py to MMCIF2Dict.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/HSExposure.py to HSExposure.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/FragmentMapper.py to FragmentMapper.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Entity.py to Entity.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Dice.py to Dice.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/DSSP.py to DSSP.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Chain.py to Chain.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/Atom.py to Atom.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/AbstractPropertyMap.py to AbstractPropertyMap.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf/mmtfio.py to mmtfio.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/PDB/mmtf/DefaultParser.py to DefaultParser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML/KGML_pathway.py to KGML_pathway.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/KGML/KGML_parser.py to KGML_parser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Map/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Gene/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Enzyme/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/Compound/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/KEGG/REST.py to REST.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM/Utilities.py to Utilities.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM/Trainer.py to Trainer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM/MarkovModel.py to MarkovModel.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/HMM/DynamicProgramming.py to DynamicProgramming.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/KGML_vis.py to KGML_vis.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/Distribution.py to Distribution.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/DisplayRepresentation.py to DisplayRepresentation.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/Comparative.py to Comparative.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/ColorSpiral.py to ColorSpiral.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Graphics/BasicChromosome.py to BasicChromosome.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Geo/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Geo/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank/utils.py to utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank/Scanner.py to Scanner.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/GenBank/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/cellosaurus.py to cellosaurus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/ScanProsite.py to ScanProsite.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/Prosite.py to Prosite.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/Prodoc.py to Prodoc.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/ExPASy/Enzyme.py to Enzyme.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/Parser.py to Parser.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss/Primer3.py to Primer3.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Emboss/Applications.py to Applications.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data/SCOPData.py to SCOPData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data/PDBData.py to PDBData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data/IUPACData.py to IUPACData.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Data/CodonTable.py to CodonTable.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Compass/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign/codonseq.py to codonseq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign/codonalignment.py to codonalignment.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/codonalign/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Cluster/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/CAPS/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/Record.py to Record.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/ParseBlastTable.py to ParseBlastTable.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/NCBIXML.py to NCBIXML.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/NCBIWWW.py to NCBIWWW.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Blast/Applications.py to Applications.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Application/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Alphabet/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/StockholmIO.py to StockholmIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/PhylipIO.py to PhylipIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/NexusIO.py to NexusIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/MsfIO.py to MsfIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/MauveIO.py to MauveIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/MafIO.py to MafIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/Interfaces.py to Interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/FastaIO.py to FastaIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/EmbossIO.py to EmbossIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/AlignIO/ClustalIO.py to ClustalIO.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/substitution_matrices/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_TCoffee.py to _TCoffee.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Probcons.py to _Probcons.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Prank.py to _Prank.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Muscle.py to _Muscle.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Mafft.py to _Mafft.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_MSAProbs.py to _MSAProbs.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Dialign.py to _Dialign.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_Clustalw.py to _Clustalw.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/Applications/_ClustalOmega.py to _ClustalOmega.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/tabular.py to tabular.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/stockholm.py to stockholm.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/sam.py to sam.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/psl.py to psl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/phylip.py to phylip.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/nexus.py to nexus.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/msf.py to msf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/mauve.py to mauve.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/maf.py to maf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/interfaces.py to interfaces.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/hhr.py to hhr.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/fasta.py to fasta.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/exonerate.py to exonerate.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/emboss.py to emboss.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/clustal.py to clustal.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/bigpsl.py to bigpsl.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/bigmaf.py to bigmaf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/bigbed.py to bigbed.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/bed.py to bed.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/a2m.py to a2m.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Align/AlignInfo.py to AlignInfo.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Affy/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Affy/CelFile.py to CelFile.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/pairwise2.py to pairwise2.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/kNN.py to kNN.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/bgzf.py to bgzf.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/_utils.py to _utils.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqRecord.py to SeqRecord.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqFeature.py to SeqFeature.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Seq.py to Seq.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/NaiveBayes.py to NaiveBayes.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/MaxEntropy.py to MaxEntropy.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/MarkovModel.py to MarkovModel.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/LogisticRegression.py to LogisticRegression.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/File.py to File.cpython-312.pyc writing byte-compilation script '/tmp/tmpgzl3ekup.py' /usr/bin/python3 /tmp/tmpgzl3ekup.py removing /tmp/tmpgzl3ekup.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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/biopython-1.81-py3.12.egg-info running install_scripts + xargs /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 + find Scripts -name '*.py' Scripts/xbbtools/xbbtools.py: updating Scripts/xbbtools/xbb_widget.py: updating Scripts/xbbtools/xbb_utils.py: updating Scripts/xbbtools/xbb_translations.py: updating Scripts/xbbtools/xbb_search.py: updating Scripts/xbbtools/xbb_help.py: updating Scripts/xbbtools/xbb_blastbg.py: updating Scripts/xbbtools/xbb_blast.py: updating Scripts/xbbtools/nextorf.py: updating Scripts/update_ncbi_codon_table.py: no change Scripts/scop_pdb.py: updating Scripts/query_pubmed.py: updating Scripts/SeqGui/SeqGui.py: no change Scripts/Restriction/rebase_update.py: updating Scripts/Restriction/ranacompiler.py: updating Scripts/Performance/biosql_performance_read.py: updating Scripts/Performance/biosql_performance_load.py: updating Scripts/PDB/hsexpo.py: updating Scripts/PDB/generate_three_to_one_dict.py: no change Scripts/GenBank/check_output_simple.py: updating Scripts/GenBank/check_output.py: updating + popd ~/build/BUILD/python-biopython-1.81 + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.81-4.fc39 --unique-debug-suffix -1.81-4.fc39.s390x --unique-debug-src-base python-biopython-1.81-4.fc39.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/python-biopython-1.81 find-debuginfo: starting Extracting debug info from 9 files DWARF-compressing 9 files sepdebugcrcfix: Updated 9 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-biopython-1.81-4.fc39.s390x 1192 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.PnRdDO + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' ~/build/BUILD/python-biopython-1.81/python3/Tests ~/build/BUILD/python-biopython-1.81 + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,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-1.81 + 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_NCBI_qblast.py test_NMR.py test_NaiveBayes.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDBList.py test_PDB_CEAligner.py test_PDB_DSSP.py test_PDB_Dice.py test_PDB_Disordered.py test_PDB_Exposure.py test_PDB_FragmentMapper.py test_PDB_KDTree.py test_PDB_MMCIF2Dict.py test_PDB_MMCIFIO.py test_PDB_MMCIFParser.py test_PDB_NACCESS.py test_PDB_PDBIO.py test_PDB_PDBParser.py test_PDB_PSEA.py test_PDB_Polypeptide.py test_PDB_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 Tutorial ++ grep -v Phylo ++ grep -v pairwise_aligner ++ grep -v Nexus ++ grep -v SubsMat ++ grep -v bgzf ++ grep -v SearchIO_blast + for test in `ls test_*.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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Ace.py test_Ace ... ok test_check_ACEParser (test_Ace.AceTestOne.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestOne.test_check_record_parser) Test to check that contig parser parses each contig into a contig. ... ok test_check_ACEParser (test_Ace.AceTestThree.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestThree.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok test_check_ACEParser (test_Ace.AceTestTwo.test_check_ACEParser) Test to check that ACEParser can parse the whole file into one record. ... ok test_check_record_parser (test_Ace.AceTestTwo.test_check_record_parser) Test to check that record parser parses each contig into a record. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.053 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages C + /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 0.018 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages C + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO.py test_AlignIO ... ok test_parsing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_parsing_empty_files) Check that parsing an empty file returns an empty list. ... ok test_phylip_reject_duplicate (test_AlignIO.TestAlignIO_exceptions.test_phylip_reject_duplicate) Check that writing duplicated IDs after truncation fails for PHYLIP. ... ok test_writing_empty_files (test_AlignIO.TestAlignIO_exceptions.test_writing_empty_files) Check that writers can cope with no alignments. ... ok test_writing_not_alignments (test_AlignIO.TestAlignIO_exceptions.test_writing_not_alignments) Check that writers reject records that are not alignments. ... ok test_reading_alignments_clustal1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal1) ... ok test_reading_alignments_clustal2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal2) ... ok test_reading_alignments_clustal3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal3) ... ok test_reading_alignments_clustal4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal4) ... ok test_reading_alignments_clustal5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal5) ... ok test_reading_alignments_clustal6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_clustal6) ... ok test_reading_alignments_emboss1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss1) ... ok test_reading_alignments_emboss2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss2) ... ok test_reading_alignments_emboss3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss3) ... ok test_reading_alignments_emboss4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss4) ... ok test_reading_alignments_emboss5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss5) ... ok test_reading_alignments_emboss6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss6) ... ok test_reading_alignments_emboss7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss7) ... ok test_reading_alignments_emboss8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_emboss8) ... ok test_reading_alignments_fasta (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta) ... ok test_reading_alignments_fasta_m10_1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_1) ... ok test_reading_alignments_fasta_m10_2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_2) ... ok test_reading_alignments_fasta_m10_3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_3) ... ok test_reading_alignments_fasta_m10_4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_4) ... ok test_reading_alignments_fasta_m10_5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_5) ... ok test_reading_alignments_fasta_m10_6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_6) ... ok test_reading_alignments_fasta_m10_7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_7) ... ok test_reading_alignments_fasta_m10_8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_fasta_m10_8) ... ok test_reading_alignments_ig (test_AlignIO.TestAlignIO_reading.test_reading_alignments_ig) ... ok test_reading_alignments_maf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf1) ... ok test_reading_alignments_maf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf2) ... ok test_reading_alignments_maf3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf3) ... ok test_reading_alignments_maf4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_maf4) ... ok test_reading_alignments_mauve (test_AlignIO.TestAlignIO_reading.test_reading_alignments_mauve) ... ok test_reading_alignments_msf1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf1) ... ok test_reading_alignments_msf2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_msf2) ... ok test_reading_alignments_nexus1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus1) ... ok test_reading_alignments_nexus2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_nexus2) ... ok test_reading_alignments_phylip1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip1) ... ok test_reading_alignments_phylip10 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip10) ... ok test_reading_alignments_phylip2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip2) ... ok test_reading_alignments_phylip3 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip3) ... ok test_reading_alignments_phylip4 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip4) ... ok test_reading_alignments_phylip5 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip5) ... ok test_reading_alignments_phylip6 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip6) ... ok test_reading_alignments_phylip7 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip7) ... ok test_reading_alignments_phylip8 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip8) ... ok test_reading_alignments_phylip9 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_phylip9) ... ok test_reading_alignments_pir (test_AlignIO.TestAlignIO_reading.test_reading_alignments_pir) ... ok test_reading_alignments_stockholm1 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm1) ... ok test_reading_alignments_stockholm2 (test_AlignIO.TestAlignIO_reading.test_reading_alignments_stockholm2) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.617 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_ClustalIO.py test_AlignIO_ClustalIO ... ok test_biopython_header (test_AlignIO_ClustalIO.TestClustalIO.test_biopython_header) Make sure we can parse the Biopython header. ... ok test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO.test_cat_one_two) ... ok test_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 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_EmbossIO.py test_AlignIO_EmbossIO ... ok test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example) ... ok test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example2) ... ok test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_example3) ... ok test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO.test_pair_plus_simple) ... ok test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO.test_simple_example) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.069 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_FastaIO.py test_AlignIO_FastaIO ... ok test_output001 (test_AlignIO_FastaIO.FastaIOTests.test_output001) Check output001.m10 file. ... ok test_output002 (test_AlignIO_FastaIO.FastaIOTests.test_output002) Check output002.m10 file. ... ok test_output003 (test_AlignIO_FastaIO.FastaIOTests.test_output003) Check output003.m10 file. ... ok test_output004 (test_AlignIO_FastaIO.FastaIOTests.test_output004) Check output004.m10 file. ... ok test_output005 (test_AlignIO_FastaIO.FastaIOTests.test_output005) Check output005.m10 file. ... ok test_output006 (test_AlignIO_FastaIO.FastaIOTests.test_output006) Check output006.m10 file. ... ok test_output007 (test_AlignIO_FastaIO.FastaIOTests.test_output007) Check output007.m10 file. ... ok test_output008 (test_AlignIO_FastaIO.FastaIOTests.test_output008) Check output008.m10 file. ... ok test_output009 (test_AlignIO_FastaIO.FastaIOTests.test_output009) Check output009.m10 file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.088 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_MauveIO.py test_AlignIO_MauveIO ... ok test_one (test_AlignIO_MauveIO.TestMauveIO.test_one) ... ok test_sequence_positions (test_AlignIO_MauveIO.TestMauveIO.test_sequence_positions) ... ok test_write_read (test_AlignIO_MauveIO.TestMauveIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_PhylipIO.py test_AlignIO_PhylipIO ... ok test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO.test_concatenation) ... ok test_five (test_AlignIO_PhylipIO.TestPhylipIO.test_five) ... ok test_four (test_AlignIO_PhylipIO.TestPhylipIO.test_four) ... ok test_one (test_AlignIO_PhylipIO.TestPhylipIO.test_one) ... ok test_six (test_AlignIO_PhylipIO.TestPhylipIO.test_six) ... ok test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO.test_two_and_three) ... ok test_write_read (test_AlignIO_PhylipIO.TestPhylipIO.test_write_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.071 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignIO_convert.py test_AlignIO_convert ... ok test_clustal_to_nexus_with_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_with_mol_type) Converting Clustal to NEXUS with a molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_AlignIO_convert.ConvertTests.test_clustal_to_nexus_without_mol_type) Converting Clustal to NEXUS without a molecule type. ... ok test_convert (test_AlignIO_convert.ConvertTests.test_convert) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.246 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_AlignInfo.py test_AlignInfo ... ok test_nucleotides (test_AlignInfo.AlignInfoTests.test_nucleotides) ... ok test_proteins (test_AlignInfo.AlignInfoTests.test_proteins) ... ok test_pseudo_count (test_AlignInfo.AlignInfoTests.test_pseudo_count) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_Alignment.py test_Align_Alignment ... ok test_nucleotide_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_nucleotide_nucleotide_str) ... ok test_protein_nucleotide_str (test_Align_Alignment.TestAlign_nucleotide_protein_str.test_protein_nucleotide_str) ... ok test_aligned (test_Align_Alignment.TestAlign_out_of_order.test_aligned) ... ok test_array (test_Align_Alignment.TestAlign_out_of_order.test_array) ... ok test_indices (test_Align_Alignment.TestAlign_out_of_order.test_indices) ... ok test_row (test_Align_Alignment.TestAlign_out_of_order.test_row) ... ok test_row_col (test_Align_Alignment.TestAlign_out_of_order.test_row_col) ... ok test_row_iterable (test_Align_Alignment.TestAlign_out_of_order.test_row_iterable) ... ok test_row_slice (test_Align_Alignment.TestAlign_out_of_order.test_row_slice) ... ok test_rows_col (test_Align_Alignment.TestAlign_out_of_order.test_rows_col) ... ok test_rows_cols (test_Align_Alignment.TestAlign_out_of_order.test_rows_cols) ... ok test_str (test_Align_Alignment.TestAlign_out_of_order.test_str) ... ok test_substitutions (test_Align_Alignment.TestAlign_out_of_order.test_substitutions) ... ok test_empty_alignment (test_Align_Alignment.TestAlignment.test_empty_alignment) ... ok test_a2m (test_Align_Alignment.TestAlignment_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_format.test_bed) ... ok test_bigbed (test_Align_Alignment.TestAlignment_format.test_bigbed) ... ok test_bigmaf (test_Align_Alignment.TestAlignment_format.test_bigmaf) ... ok test_bigpsl (test_Align_Alignment.TestAlignment_format.test_bigpsl) ... ok test_clustal (test_Align_Alignment.TestAlignment_format.test_clustal) ... ok test_emboss (test_Align_Alignment.TestAlignment_format.test_emboss) ... ok test_exonerate (test_Align_Alignment.TestAlignment_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_format.test_fasta) ... ok test_hhr (test_Align_Alignment.TestAlignment_format.test_hhr) ... ok test_maf (test_Align_Alignment.TestAlignment_format.test_maf) ... ok test_mauve (test_Align_Alignment.TestAlignment_format.test_mauve) ... ok test_msf (test_Align_Alignment.TestAlignment_format.test_msf) ... ok test_nexus (test_Align_Alignment.TestAlignment_format.test_nexus) ... ok test_phylip (test_Align_Alignment.TestAlignment_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_format.test_sam) ... ok test_stockholm (test_Align_Alignment.TestAlignment_format.test_stockholm) ... ok test_tabular (test_Align_Alignment.TestAlignment_format.test_tabular) ... ok test_a2m (test_Align_Alignment.TestAlignment_pairwise_format.test_a2m) ... ok test_bed (test_Align_Alignment.TestAlignment_pairwise_format.test_bed) ... ok test_clustal (test_Align_Alignment.TestAlignment_pairwise_format.test_clustal) ... ok test_exonerate (test_Align_Alignment.TestAlignment_pairwise_format.test_exonerate) ... ok test_fasta (test_Align_Alignment.TestAlignment_pairwise_format.test_fasta) ... ok test_maf (test_Align_Alignment.TestAlignment_pairwise_format.test_maf) ... ok test_phylip (test_Align_Alignment.TestAlignment_pairwise_format.test_phylip) ... ok test_psl (test_Align_Alignment.TestAlignment_pairwise_format.test_psl) ... ok test_sam (test_Align_Alignment.TestAlignment_pairwise_format.test_sam) ... ok test_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 0.369 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_a2m.py test_Align_a2m ... ok test_clustalw (test_Align_a2m.TestA2MReadingWriting.test_clustalw) ... ok test_empty (test_Align_a2m.TestA2MReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_a2m.TestA2MReadingWriting.test_kalign) ... ok test_msaprobs (test_Align_a2m.TestA2MReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_a2m.TestA2MReadingWriting.test_muscle) ... ok test_probcons (test_Align_a2m.TestA2MReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_bed.py test_Align_bed ... ok test_reading (test_Align_bed.TestAlign_bed12.test_reading) Test parsing alignments in file formats BED3 through BED12. ... ok test_writing (test_Align_bed.TestAlign_bed12.test_writing) Test writing the alignments in bed12.bed as BED3 through BED12. ... ok test_reading_psl_34_001 (test_Align_bed.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.bed. ... ok test_reading_psl_34_003 (test_Align_bed.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.bed. ... ok test_reading_psl_34_004 (test_Align_bed.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.bed. ... ok test_reading_psl_34_005 (test_Align_bed.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.bed. ... ok test_writing_psl_34_001 (test_Align_bed.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.bed. ... ok test_writing_psl_34_003 (test_Align_bed.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.bed. ... ok test_writing_psl_34_004 (test_Align_bed.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.bed. ... ok test_writing_psl_34_005 (test_Align_bed.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.bed. ... ok test_reading (test_Align_bed.TestAlign_dna_rna.test_reading) Test parsing dna_rna.bed. ... ok test_writing (test_Align_bed.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.bed. ... ok test_reading_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.bed. ... ok test_reading_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.bed. ... ok test_writing_psl_35_001 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.bed. ... ok test_writing_psl_35_002 (test_Align_bed.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.bed. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.187 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 ---------------------------------------------------------------------- Ran 1 test in 0.141 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.358 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.268 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_clustal.py test_Align_clustal ... ok test_clustalw (test_Align_clustal.TestClustalReadingWriting.test_clustalw) ... ok test_empty (test_Align_clustal.TestClustalReadingWriting.test_empty) Checking empty file. ... ok test_kalign (test_Align_clustal.TestClustalReadingWriting.test_kalign) Make sure we can parse the Kalign header. ... ok test_msaprobs (test_Align_clustal.TestClustalReadingWriting.test_msaprobs) ... ok test_muscle (test_Align_clustal.TestClustalReadingWriting.test_muscle) ... ok test_probcons (test_Align_clustal.TestClustalReadingWriting.test_probcons) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.113 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.116 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_exonerate.py test_Align_exonerate ... ok test_exn_22_m_affine_local_cigar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_cigar) Test parsing exn_22_m_affine_local_cigar.exn. ... ok test_exn_22_m_affine_local_vulgar (test_Align_exonerate.Exonerate_affine_local.test_exn_22_m_affine_local_vulgar) Test parsing exn_22_m_affine_local_vulgar.exn. ... ok test_exn_22_m_cdna2genome_cigar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_cigar) Test parsing exn_22_m_cdna2genome_cigar.exn. ... ok test_exn_22_m_cdna2genome_vulgar (test_Align_exonerate.Exonerate_cdna2genome.test_exn_22_m_cdna2genome_vulgar) Test parsing exn_22_m_cdna2genome_vulgar.exn. ... ok test_exn_22_m_coding2coding_cigar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_cigar) Test parsing exn_22_m_coding2coding_cigar.exn. ... ok test_exn_22_m_coding2coding_vulgar (test_Align_exonerate.Exonerate_coding2coding.test_exn_22_m_coding2coding_vulgar) Test parsing exn_22_m_coding2coding_vulgar.exn. ... ok test_exn_22_m_coding2coding_fshifts_cigar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_cigar) Test parsing exn_22_m_cigar_fshifts.exn). ... ok test_exn_22_m_coding2coding_fshifts_vulgar (test_Align_exonerate.Exonerate_coding2coding_fshifts.test_exn_22_m_coding2coding_fshifts_vulgar) Test parsing exn_22_o_vulgar_fshifts.exn. ... ok test_exn_22_m_coding2genome_cigar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_cigar) Test parsing exn_22_m_coding2genome_cigar.exn. ... ok test_exn_22_m_coding2genome_vulgar (test_Align_exonerate.Exonerate_coding2genome.test_exn_22_m_coding2genome_vulgar) Test parsing exn_22_m_coding2genome_vulgar.exn. ... ok test_exn_22_m_dna2protein_cigar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_cigar) Test parsing exn_22_m_dna2protein_cigar.exn. ... ok test_exn_22_m_dna2protein_vulgar (test_Align_exonerate.Exonerate_dna2protein.test_exn_22_m_dna2protein_vulgar) Test parsing exn_22_m_dna2protein_vulgar.exn. ... ok test_exn_22_m_est2genome_cigar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_cigar) Test parsing exn_22_m_est2genome_cigar.exn. ... ok test_exn_22_m_est2genome_vulgar (test_Align_exonerate.Exonerate_est2genome.test_exn_22_m_est2genome_vulgar) Test parsing exn_22_m_est2genome_vulgar.exn. ... ok test_exn_22_m_genome2genome_cigar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_cigar) Test parsing exn_22_o_vulgar_cigar.exn. ... ok test_exn_22_m_genome2genome_vulgar (test_Align_exonerate.Exonerate_genome2genome.test_exn_22_m_genome2genome_vulgar) Test parsing exn_22_o_vulgar.exn. ... ok test_exn_22_q_multiple_cigar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_cigar) Test parsing exn_22_q_multiple_cigar.exn. ... ok test_exn_22_q_multiple_vulgar (test_Align_exonerate.Exonerate_multiple.test_exn_22_q_multiple_vulgar) Test parsing exn_22_q_multiple_vulgar.exn. ... ok test_exn_22_m_ner_cigar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_cigar) Test parsing exonerate output (exn_22_m_ner_cigar.exn). ... ok test_exn_22_m_ner_vulgar (test_Align_exonerate.Exonerate_ner.test_exn_22_m_ner_vulgar) Test parsing exonerate output (exn_22_m_ner_vulgar.exn). ... ok test_exn_22_q_none (test_Align_exonerate.Exonerate_none.test_exn_22_q_none) Test parsing exonerate output (exn_22_q_none.exn). ... ok test_exn_22_m_protein2dna_cigar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_cigar) Test parsing exonerate output (exn_22_m_protein2dna_cigar.exn). ... ok test_exn_22_m_protein2dna_vulgar (test_Align_exonerate.Exonerate_protein2dna.test_exn_22_m_protein2dna_vulgar) Test parsing exonerate output (exn_22_m_protein2dna_vulgar.exn). ... ok test_exn_22_m_protein2dna_fshifts_cigar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_cigar) Test parsing exonerate output (exn_22_o_cigar_fshifts2.exn). ... ok test_exn_22_m_protein2dna_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2dna_fshifts.test_exn_22_m_protein2dna_fshifts_vulgar) Test parsing exonerate output (exn_22_o_vulgar_fshifts2.exn). ... ok test_exn_22_m_protein2genome_cigar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_cigar) Test parsing exn_22_m_protein2genome_cigar.exn. ... ok test_exn_22_m_protein2genome_vulgar (test_Align_exonerate.Exonerate_protein2genome.test_exn_22_m_protein2genome_vulgar) Test parsing exn_22_m_protein2genome_vulgar.exn. ... ok test_exn_24_protein2genome_met_intron_cigar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_cigar) Test parsing exn_24_m_protein2genome_met_intron_cigar.exn. ... ok test_exn_24_protein2genome_met_intron_vulgar (test_Align_exonerate.Exonerate_protein2genome_met_intron.test_exn_24_protein2genome_met_intron_vulgar) Test parsing exn_24_m_protein2genome_met_intron_vulgar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_cigar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_cigar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_cigar.exn. ... ok test_exn_24_m_protein2genome_revcomp_fshifts_vulgar (test_Align_exonerate.Exonerate_protein2genome_revcomp_fshifts.test_exn_24_m_protein2genome_revcomp_fshifts_vulgar) Test parsing exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn. ... ok test_exn_22_m_ungapped_cigar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_cigar) Test parsing exn_22_m_ungapped_cigar.exn. ... ok test_exn_22_m_ungapped_vulgar (test_Align_exonerate.Exonerate_ungapped.test_exn_22_m_ungapped_vulgar) Test parsing exn_22_m_ungapped_vulgar.exn. ... ok test_exn_22_m_ungapped_trans_cigar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_cigar) Test parsing exn_22_m_ungapped_trans_cigar.exn. ... ok test_exn_22_m_ungapped_trans_vulgar (test_Align_exonerate.Exonerate_ungapped_trans.test_exn_22_m_ungapped_trans_vulgar) Test parsing exn_22_m_ungapped_trans_vulgar.exn. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.186 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.089 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.369 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_maf.py test_Align_maf ... ok test_reading_bug2453 (test_Align_maf.TestAlign_reading.test_reading_bug2453) Test parsing bug2453.maf. ... ok test_reading_bundle_without_target (test_Align_maf.TestAlign_reading.test_reading_bundle_without_target) Test parsing bundle_without_target.maf. ... ok test_reading_length_coords_mismatch (test_Align_maf.TestAlign_reading.test_reading_length_coords_mismatch) Test parsing inconsistent MAF file length_coords_mismatch.maf. ... ok test_reading_missing_signature (test_Align_maf.TestAlign_reading.test_reading_missing_signature) Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature. ... ok test_reading_ucsc_mm9_chr10 (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10) Test parsing MAF file ucsc_mm9_chr10.maf. ... ok test_reading_ucsc_mm9_chr10_bad (test_Align_maf.TestAlign_reading.test_reading_ucsc_mm9_chr10_bad) Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size. ... ok test_reading_ucsc_test (test_Align_maf.TestAlign_reading.test_reading_ucsc_test) Test parsing ucsc_test.maf. ... ok test_writing_bug2453 (test_Align_maf.TestAlign_writing.test_writing_bug2453) Test reading and writing bug2453.maf. ... ok test_writing_bundle_without_target (test_Align_maf.TestAlign_writing.test_writing_bundle_without_target) Test reading and writing bundle_without_target.maf. ... ok test_writing_ucsc_mm9_chr10 (test_Align_maf.TestAlign_writing.test_writing_ucsc_mm9_chr10) Test reading and writing ucsc_mm9_chr10.maf. ... ok test_writing_ucsc_test (test_Align_maf.TestAlign_writing.test_writing_ucsc_test) Test reading and writing ucsc_test.maf. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.482 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_mauve.py test_Align_mauve ... ok test_parse (test_Align_mauve.TestCombinedFile.test_parse) ... ok test_write_read (test_Align_mauve.TestCombinedFile.test_write_read) ... ok test_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 0.104 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /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 0.070 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_nexus.py test_Align_nexus ... ok test_empty (test_Align_nexus.TestNexusBasic.test_empty) ... ok test_nexus1 (test_Align_nexus.TestNexusReading.test_nexus1) ... ok test_nexus2 (test_Align_nexus.TestNexusReading.test_nexus2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_phylip.py test_Align_phylip ... ok test_five_and_six (test_Align_phylip.TestPhylipReading.test_five_and_six) ... ok test_four (test_Align_phylip.TestPhylipReading.test_four) ... ok test_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 0.101 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_psl.py test_Align_psl ... ok test_reading_psl_34_001 (test_Align_psl.TestAlign_dna.test_reading_psl_34_001) Test parsing psl_34_001.psl and pslx_34_001.pslx. ... ok test_reading_psl_34_002 (test_Align_psl.TestAlign_dna.test_reading_psl_34_002) Test parsing psl_34_002.psl and pslx_34_002.pslx. ... ok test_reading_psl_34_003 (test_Align_psl.TestAlign_dna.test_reading_psl_34_003) Test parsing psl_34_003.psl and pslx_34_003.pslx. ... ok test_reading_psl_34_004 (test_Align_psl.TestAlign_dna.test_reading_psl_34_004) Test parsing psl_34_004.psl and pslx_34_004.pslx. ... ok test_reading_psl_34_005 (test_Align_psl.TestAlign_dna.test_reading_psl_34_005) Test parsing psl_34_005.psl and pslx_34_005.pslx. ... ok test_writing_psl_34_001 (test_Align_psl.TestAlign_dna.test_writing_psl_34_001) Test writing the alignments in psl_34_001.psl. ... ok test_writing_psl_34_002 (test_Align_psl.TestAlign_dna.test_writing_psl_34_002) Test writing the alignments in psl_34_002.psl. ... ok test_writing_psl_34_003 (test_Align_psl.TestAlign_dna.test_writing_psl_34_003) Test writing the alignments in psl_34_003.psl. ... ok test_writing_psl_34_004 (test_Align_psl.TestAlign_dna.test_writing_psl_34_004) Test writing the alignments in psl_34_004.psl. ... ok test_writing_psl_34_005 (test_Align_psl.TestAlign_dna.test_writing_psl_34_005) Test writing the alignments in psl_34_005.psl. ... ok test_reading (test_Align_psl.TestAlign_dna_rna.test_reading) Test parsing dna_rna.psl. ... ok test_writing (test_Align_psl.TestAlign_dna_rna.test_writing) Test writing the alignments in dna_rna.psl. ... ok test_reading_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_001) Test parsing psl_35_001.psl and pslx_35_001.pslx. ... ok test_reading_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_reading_psl_35_002) Test parsing psl_35_002.psl. ... ok test_writing_psl_35_001 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_001) Test writing the alignments in psl_35_001.psl. ... ok test_writing_psl_35_002 (test_Align_psl.TestAlign_dnax_prot.test_writing_psl_35_002) Test writing the alignments in psl_35_002.psl. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.326 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.433 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.744 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Align_tabular.py test_Align_tabular ... ok test_2226_tblastn_001 (test_Align_tabular.TestBlast.test_2226_tblastn_001) ... ok test_2226_tblastn_002 (test_Align_tabular.TestBlast.test_2226_tblastn_002) ... ok test_2226_tblastn_003 (test_Align_tabular.TestBlast.test_2226_tblastn_003) ... ok test_2226_tblastn_004 (test_Align_tabular.TestBlast.test_2226_tblastn_004) ... ok test_2226_tblastn_005 (test_Align_tabular.TestBlast.test_2226_tblastn_005) ... ok test_2226_tblastn_007 (test_Align_tabular.TestBlast.test_2226_tblastn_007) ... ok test_2226_tblastn_008 (test_Align_tabular.TestBlast.test_2226_tblastn_008) ... ok test_2226_tblastn_009 (test_Align_tabular.TestBlast.test_2226_tblastn_009) ... ok test_2226_tblastn_010 (test_Align_tabular.TestBlast.test_2226_tblastn_010) ... ok test_2226_tblastn_011 (test_Align_tabular.TestBlast.test_2226_tblastn_011) ... ok test_2226_tblastn_012 (test_Align_tabular.TestBlast.test_2226_tblastn_012) ... ok test_2228_tblastn_001 (test_Align_tabular.TestBlast.test_2228_tblastn_001) ... ok test_2228_tblastx_001 (test_Align_tabular.TestBlast.test_2228_tblastx_001) ... ok test_empty (test_Align_tabular.TestFastaBasic.test_empty) ... ok test_m8CB (test_Align_tabular.TestFastaNucleotide.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaNucleotide.test_m8CC) ... ok test_m8CB (test_Align_tabular.TestFastaProtein.test_m8CB) ... ok test_m8CC (test_Align_tabular.TestFastaProtein.test_m8CC) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.512 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Application.py test_Application ... ok test_echo (test_Application.TestApp.test_echo) ... ok test_echo_capture_both (test_Application.TestApp.test_echo_capture_both) ... ok test_echo_capture_neither (test_Application.TestApp.test_echo_capture_neither) ... ok test_echo_capture_stderr (test_Application.TestApp.test_echo_capture_stderr) ... ok test_echo_capture_stdout (test_Application.TestApp.test_echo_capture_stdout) ... ok test_echo_file_both (test_Application.TestApp.test_echo_file_both) ... ok test_echo_file_same (test_Application.TestApp.test_echo_file_same) ... ok test_echo_file_stderr (test_Application.TestApp.test_echo_file_stderr) ... ok test_echo_file_stdout (test_Application.TestApp.test_echo_file_stdout) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.033 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BWA_tool.py test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb.py test_BioSQL_MySQLdb ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.162 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_MySQLdb_online.py test_BioSQL_MySQLdb_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.110 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector.py test_BioSQL_mysql_connector ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_mysql_connector_online.py test_BioSQL_mysql_connector_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.111 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2.py test_BioSQL_psycopg2 ... skipping. BioSQL test configuration file biosql.ini missing (see biosql.ini.sample) ---------------------------------------------------------------------- Ran 1 test in 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_psycopg2_online.py test_BioSQL_psycopg2_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.107 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3.py test_BioSQL_sqlite3 ... ok test_SeqIO_loading (common_BioSQL.AutoSeqIOTests.test_SeqIO_loading) ... ok test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest.test_backwards_compatibility) Check can re-use an old BioSQL SQLite3 database. ... ok test_NC_000932 (common_BioSQL.ClosedLoopTest.test_NC_000932) From GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok test_NC_005816 (common_BioSQL.ClosedLoopTest.test_NC_005816) From GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok test_NT_019265 (common_BioSQL.ClosedLoopTest.test_NT_019265) From GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok test_arab1 (common_BioSQL.ClosedLoopTest.test_arab1) From GenBank file to BioSQL and back to a GenBank file, arab1. ... ok test_cor6_6 (common_BioSQL.ClosedLoopTest.test_cor6_6) From GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok test_no_ref (common_BioSQL.ClosedLoopTest.test_no_ref) From GenBank file to BioSQL and back to a GenBank file, noref. ... ok test_one_of (common_BioSQL.ClosedLoopTest.test_one_of) From GenBank file to BioSQL and back to a GenBank file, one_of. ... ok test_protein_refseq2 (common_BioSQL.ClosedLoopTest.test_protein_refseq2) From GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok test_del_db_items (common_BioSQL.DeleteTest.test_del_db_items) Check all associated data is deleted from an item. ... ok test_server (common_BioSQL.DeleteTest.test_server) Check BioSeqDatabase methods. ... ok test_duplicate_id_load (common_BioSQL.DupLoadTest.test_duplicate_id_load) Make sure can't import records with same ID (in one go). ... ok test_duplicate_load (common_BioSQL.DupLoadTest.test_duplicate_load) Make sure can't import a single record twice (in one go). ... ok test_duplicate_load2 (common_BioSQL.DupLoadTest.test_duplicate_load2) Make sure can't import a single record twice (in steps). ... ok test_record_loading (common_BioSQL.InDepthLoadTest.test_record_loading) Make sure all records are correctly loaded. ... ok test_reload (common_BioSQL.InDepthLoadTest.test_reload) Make sure can't reimport existing records. ... ok test_seq_feature (common_BioSQL.InDepthLoadTest.test_seq_feature) In depth check that SeqFeatures are transmitted through the db. ... ok test_transfer (common_BioSQL.InDepthLoadTest.test_transfer) Make sure can load record into another namespace. ... ok test_load_database (common_BioSQL.LoaderTest.test_load_database) Load SeqRecord objects into a BioSQL database. ... ok test_cross_retrieval_of_items (common_BioSQL.MultiReadTest.test_cross_retrieval_of_items) Test that valid ids can't be retrieved between namespaces. ... ok test_get_db_items (common_BioSQL.MultiReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_server (common_BioSQL.MultiReadTest.test_server) Check BioSeqDatabase methods. ... ok test_get_db_items (common_BioSQL.ReadTest.test_get_db_items) Check list, keys, length etc. ... ok test_lookup_items (common_BioSQL.ReadTest.test_lookup_items) Test retrieval of items using various ids. ... ok test_server (common_BioSQL.ReadTest.test_server) Check BioSeqDatabase methods. ... ok test_addition (common_BioSQL.SeqInterfaceTest.test_addition) Check can add Seq objects from BioSQL together. ... ok test_convert (common_BioSQL.SeqInterfaceTest.test_convert) Check can turn a Seq object from BioSQL into a Seq or MutableSeq. ... ok test_eq (common_BioSQL.SeqInterfaceTest.test_eq) ... ok test_ge (common_BioSQL.SeqInterfaceTest.test_ge) ... ok test_gt (common_BioSQL.SeqInterfaceTest.test_gt) ... ok test_le (common_BioSQL.SeqInterfaceTest.test_le) ... ok test_lt (common_BioSQL.SeqInterfaceTest.test_lt) ... ok test_multiplication (common_BioSQL.SeqInterfaceTest.test_multiplication) Check can multiply Seq objects from BioSQL by integers. ... ok test_ne (common_BioSQL.SeqInterfaceTest.test_ne) ... ok test_record_slicing (common_BioSQL.SeqInterfaceTest.test_record_slicing) Check that slices of DBSeqRecord are retrieved properly. ... ok test_seq (common_BioSQL.SeqInterfaceTest.test_seq) Make sure Seqs from BioSQL implement the right interface. ... ok test_seq_features (common_BioSQL.SeqInterfaceTest.test_seq_features) Check SeqFeatures of a sequence. ... ok test_seq_record (common_BioSQL.SeqInterfaceTest.test_seq_record) Make sure SeqRecords from BioSQL implement the right interface. ... ok test_seq_slicing (common_BioSQL.SeqInterfaceTest.test_seq_slicing) Check that slices of sequences are retrieved properly. ... ok test_ambiguous_location (common_BioSQL.SwissProtUnknownPositionTest.test_ambiguous_location) Loaded uniprot-xml with ambiguous location in BioSQL. ... ok test_add (common_BioSQL.TestBaseClassMethods.test_add) ... ok test_bytes (common_BioSQL.TestBaseClassMethods.test_bytes) ... ok test_contains (common_BioSQL.TestBaseClassMethods.test_contains) ... ok test_count (common_BioSQL.TestBaseClassMethods.test_count) ... ok test_endswith (common_BioSQL.TestBaseClassMethods.test_endswith) ... ok test_find (common_BioSQL.TestBaseClassMethods.test_find) ... ok test_hash (common_BioSQL.TestBaseClassMethods.test_hash) ... ok test_index (common_BioSQL.TestBaseClassMethods.test_index) ... ok test_lower (common_BioSQL.TestBaseClassMethods.test_lower) ... ok test_lstrip (common_BioSQL.TestBaseClassMethods.test_lstrip) ... ok test_mul (common_BioSQL.TestBaseClassMethods.test_mul) ... ok test_radd (common_BioSQL.TestBaseClassMethods.test_radd) ... ok test_replace (common_BioSQL.TestBaseClassMethods.test_replace) ... ok test_repr (common_BioSQL.TestBaseClassMethods.test_repr) ... ok test_rfind (common_BioSQL.TestBaseClassMethods.test_rfind) ... ok test_rindex (common_BioSQL.TestBaseClassMethods.test_rindex) ... ok test_rsplit (common_BioSQL.TestBaseClassMethods.test_rsplit) ... ok test_rstrip (common_BioSQL.TestBaseClassMethods.test_rstrip) ... ok test_split (common_BioSQL.TestBaseClassMethods.test_split) ... ok test_startswith (common_BioSQL.TestBaseClassMethods.test_startswith) ... ok test_str (common_BioSQL.TestBaseClassMethods.test_str) ... ok test_strip (common_BioSQL.TestBaseClassMethods.test_strip) ... ok test_translate (common_BioSQL.TestBaseClassMethods.test_translate) ... ok test_upper (common_BioSQL.TestBaseClassMethods.test_upper) ... ok test_NC_000932 (common_BioSQL.TransferTest.test_NC_000932) From GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok test_NC_005816 (common_BioSQL.TransferTest.test_NC_005816) From GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok test_NT_019265 (common_BioSQL.TransferTest.test_NT_019265) From GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok test_arab1 (common_BioSQL.TransferTest.test_arab1) From GenBank file to BioSQL, then again to a new namespace, arab1. ... ok test_cor6_6 (common_BioSQL.TransferTest.test_cor6_6) From GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok test_no_ref (common_BioSQL.TransferTest.test_no_ref) From GenBank file to BioSQL, then again to a new namespace, noref. ... ok test_one_of (common_BioSQL.TransferTest.test_one_of) From GenBank file to BioSQL, then again to a new namespace, one_of. ... ok test_protein_refseq2 (common_BioSQL.TransferTest.test_protein_refseq2) From GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok ---------------------------------------------------------------------- Ran 1 test in 4.279 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_BioSQL_sqlite3_online.py test_BioSQL_sqlite3_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.106 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Blast_Record.py test_Blast_Record ... ok test_str (test_Blast_Record.TestHsp.test_str) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.060 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_CAPS.py test_CAPS ... ok test (test_CAPS.TestCAPS.test) ... ok testNoCAPS (test_CAPS.TestCAPS.testNoCAPS) ... ok testNoCAPS_msa (test_CAPS.TestCAPS.testNoCAPS_msa) ... ok test_msa (test_CAPS.TestCAPS.test_msa) ... ok test_trivial (test_CAPS.TestCAPS.test_trivial) ... ok test_trivial_msa (test_CAPS.TestCAPS.test_trivial_msa) ... ok test_uneven (test_CAPS.TestCAPS.test_uneven) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.225 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Chi2.py test_Chi2 ... ok test_cdf_chi2 (test_Chi2.ModTest.test_cdf_chi2) ... ok test_incomplete_gamma (test_Chi2.ModTest.test_incomplete_gamma) ... ok test_ln_gamma (test_Chi2.ModTest.test_ln_gamma) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ClustalOmega_tool.py test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.095 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Clustalw_tool.py test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.053 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ColorSpiral.py test_ColorSpiral ... ok test_dict (test_ColorSpiral.DictTest.test_dict) get_color_dict() for classes A-D, no jitter. ... ok test_colorlist (test_ColorSpiral.SpiralTest.test_colorlist) Get set of eight colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SpiralTest.test_colorspiral) Get set of 16 colours, no jitter, using ColorSpiral. ... ok test_colorspiral (test_ColorSpiral.SquareTest.test_colorspiral) Set of 625 colours, with jitter, using get_colors(). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages C + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Compass.py test_Compass ... ok testAlignmentParsingOne (test_Compass.CompassTest.testAlignmentParsingOne) ... ok testAlignmentParsingTwo (test_Compass.CompassTest.testAlignmentParsingTwo) ... ok testCompassIteratorEasy (test_Compass.CompassTest.testCompassIteratorEasy) ... ok testCompassIteratorHard (test_Compass.CompassTest.testCompassIteratorHard) ... ok testCompassParser (test_Compass.CompassTest.testCompassParser) ... ok testCompassScanAndConsume (test_Compass.CompassTest.testCompassScanAndConsume) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Consensus.py test_Consensus ... ok test_bitstring (test_Consensus.BitStringTest.test_bitstring) ... ok test_bootstrap (test_Consensus.BootstrapTest.test_bootstrap) ... ok test_bootstrap_consensus (test_Consensus.BootstrapTest.test_bootstrap_consensus) ... ok test_bootstrap_consensus_msa (test_Consensus.BootstrapTest.test_bootstrap_consensus_msa) ... ok test_bootstrap_trees (test_Consensus.BootstrapTest.test_bootstrap_trees) ... ok test_bootstrap_trees_msa (test_Consensus.BootstrapTest.test_bootstrap_trees_msa) ... ok test_adam_consensus (test_Consensus.ConsensusTest.test_adam_consensus) ... ok test_count_clades (test_Consensus.ConsensusTest.test_count_clades) ... ok test_get_support (test_Consensus.ConsensusTest.test_get_support) ... ok test_majority_consensus (test_Consensus.ConsensusTest.test_majority_consensus) ... ok test_strict_consensus (test_Consensus.ConsensusTest.test_strict_consensus) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.737 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Dialign_tool.py test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EMBL_unittest.py test_EMBL_unittest ... ok test_embl_0_line (test_EMBL_unittest.EMBLTests.test_embl_0_line) Test SQ line with 0 length sequence. ... ok test_embl_content_after_co (test_EMBL_unittest.EMBLTests.test_embl_content_after_co) Test a ValueError is thrown by content after a CO line. ... ok test_embl_no_coords (test_EMBL_unittest.EMBLTests.test_embl_no_coords) Test sequence lines without coordinates. ... ok test_embl_wrong_dr_line (test_EMBL_unittest.EMBLTests.test_embl_wrong_dr_line) Test files with wrong DR lines. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.087 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Emboss.py test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss. ---------------------------------------------------------------------- Ran 1 test in 0.113 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EmbossPhylipNew.py test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools. ---------------------------------------------------------------------- Ran 1 test in 0.091 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_EmbossPrimer.py test_EmbossPrimer ... ok test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest.test_in_depth_single_parse) Make sure we get info right from a single primer find. ... ok test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest.test_indepth_regular_parse) Make sure we get the data from normal primer3 files okay. ... ok test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest.test_internal_oligo_single_parse) Make sure we can parse an internal oligo file correctly. ... ok test_multi_record_full (test_EmbossPrimer.Primer3ParseTest.test_multi_record_full) Test parsing multiple primer sets (NirK full). ... ok test_multi_record_fwd (test_EmbossPrimer.Primer3ParseTest.test_multi_record_fwd) Test parsing multiple primer sets (NirK forward). ... ok test_simple_parse (test_EmbossPrimer.Primer3ParseTest.test_simple_parse) Make sure that we can use all single target primer3 files. ... ok test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest.test_primer_representation) Make sure we can output primer information correctly. ... ok test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest.test_in_depth_normal_parse) Make sure the output from a simple primersearch file is correct. ... ok test_simple_parse (test_EmbossPrimer.PrimersearchParseTest.test_simple_parse) Make sure that we can parse all primersearch files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.015 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez.py test_Entrez ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Entrez/__init__.py:694: 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 ---------------------------------------------------------------------- Ran 1 test in 4.160 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_online.py test_Entrez_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.081 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Entrez_parser.py test_Entrez_parser ... ok test_efetch_schemas (test_Entrez_parser.EFetchTest.test_efetch_schemas) Test parsing XML using Schemas. ... ok test_fasta (test_Entrez_parser.EFetchTest.test_fasta) Test error handling when presented with Fasta non-XML data. ... ok test_genbank (test_Entrez_parser.EFetchTest.test_genbank) Test error handling when presented with GenBank non-XML data. ... ok test_nucleotide1 (test_Entrez_parser.EFetchTest.test_nucleotide1) Test parsing XML returned by EFetch, Nucleotide database (first test). ... ok test_nucleotide2 (test_Entrez_parser.EFetchTest.test_nucleotide2) Test parsing XML returned by EFetch, Nucleotide database (second test). ... ok test_omim (test_Entrez_parser.EFetchTest.test_omim) Test parsing XML returned by EFetch, OMIM database. ... ok test_pmc (test_Entrez_parser.EFetchTest.test_pmc) Test parsing XML returned by EFetch from PubMed Central. ... ok test_protein (test_Entrez_parser.EFetchTest.test_protein) Test parsing XML returned by EFetch, Protein database. ... ok test_pubmed1 (test_Entrez_parser.EFetchTest.test_pubmed1) Test parsing XML returned by EFetch, PubMed database (first test). ... ok test_pubmed2 (test_Entrez_parser.EFetchTest.test_pubmed2) Test parsing XML returned by EFetch, PubMed database (second test). ... ok test_pubmed_html (test_Entrez_parser.EFetchTest.test_pubmed_html) Test error handling when presented with HTML (so XML-like) data. ... ok test_pubmed_html_escaping (test_Entrez_parser.EFetchTest.test_pubmed_html_escaping) Test parsing XML returned by EFetch, PubMed database with HTML tags and HTML escape characters. ... ok test_pubmed_html_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with both HTML and MathML tags. ... ok test_pubmed_html_tags (test_Entrez_parser.EFetchTest.test_pubmed_html_tags) Test parsing XML returned by EFetch, PubMed database with HTML tags. ... ok test_pubmed_mathml_tags (test_Entrez_parser.EFetchTest.test_pubmed_mathml_tags) Test parsing XML returned by EFetch, PubMed database, with extensive MathML tags. ... ok test_taxonomy (test_Entrez_parser.EFetchTest.test_taxonomy) Test parsing XML returned by EFetch, Taxonomy database. ... ok test_truncated_xml (test_Entrez_parser.EFetchTest.test_truncated_xml) Test error handling for a truncated XML declaration. ... ok test_xml_without_declaration (test_Entrez_parser.EFetchTest.test_xml_without_declaration) Test error handling for a missing XML declaration. ... ok test_xml_without_definition (test_Entrez_parser.EFetchTest.test_xml_without_definition) Test error handling for a missing DTD or XML Schema. ... ok test_egquery1 (test_Entrez_parser.EGQueryTest.test_egquery1) Test parsing XML output returned by EGQuery (first test). ... ok test_egquery2 (test_Entrez_parser.EGQueryTest.test_egquery2) Test parsing XML output returned by EGQuery (second test). ... ok test_corrupted (test_Entrez_parser.EInfoTest.test_corrupted) Test if corrupted XML is handled correctly. ... ok test_list (test_Entrez_parser.EInfoTest.test_list) Test parsing database list returned by EInfo. ... ok test_pubmed1 (test_Entrez_parser.EInfoTest.test_pubmed1) Test parsing database info returned by EInfo. ... ok test_pubmed2 (test_Entrez_parser.EInfoTest.test_pubmed2) Test validating the XML against the DTD. ... ok test_pubmed3 (test_Entrez_parser.EInfoTest.test_pubmed3) Test non-validating parser on XML with an inconsistent DTD. ... ok test_medline (test_Entrez_parser.ELinkTest.test_medline) Test parsing medline indexed articles returned by ELink. ... ok test_nucleotide (test_Entrez_parser.ELinkTest.test_nucleotide) Test parsing Nucleotide to Protein links returned by ELink. ... ok test_pubmed1 (test_Entrez_parser.ELinkTest.test_pubmed1) Test parsing pubmed links returned by ELink (first test). ... ok test_pubmed2 (test_Entrez_parser.ELinkTest.test_pubmed2) Test parsing pubmed links returned by ELink (second test). ... ok test_pubmed3 (test_Entrez_parser.ELinkTest.test_pubmed3) Test parsing pubmed link returned by ELink (third test). ... ok test_pubmed4 (test_Entrez_parser.ELinkTest.test_pubmed4) Test parsing pubmed links returned by ELink (fourth test). ... ok test_pubmed5 (test_Entrez_parser.ELinkTest.test_pubmed5) Test parsing pubmed links returned by ELink (fifth test). ... ok test_pubmed6 (test_Entrez_parser.ELinkTest.test_pubmed6) Test parsing pubmed links returned by ELink (sixth test). ... ok test_epost (test_Entrez_parser.EPostTest.test_epost) Test parsing XML returned by EPost. ... ok test_invalid (test_Entrez_parser.EPostTest.test_invalid) Test parsing XML returned by EPost with invalid id (overflow tag). ... ok test_wrong (test_Entrez_parser.EPostTest.test_wrong) Test parsing XML returned by EPost with incorrect arguments. ... ok test_journals (test_Entrez_parser.ESearchTest.test_journals) Test parsing XML returned by ESearch from the Journals database. ... ok test_notfound (test_Entrez_parser.ESearchTest.test_notfound) Test parsing XML returned by ESearch when no items were found. ... ok test_nucleotide (test_Entrez_parser.ESearchTest.test_nucleotide) Test parsing XML returned by ESearch from the Nucleotide database. ... ok test_pmc (test_Entrez_parser.ESearchTest.test_pmc) Test parsing XML returned by ESearch from PubMed Central. ... ok test_protein (test_Entrez_parser.ESearchTest.test_protein) Test parsing XML returned by ESearch from the Protein database. ... ok test_pubmed1 (test_Entrez_parser.ESearchTest.test_pubmed1) Test parsing XML returned by ESearch from PubMed (first test). ... ok test_pubmed2 (test_Entrez_parser.ESearchTest.test_pubmed2) Test parsing XML returned by ESearch from PubMed (second test). ... ok test_pubmed3 (test_Entrez_parser.ESearchTest.test_pubmed3) Test parsing XML returned by ESearch from PubMed (third test). ... ok test_espell (test_Entrez_parser.ESpellTest.test_espell) Test parsing XML output returned by ESpell. ... ok test_integer_none (test_Entrez_parser.ESummaryTest.test_integer_none) Test parsing ESummary XML where an Integer is not defined. ... ok test_journals (test_Entrez_parser.ESummaryTest.test_journals) Test parsing XML returned by ESummary from the Journals database. ... ok test_nucleotide (test_Entrez_parser.ESummaryTest.test_nucleotide) Test parsing XML returned by ESummary from the Nucleotide database. ... ok test_protein (test_Entrez_parser.ESummaryTest.test_protein) Test parsing XML returned by ESummary from the Protein database. ... ok test_pubmed (test_Entrez_parser.ESummaryTest.test_pubmed) Test parsing XML returned by ESummary from PubMed. ... ok test_structure (test_Entrez_parser.ESummaryTest.test_structure) Test parsing XML returned by ESummary from the Structure database. ... ok test_taxonomy (test_Entrez_parser.ESummaryTest.test_taxonomy) Test parsing XML returned by ESummary from the Taxonomy database. ... ok test_unists (test_Entrez_parser.ESummaryTest.test_unists) Test parsing XML returned by ESummary from the UniSTS database. ... ok test_wrong (test_Entrez_parser.ESummaryTest.test_wrong) Test parsing XML returned by ESummary with incorrect arguments. ... ok test_BytesIO (test_Entrez_parser.GeneralTests.test_BytesIO) Test parsing a BytesIO 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 ---------------------------------------------------------------------- Ran 1 test in 0.815 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Enzyme.py test_Enzyme ... ok test_lactate (test_Enzyme.TestEnzyme.test_lactate) Parsing ENZYME record for lactate racemase (5.1.2.1). ... ok test_lipoprotein (test_Enzyme.TestEnzyme.test_lipoprotein) Parsing ENZYME record for lipoprotein lipase (3.1.1.34). ... ok test_parse_many (test_Enzyme.TestEnzyme.test_parse_many) Check parse function with multiple records. ... ok test_parse_one (test_Enzyme.TestEnzyme.test_parse_one) Check parse function with one record. ... ok test_parse_zero (test_Enzyme.TestEnzyme.test_parse_zero) ... ok test_proline (test_Enzyme.TestEnzyme.test_proline) Parsing ENZYME record for proline racemase (5.1.1.4). ... ok test_valine (test_Enzyme.TestEnzyme.test_valine) Parsing ENZYME record for valine decarboxylase (4.1.1.14). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ExPASy.py test_ExPASy ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.008 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Fasttree_tool.py test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.133 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_File.py test_File ... ok test_custom_path_like_object (test_File.AsHandleTestCase.test_custom_path_like_object) Test as_handle with a custom path-like object. ... ok test_handle (test_File.AsHandleTestCase.test_handle) Test as_handle with a file-like object argument. ... ok test_path_object (test_File.AsHandleTestCase.test_path_object) Test as_handle with a pathlib.Path object. ... ok test_string_path (test_File.AsHandleTestCase.test_string_path) Test as_handle with a string path argument. ... ok test_stringio (test_File.AsHandleTestCase.test_stringio) Testing passing StringIO handles. ... ok test_instance_exception (test_File.BaseClassTests.test_instance_exception) ... ok test_bgzf (test_File.RandomAccess.test_bgzf) Test BGZF compressed file. ... ok test_gzip (test_File.RandomAccess.test_gzip) Test gzip compressed file. ... ok test_plain (test_File.RandomAccess.test_plain) Test plain text file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenBank.py test_GenBank ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: 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 ---------------------------------------------------------------------- Ran 1 test in 0.357 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GenomeDiagram.py test_GenomeDiagram ... ok test_color_conversions (test_GenomeDiagram.ColorsTest.test_color_conversions) Test color translations. ... ok test_add_track (test_GenomeDiagram.DiagramTest.test_add_track) Add track. ... ok test_add_track_error (test_GenomeDiagram.DiagramTest.test_add_track_error) Test adding unspecified track. ... ok test_add_track_to_occupied_level (test_GenomeDiagram.DiagramTest.test_add_track_to_occupied_level) Add track to occupied level. ... ok test_del_tracks (test_GenomeDiagram.DiagramTest.test_del_tracks) Delete track. ... ok test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_methods_pdf) Construct and draw PDF using method approach. ... ok test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest.test_diagram_via_object_pdf) Construct and draw PDF using object approach. ... ok test_get_tracks (test_GenomeDiagram.DiagramTest.test_get_tracks) Get track. ... ok test_move_track (test_GenomeDiagram.DiagramTest.test_move_track) Move a track. ... ok test_partial_diagram (test_GenomeDiagram.DiagramTest.test_partial_diagram) Construct and draw SVG and PDF for just part of a SeqRecord. ... ok test_renumber (test_GenomeDiagram.DiagramTest.test_renumber) Test renumbering tracks. ... ok test_str (test_GenomeDiagram.DiagramTest.test_str) Test diagram's info as string. ... ok test_write_arguments (test_GenomeDiagram.DiagramTest.test_write_arguments) Check how the write methods respond to output format arguments. ... ok test_limits (test_GenomeDiagram.GraphTest.test_limits) Check line graphs. ... ok test_slicing (test_GenomeDiagram.GraphTest.test_slicing) Check GraphData slicing. ... ok test_label_default (test_GenomeDiagram.LabelTest.test_label_default) Feature labels - default. ... ok test_all_sigils (test_GenomeDiagram.SigilsTest.test_all_sigils) All sigils. ... ok test_arrow_heads (test_GenomeDiagram.SigilsTest.test_arrow_heads) Feature arrow sigils, varying heads. ... ok test_arrow_shafts (test_GenomeDiagram.SigilsTest.test_arrow_shafts) Feature arrow sigils, varying shafts. ... ok test_big_arrow_shafts (test_GenomeDiagram.SigilsTest.test_big_arrow_shafts) Feature big-arrow sigils, varying shafts. ... ok test_labels (test_GenomeDiagram.SigilsTest.test_labels) Feature labels. ... ok test_long_arrow_heads (test_GenomeDiagram.SigilsTest.test_long_arrow_heads) Feature ARROW sigil heads within bounding box. ... ok test_long_bigarrow_heads (test_GenomeDiagram.SigilsTest.test_long_bigarrow_heads) Feature BIGARROW sigil heads within bounding box. ... ok test_long_jaggy (test_GenomeDiagram.SigilsTest.test_long_jaggy) Feature JAGGY sigil heads within bounding box. ... ok test_long_octo_heads (test_GenomeDiagram.SigilsTest.test_long_octo_heads) Feature OCTO sigil heads within bounding box. ... ok test_short_arrow (test_GenomeDiagram.SigilsTest.test_short_arrow) Feature arrow sigil heads within bounding box. ... ok test_short_bigarrow (test_GenomeDiagram.SigilsTest.test_short_bigarrow) Feature big-arrow sigil heads within bounding box. ... ok test_short_jaggy (test_GenomeDiagram.SigilsTest.test_short_jaggy) Feature arrow sigil heads within bounding box. ... ok test_short_octo (test_GenomeDiagram.SigilsTest.test_short_octo) Feature big-arrow sigil heads within bounding box. ... ok ---------------------------------------------------------------------- Ran 1 test in 4.005 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsBitmaps.py test_GraphicsBitmaps ... skipping. Reportlab module rlPyCairo unavailable cannot import desired renderPM backend rlPyCairo Seek advice at the users list see https://pairlist2.pair.net/mailman/listinfo/reportlab-users ---------------------------------------------------------------------- Ran 1 test in 0.158 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsChromosome.py test_GraphicsChromosome ... ok test_add_count (test_GraphicsChromosome.ChromosomeCountTest.test_add_count) Add counts to specific chromosome segments. ... ok test_add_label (test_GraphicsChromosome.ChromosomeCountTest.test_add_label) Add labels to chromosome segments. ... ok test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest.test_color_from_count) Retrieve a color from a count number with the default color scheme. ... ok test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest.test_fill_chromosome) Test filling out the information on a chromosome. ... ok test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest.test_get_segment_info) Test retrieval of segment information. ... ok test_set_scale (test_GraphicsChromosome.ChromosomeCountTest.test_set_scale) Set the scale for a chromosome segment. ... ok test_random_organism (test_GraphicsChromosome.OrganismGraphicTest.test_random_organism) Generate an organism with random chromosome info. ... ok test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism) Test the basic functionality of drawing an organism. ... ok test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_pdf) Output a simple organism to a PDF file. ... ok test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_ps) Output a simple organism to a postscript file. ... ok test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest.test_simple_organism_svg) Output a simple organism to an SVG file. ... ok test_widget (test_GraphicsChromosome.OrganismGraphicTest.test_widget) Try widget derived functionality. ... ok test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_seqfeatures) Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis. ... ok test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest.test_simple_tRNA_tuples) Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.899 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsDistribution.py test_GraphicsDistribution ... ok test_multi_page (test_GraphicsDistribution.BarChartTest.test_multi_page) Create a page with multiple distributions on it. ... ok test_simple_page (test_GraphicsDistribution.BarChartTest.test_simple_page) Test displaying a page with single distribution. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.214 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_GraphicsGeneral.py test_GraphicsGeneral ... ok test_simple_scatter_plot_1 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_1) Test creation of a simple ScatterPlot with one list. ... ok test_simple_scatter_plot_7 (test_GraphicsGeneral.ComparativeTest.test_simple_scatter_plot_7) Test creation of a simple ScatterPlot with more lists. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.264 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMCasino.py test_HMMCasino ... ok test_baum_welch_training_standard (test_HMMCasino.TestHMMCasino.test_baum_welch_training_standard) Standard Training with known states. ... ok test_baum_welch_training_without (test_HMMCasino.TestHMMCasino.test_baum_welch_training_without) Baum-Welch training without known state sequences. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.201 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_HMMGeneral.py test_HMMGeneral ... ok test_log_likelihood (test_HMMGeneral.AbstractTrainerTest.test_log_likelihood) Calculate log likelihood. ... ok test_ml_estimator (test_HMMGeneral.AbstractTrainerTest.test_ml_estimator) Test the maximum likelihood estimator for simple cases. ... ok test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest.test_allow_transition) Testing allow_transition. ... ok test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest.test_non_ergodic) Non-ergodic model (meaning that some transitions are not allowed). ... ok test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest.test_simple_hmm) Test a simple model with 2 states and 2 symbols. ... ok test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_from) Testing the calculation of transitions_from. ... ok test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest.test_transitions_to) Testing the calculation of transitions_to. ... ok test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest.test_allow_all_transitions) Testing allow_all_transitions. ... ok test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_equal_probabilities) ... ok test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_initial_probabilities) ... ok test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest.test_set_random_probabilities) ... ok test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest.test_test_initialize) Making sure MarkovModelBuilder is initialized correctly. ... ok test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest.test_calculate_s_value) Testing the calculation of s values. ... ok test_empty_state_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_empty_state_training_sequence) ... ok test_invalid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_invalid_training_sequence) ... ok test_valid_training_sequence (test_HMMGeneral.TrainingSequenceTest.test_valid_training_sequence) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.065 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG.py test_KEGG ... ok test_irregular (test_KEGG.CompoundTests.test_irregular) compound.irregular tests. ... ok test_mass (test_KEGG.CompoundTests.test_mass) record.mass tests. ... ok test_sample (test_KEGG.CompoundTests.test_sample) compound.sample tests. ... ok test_4letter (test_KEGG.EnzymeTests.test_4letter) enzyme.4letter tests. ... ok test_exceptions (test_KEGG.EnzymeTests.test_exceptions) enzyme.exceptions tests. ... ok test_irregular (test_KEGG.EnzymeTests.test_irregular) enzyme.irregular tests. ... ok test_new (test_KEGG.EnzymeTests.test_new) enzyme.new tests. ... ok test_sample (test_KEGG.EnzymeTests.test_sample) enzyme.sample tests. ... ok test_map00950 (test_KEGG.MapTests.test_map00950) map00950.rea tests. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.129 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KEGG_online.py test_KEGG_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics.py test_KGML_graphics ... ok test_render_KGML_basic (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_basic) Basic rendering of KGML: write to PDF without modification. ... ok test_render_KGML_modify (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_modify) Rendering of KGML to PDF, with modification. ... ok test_render_KGML_transparency (test_KGML_graphics.KGMLPathwayTest.test_render_KGML_transparency) Rendering of KGML to PDF, with color alpha channel. ... ok ---------------------------------------------------------------------- Ran 1 test in 7.561 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_graphics_online.py test_KGML_graphics_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.045 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KGML_nographics.py test_KGML_nographics ... ok test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest.test_read_and_write_KGML_files) Read KGML from, and write KGML to, local files. ... ok ---------------------------------------------------------------------- Ran 1 test in 1.031 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_KeyWList.py test_KeyWList ... ok test_parse (test_KeyWList.KeyWListTest.test_parse) Test parsing keywlist.txt works. ... ok test_parse2 (test_KeyWList.KeyWListTest.test_parse2) Parsing keywlist2.txt (without header and footer). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_LogisticRegression.py test_LogisticRegression ... ok test_calculate_model (test_LogisticRegression.TestLogisticRegression.test_calculate_model) ... ok test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression.test_calculate_model_with_update_callback) ... ok test_calculate_probability (test_LogisticRegression.TestLogisticRegression.test_calculate_probability) ... ok test_classify (test_LogisticRegression.TestLogisticRegression.test_classify) ... ok test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression.test_dimensionality_of_input_xs) ... ok test_leave_one_out (test_LogisticRegression.TestLogisticRegression.test_leave_one_out) ... ok test_model_accuracy (test_LogisticRegression.TestLogisticRegression.test_model_accuracy) ... ok test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression.test_xs_and_ys_input_parameter_lengths) ... ok test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression.test_ys_input_class_assignments) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.050 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MSAProbs_tool.py test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.115 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MafIO_index.py test_MafIO_index ... ok test_bundle_without_target (test_MafIO_index.NewIndexTest.test_bundle_without_target) ... ok test_good_big (test_MafIO_index.NewIndexTest.test_good_big) ... ok test_good_small (test_MafIO_index.NewIndexTest.test_good_small) ... ok test_length_coords_mismatch (test_MafIO_index.NewIndexTest.test_length_coords_mismatch) ... ok test_old (test_MafIO_index.PreBuiltIndexTest.test_old) ... ok test_old_corrupt_index (test_MafIO_index.PreBuiltIndexTest.test_old_corrupt_index) ... ok test_old_file_not_found (test_MafIO_index.PreBuiltIndexTest.test_old_file_not_found) ... ok test_old_invalid_sqlite (test_MafIO_index.PreBuiltIndexTest.test_old_invalid_sqlite) ... ok test_old_unfinished_index (test_MafIO_index.PreBuiltIndexTest.test_old_unfinished_index) ... ok test_old_wrong_filename (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_filename) ... ok test_old_wrong_target_seqname (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_target_seqname) ... ok test_old_wrong_version (test_MafIO_index.PreBuiltIndexTest.test_old_wrong_version) ... ok test_region2bin (test_MafIO_index.StaticMethodTest.test_region2bin) ... ok test_ucscbin (test_MafIO_index.StaticMethodTest.test_ucscbin) ... ok test_records_begin (test_MafIO_index.TestGetRecord.test_records_begin) ... ok test_records_end (test_MafIO_index.TestGetRecord.test_records_end) ... ok test_incorrect_bundle_coords (test_MafIO_index.TestSearchBadMAF.test_incorrect_bundle_coords) ... ok test_correct_block_boundary (test_MafIO_index.TestSearchGoodMAF.test_correct_block_boundary) Following issues 504 and 1086. ... ok test_correct_block_length (test_MafIO_index.TestSearchGoodMAF.test_correct_block_length) Following issues 504 and 1086. ... ok test_correct_retrieval_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_correct_retrieval_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_2) ... ok test_correct_retrieval_3 (test_MafIO_index.TestSearchGoodMAF.test_correct_retrieval_3) Following issue 1083. ... ok test_correct_spliced_sequences_1 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_1) Checking that spliced sequences are correct. ... ok test_correct_spliced_sequences_2 (test_MafIO_index.TestSearchGoodMAF.test_correct_spliced_sequences_2) Checking that spliced sequences are correct. ... ok test_invalid_exon_count (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_count) ... ok test_invalid_exon_schema (test_MafIO_index.TestSearchGoodMAF.test_invalid_exon_schema) ... ok test_invalid_type_1 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_1) ... ok test_invalid_type_2 (test_MafIO_index.TestSearchGoodMAF.test_invalid_type_2) ... ok test_bundle_without_target (test_MafIO_index.TestSpliceBadMAF.test_bundle_without_target) ... ok test_inconsistent_strand (test_MafIO_index.TestSpliceBadMAF.test_inconsistent_strand) ... ok test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF.test_correct_retrieval_1) Correct retrieval of Cnksr3 in mouse. ... ok test_invalid_strand (test_MafIO_index.TestSpliceGoodMAF.test_invalid_strand) ... ok test_no_alignment (test_MafIO_index.TestSpliceGoodMAF.test_no_alignment) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.191 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Mafft_tool.py test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_MarkovModel.py test_MarkovModel ... ok test_argmaxes (test_MarkovModel.TestMarkovModel.test_argmaxes) ... ok test_backward (test_MarkovModel.TestMarkovModel.test_backward) ... ok test_baum_welch (test_MarkovModel.TestMarkovModel.test_baum_welch) ... ok test_forward (test_MarkovModel.TestMarkovModel.test_forward) ... ok test_logsum_and_exp_logsum (test_MarkovModel.TestMarkovModel.test_logsum_and_exp_logsum) ... ok test_logvecadd (test_MarkovModel.TestMarkovModel.test_logvecadd) ... ok test_mle (test_MarkovModel.TestMarkovModel.test_mle) ... ok test_normalize_and_copy_and_check (test_MarkovModel.TestMarkovModel.test_normalize_and_copy_and_check) ... ok test_random_norm (test_MarkovModel.TestMarkovModel.test_random_norm) ... ok test_readline_and_check_start (test_MarkovModel.TestMarkovModel.test_readline_and_check_start) ... ok test_save_and_load (test_MarkovModel.TestMarkovModel.test_save_and_load) ... ok test_topcoder1 (test_MarkovModel.TestMarkovModel.test_topcoder1) ... ok test_topcoder2 (test_MarkovModel.TestMarkovModel.test_topcoder2) ... ok test_topcoder3 (test_MarkovModel.TestMarkovModel.test_topcoder3) ... ok test_topcoder4 (test_MarkovModel.TestMarkovModel.test_topcoder4) ... ok test_topcoder5 (test_MarkovModel.TestMarkovModel.test_topcoder5) ... ok test_train_bw (test_MarkovModel.TestMarkovModel.test_train_bw) ... ok test_train_visible (test_MarkovModel.TestMarkovModel.test_train_visible) ... ok test_uniform_norm (test_MarkovModel.TestMarkovModel.test_uniform_norm) ... ok test_viterbi (test_MarkovModel.TestMarkovModel.test_viterbi) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.185 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Medline.py test_Medline ... ok test_multiline_mesh (test_Medline.TestMedline.test_multiline_mesh) ... ok test_parse (test_Medline.TestMedline.test_parse) ... ok test_read (test_Medline.TestMedline.test_read) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Muscle_tool.py test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.103 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 ---------------------------------------------------------------------- Ran 1 test in 0.560 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBIXML.py test_NCBIXML ... ok test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastn_001) Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001). ... ok test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastp_001) Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001). ... ok test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_blastx_001) Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001). ... ok test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastn_001) Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001). ... ok test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2212L_tblastx_001) Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001). ... ok test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_blastp_001) Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001). ... ok test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML.test_xml_2218L_rpsblast_001) Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001). ... ok test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_001) Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001). ... ok test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML.test_xml_2218_blastp_002) Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002). ... ok test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastp_001) Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001). ... ok test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML.test_xml_2222_blastx_001) Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001). ... ok test_xml_2900_blastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v1) ... ok test_xml_2900_blastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastn_001_v2) ... ok test_xml_2900_blastp_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v1) ... ok test_xml_2900_blastp_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastp_001_v2) ... ok test_xml_2900_blastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v1) ... ok test_xml_2900_blastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_blastx_001_v2) ... ok test_xml_2900_tblastn_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v1) ... ok test_xml_2900_tblastn_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastn_001_v2) ... ok test_xml_2900_tblastx_001_v1 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v1) ... ok test_xml_2900_tblastx_001_v2 (test_NCBIXML.TestNCBIXML.test_xml_2900_tblastx_001_v2) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.720 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBI_BLAST_tools.py test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.017 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NCBI_qblast.py test_NCBI_qblast ... ok test_blastp_nr_actin (test_NCBI_qblast.TestQblast.test_blastp_nr_actin) ... ok test_discomegablast (test_NCBI_qblast.TestQblast.test_discomegablast) ... ok test_error_conditions (test_NCBI_qblast.TestQblast.test_error_conditions) Test if exceptions were properly handled. ... ok test_orchid_est (test_NCBI_qblast.TestQblast.test_orchid_est) ... ok test_parse_qblast_ref_page (test_NCBI_qblast.TestQblast.test_parse_qblast_ref_page) ... ok test_pcr_primers (test_NCBI_qblast.TestQblast.test_pcr_primers) ... ok test_short_query (test_NCBI_qblast.TestQblast.test_short_query) Test SHORT_QUERY_ADJUST parameter. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NMR.py test_NMR ... ok test_noetools (test_NMR.NmrTests.test_noetools) Self test for NMR.NOEtools. ... ok test_xpktools (test_NMR.NmrTests.test_xpktools) Self test for NMR.xpktools. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.022 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_NaiveBayes.py test_NaiveBayes ... ok test_car_data (test_NaiveBayes.CarTest.test_car_data) Simple example using car data. ... ok test_calculate_function_with_scale (test_NaiveBayes.NaiveBayesTest.test_calculate_function_with_scale) ... ok test_calculate_function_wrong_dimensionality (test_NaiveBayes.NaiveBayesTest.test_calculate_function_wrong_dimensionality) ... ok test_classify_function (test_NaiveBayes.NaiveBayesTest.test_classify_function) ... ok test_train_function_input_lengths (test_NaiveBayes.NaiveBayesTest.test_train_function_input_lengths) ... ok test_train_function_no_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_no_training_set) ... ok test_train_function_uneven_dimension_of_training_set (test_NaiveBayes.NaiveBayesTest.test_train_function_uneven_dimension_of_training_set) ... ok test_train_function_with_priors (test_NaiveBayes.NaiveBayesTest.test_train_function_with_priors) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_baseml.py test_PAML_baseml ... ok testAlignmentExists (test_PAML_baseml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_baseml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_baseml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_baseml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_baseml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_baseml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_baseml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_baseml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_baseml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_baseml.ModTest.testPamlErrorsCaught) ... ok testParseAllVersions (test_PAML_baseml.ModTest.testParseAllVersions) ... ok testParseAlpha1Rho1 (test_PAML_baseml.ModTest.testParseAlpha1Rho1) ... ok testParseModel (test_PAML_baseml.ModTest.testParseModel) ... ok testParseNhomo (test_PAML_baseml.ModTest.testParseNhomo) ... ok testParseSEs (test_PAML_baseml.ModTest.testParseSEs) ... ok testResultsExist (test_PAML_baseml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_baseml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_baseml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_baseml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_baseml.ModTest.testTreeFileValid) ... ok testTreeSpecified (test_PAML_baseml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_baseml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.305 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_codeml.py test_PAML_codeml ... ok testAlignmentExists (test_PAML_codeml.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_codeml.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_codeml.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_codeml.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_codeml.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_codeml.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_codeml.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_codeml.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_codeml.ModTest.testOutputFileSpecified) ... ok testPamlErrorsCaught (test_PAML_codeml.ModTest.testPamlErrorsCaught) ... ok testParseAA (test_PAML_codeml.ModTest.testParseAA) ... ok testParseAAPairwise (test_PAML_codeml.ModTest.testParseAAPairwise) ... ok testParseAllNSsites (test_PAML_codeml.ModTest.testParseAllNSsites) ... ok testParseBranchSiteA (test_PAML_codeml.ModTest.testParseBranchSiteA) ... ok testParseCladeModelC (test_PAML_codeml.ModTest.testParseCladeModelC) ... ok testParseFreeRatio (test_PAML_codeml.ModTest.testParseFreeRatio) ... ok testParseM2arel (test_PAML_codeml.ModTest.testParseM2arel) ... ok testParseNSsite3 (test_PAML_codeml.ModTest.testParseNSsite3) ... ok testParseNgene2Mgene02 (test_PAML_codeml.ModTest.testParseNgene2Mgene02) ... ok testParseNgene2Mgene1 (test_PAML_codeml.ModTest.testParseNgene2Mgene1) ... ok testParseNgene2Mgene34 (test_PAML_codeml.ModTest.testParseNgene2Mgene34) ... ok testParsePairwise (test_PAML_codeml.ModTest.testParsePairwise) ... ok testParseSEs (test_PAML_codeml.ModTest.testParseSEs) ... ok testParseSitesParamsForPairwise (test_PAML_codeml.ModTest.testParseSitesParamsForPairwise) Verify that pairwise site estimates are indeed parsed. Fixes #483. ... ok testResultsExist (test_PAML_codeml.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_codeml.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_codeml.ModTest.testResultsValid) ... ok testTreeExists (test_PAML_codeml.ModTest.testTreeExists) ... ok testTreeFileValid (test_PAML_codeml.ModTest.testTreeFileValid) ... ok testTreeParseVersatility (test_PAML_codeml.ModTest.testTreeParseVersatility) Test finding trees in the results. ... ok testTreeSpecified (test_PAML_codeml.ModTest.testTreeSpecified) ... ok testWorkingDirValid (test_PAML_codeml.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.997 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_tools.py test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.119 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PAML_yn00.py test_PAML_yn00 ... ok testAlignmentExists (test_PAML_yn00.ModTest.testAlignmentExists) ... ok testAlignmentFileIsValid (test_PAML_yn00.ModTest.testAlignmentFileIsValid) ... ok testAlignmentSpecified (test_PAML_yn00.ModTest.testAlignmentSpecified) ... ok testCtlFileExistsOnRead (test_PAML_yn00.ModTest.testCtlFileExistsOnRead) ... ok testCtlFileExistsOnRun (test_PAML_yn00.ModTest.testCtlFileExistsOnRun) ... ok testCtlFileValidOnRead (test_PAML_yn00.ModTest.testCtlFileValidOnRead) ... ok testCtlFileValidOnRun (test_PAML_yn00.ModTest.testCtlFileValidOnRun) ... ok testOptionExists (test_PAML_yn00.ModTest.testOptionExists) ... ok testOutputFileSpecified (test_PAML_yn00.ModTest.testOutputFileSpecified) ... ok testParseAllVersions (test_PAML_yn00.ModTest.testParseAllVersions) ... ok testParseDottedNames (test_PAML_yn00.ModTest.testParseDottedNames) ... ok testParseDottedNumNames (test_PAML_yn00.ModTest.testParseDottedNumNames) ... ok testParseLongNames (test_PAML_yn00.ModTest.testParseLongNames) ... ok testResultsExist (test_PAML_yn00.ModTest.testResultsExist) ... ok testResultsParsable (test_PAML_yn00.ModTest.testResultsParsable) ... ok testResultsValid (test_PAML_yn00.ModTest.testResultsValid) ... ok testWorkingDirValid (test_PAML_yn00.ModTest.testWorkingDirValid) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.139 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDBList.py test_PDBList ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_CEAligner.py test_PDB_CEAligner ... ok test_cealigner (test_PDB_CEAligner.CEAlignerTests.test_cealigner) Test aligning 7CFN on 6WQA. ... ok test_cealigner_no_transform (test_PDB_CEAligner.CEAlignerTests.test_cealigner_no_transform) Test aligning 7CFN on 6WQA without transforming 7CFN. ... ok test_cealigner_nucleic (test_PDB_CEAligner.CEAlignerTests.test_cealigner_nucleic) Test aligning 1LCD on 1LCD. ... ok ---------------------------------------------------------------------- Ran 1 test in 3.242 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_DSSP.py test_PDB_DSSP ... ok test_DSSP_RSA (test_PDB_DSSP.DSSP_test.test_DSSP_RSA) Tests the usage of different ASA tables. ... ok test_DSSP_file (test_PDB_DSSP.DSSP_test.test_DSSP_file) Test parsing of pregenerated DSSP. ... ok test_DSSP_hbonds (test_PDB_DSSP.DSSP_test.test_DSSP_hbonds) Test parsing of DSSP hydrogen bond information. ... ok test_DSSP_in_model_obj (test_PDB_DSSP.DSSP_test.test_DSSP_in_model_obj) All elements correctly added to xtra attribute of input model object. ... ok test_DSSP_noheader_file (test_PDB_DSSP.DSSP_test.test_DSSP_noheader_file) Test parsing of pregenerated DSSP missing header information. ... ok setUpClass (test_PDB_DSSP.DSSP_tool_test) ... skipped 'Install dssp if you want to use it from Biopython.' ---------------------------------------------------------------------- Ran 1 test in 0.234 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Dice.py test_PDB_Dice ... ok test_dice (test_PDB_Dice.DiceTests.test_dice) Self test for PDB.Dice module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.104 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.110 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Exposure.py test_PDB_Exposure ... ok test_ExposureCN (test_PDB_Exposure.Exposure.test_ExposureCN) HSExposureCN. ... ok test_HSExposureCA (test_PDB_Exposure.Exposure.test_HSExposureCA) HSExposureCA. ... ok test_HSExposureCB (test_PDB_Exposure.Exposure.test_HSExposureCB) HSExposureCB. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.471 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_FragmentMapper.py test_PDB_FragmentMapper ... ok test_fragment_mapper (test_PDB_FragmentMapper.FragmentMapperTests.test_fragment_mapper) Self test for FragmentMapper module. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.135 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_KDTree.py test_PDB_KDTree ... ok test_KDTree_exceptions (test_PDB_KDTree.KDTreeTest.test_KDTree_exceptions) ... ok test_KDTree_neighbor_search_manual (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_manual) Test all fixed radius neighbor search. ... ok test_KDTree_neighbor_search_simple (test_PDB_KDTree.KDTreeTest.test_KDTree_neighbor_search_simple) Test all fixed radius neighbor search. ... ok test_KDTree_point_search (test_PDB_KDTree.KDTreeTest.test_KDTree_point_search) Test searching all points within a certain radius of center. ... ok test_neighbor_search (test_PDB_KDTree.NeighborTest.test_neighbor_search) NeighborSearch: Find nearby randomly generated coordinates. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.106 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIF2Dict.py test_PDB_MMCIF2Dict ... ok test_MMCIF2dict (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_MMCIF2dict) ... ok test_inline_comments (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_inline_comments) Comments may begin outside of column 1 if preceded by whitespace. ... ok test_loop_keyword_case_insensitive (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_loop_keyword_case_insensitive) Comments may begin outside of column 1. ... ok test_quotefix (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_quotefix) ... ok test_splitline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_splitline) ... ok test_token_after_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_token_after_multiline) Multi-line string followed by token on the same line. ... ok test_truncated_multiline (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_truncated_multiline) ... ok test_underscores (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_underscores) ... ok test_verbatim_block (test_PDB_MMCIF2Dict.MMCIF2dictTests.test_verbatim_block) Verbatim blocks parsed correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.117 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 ---------------------------------------------------------------------- Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] Operating system: posix linux Ran 1 test in 0.329 seconds 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_MMCIFParser.py test_PDB_MMCIFParser ... ok test_conversion (test_PDB_MMCIFParser.CIFtoPDB.test_conversion) Parse 1LCD.cif, write 1LCD.pdb, parse again and compare. ... ok test_conversion_not_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_not_preserve_numbering) Convert mmCIF to PDB and renumber atom serials. ... ok test_conversion_preserve_numbering (test_PDB_MMCIFParser.CIFtoPDB.test_conversion_preserve_numbering) Convert mmCIF to PDB and preserve original serial numbering. ... ok testModels (test_PDB_MMCIFParser.ParseReal.testModels) Test file with multiple models. ... ok test_filehandle (test_PDB_MMCIFParser.ParseReal.test_filehandle) Test if the parser can handle file handle as well as filename. ... ok test_header (test_PDB_MMCIFParser.ParseReal.test_header) Test if the parser populates header data. ... ok test_insertions (test_PDB_MMCIFParser.ParseReal.test_insertions) Test file with residue insertion codes. ... ok test_parsers (test_PDB_MMCIFParser.ParseReal.test_parsers) Extract polypeptides from 1A80. ... ok test_point_mutations_fast (test_PDB_MMCIFParser.ParseReal.test_point_mutations_fast) Test if FastMMCIFParser can parse point mutations correctly. ... ok test_point_mutations_main (test_PDB_MMCIFParser.ParseReal.test_point_mutations_main) Test if MMCIFParser parse point mutations correctly. ... ok test_with_anisotrop (test_PDB_MMCIFParser.ParseReal.test_with_anisotrop) ... ok ---------------------------------------------------------------------- Ran 1 test in 1.459 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_NACCESS.py test_PDB_NACCESS ... ok test_NACCESS (test_PDB_NACCESS.NACCESS_test.test_NACCESS) Test calling NACCESS from Bio.PDB. ... skipped 'Install naccess if you want to use it from Biopython.' test_NACCESS_asa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_asa_file) Test parsing of pregenerated asa NACCESS file. ... ok test_NACCESS_rsa_file (test_PDB_NACCESS.NACCESS_test.test_NACCESS_rsa_file) Test parsing of pregenerated rsa NACCESS file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.089 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBIO.py test_PDB_PDBIO ... ok test_model_numbering (test_PDB_PDBIO.WriteTest.test_model_numbering) Preserve model serial numbers during I/O. ... ok test_pdbio_missing_occupancy (test_PDB_PDBIO.WriteTest.test_pdbio_missing_occupancy) Write PDB file with missing occupancy. ... ok test_pdbio_pdb_format_limits (test_PDB_PDBIO.WriteTest.test_pdbio_pdb_format_limits) Test raising error when structure cannot meet PDB format limits. ... ok test_pdbio_select (test_PDB_PDBIO.WriteTest.test_pdbio_select) Write a selection of the structure using a Select subclass. ... ok test_pdbio_write_auto_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_auto_numbering) Test writing PDB and do not preserve atom numbering. ... ok test_pdbio_write_custom_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_custom_residue) Write a chainless residue using PDBIO. ... ok test_pdbio_write_preserve_numbering (test_PDB_PDBIO.WriteTest.test_pdbio_write_preserve_numbering) Test writing PDB and preserve atom numbering. ... ok test_pdbio_write_residue (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue) Write a single residue using PDBIO. ... ok test_pdbio_write_residue_w_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_w_chain) Write a single residue (chain id == X) using PDBIO. ... ok test_pdbio_write_residue_wout_chain (test_PDB_PDBIO.WriteTest.test_pdbio_write_residue_wout_chain) Write a single orphan residue using PDBIO. ... ok test_pdbio_write_structure (test_PDB_PDBIO.WriteTest.test_pdbio_write_structure) Write a full structure using PDBIO. ... ok test_pdbio_write_truncated (test_PDB_PDBIO.WriteTest.test_pdbio_write_truncated) Test parsing of truncated lines. ... ok test_pdbio_write_unk_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_unk_element) PDBIO raises PDBIOException when writing unrecognised atomic elements. ... ok test_pdbio_write_x_element (test_PDB_PDBIO.WriteTest.test_pdbio_write_x_element) Write a structure with atomic element X with PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.297 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PDBParser.py test_PDB_PDBParser ... ok test_1_flawedpdb_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_1_flawedpdb_permissive) Parse a flawed PDB file in permissive mode: check warnings. ... ok test_2_flawedpdb_strict (test_PDB_PDBParser.FlawedPDB_tests.test_2_flawedpdb_strict) Parse a flawed PDB file in permissive mode: check errors. ... ok test_3_bad_xyz_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_3_bad_xyz_permissive) Parse an entry with bad x,y,z value with PERMISSIVE=True. ... ok test_4_bad_xyz_strict (test_PDB_PDBParser.FlawedPDB_tests.test_4_bad_xyz_strict) Parse an entry with bad x,y,z value with PERMISSIVE=False. ... ok test_5_missing_occupancy_permissive (test_PDB_PDBParser.FlawedPDB_tests.test_5_missing_occupancy_permissive) Parse file with missing occupancy with PERMISSIVE=True. ... ok test_6_missing_occupancy_strict (test_PDB_PDBParser.FlawedPDB_tests.test_6_missing_occupancy_strict) Parse file with missing occupancy with PERMISSIVE=False. ... ok test_structure_details (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_details) Verify details of the parsed example PDB file. ... ok test_structure_integrity (test_PDB_PDBParser.ParseDummyPDB_test.test_structure_integrity) Verify the structure of the parsed example PDB file. ... ok test_1A8O_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_1A8O_strict) Parse 1A8O.pdb file in strict mode. ... ok test_SMCRA (test_PDB_PDBParser.ParseRealPDB_tests.test_SMCRA) Walk down the structure hierarchy and test parser reliability. ... ok test_duplicated_residue_permissive (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_permissive) Catch exception on duplicated residue. ... ok test_duplicated_residue_strict (test_PDB_PDBParser.ParseRealPDB_tests.test_duplicated_residue_strict) Throw exception on duplicated residue. ... ok test_empty (test_PDB_PDBParser.ParseRealPDB_tests.test_empty) Parse an empty file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.134 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_PSEA.py test_PDB_PSEA ... skipping. Download and install psea from ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. Make sure that psea is on path ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Polypeptide.py test_PDB_Polypeptide ... ok test_cappbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real) Test CaPPBuilder on real PDB file. ... ok test_cappbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_real_nonstd) Test CaPPBuilder on real PDB file allowing non-standard amino acids. ... ok test_cappbuilder_tau (test_PDB_Polypeptide.PolypeptideTests.test_cappbuilder_tau) Test tau angles calculated with CaPPBuilder. ... ok test_ppbuilder_real (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real) Test PPBuilder on real PDB file. ... ok test_ppbuilder_real_nonstd (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_real_nonstd) Test PPBuilder on real PDB file allowing non-standard amino acids. ... ok test_ppbuilder_torsion (test_PDB_Polypeptide.PolypeptideTests.test_ppbuilder_torsion) Test phi/psi angles calculated with PPBuilder. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_ResidueDepth.py test_PDB_ResidueDepth ... ok setUpClass (test_PDB_ResidueDepth.MSMS_tests) ... skipped 'Install MSMS if you want to use it from Biopython.' test_pdb_to_xyzr (test_PDB_ResidueDepth.ResidueDepth_tests.test_pdb_to_xyzr) Test generation of xyzr (atomic radii) file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SASA.py test_PDB_SASA ... ok test_custom_radii (test_PDB_SASA.TestShrakeRupley.test_custom_radii) Run Shrake-Rupley with custom radii. ... ok test_default_algorithm (test_PDB_SASA.TestShrakeRupley.test_default_algorithm) Run Shrake-Rupley with default parameters. ... ok test_fail_compute_entity_level (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_level) Raise exception on input Atom entity. ... ok test_fail_compute_entity_type (test_PDB_SASA.TestShrakeRupley.test_fail_compute_entity_type) Raise exception on unsupported entity type. ... ok test_fail_compute_level_1 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_1) Raise exception on invalid level parameter: X. ... ok test_fail_compute_level_2 (test_PDB_SASA.TestShrakeRupley.test_fail_compute_level_2) Raise exception on invalid level parameter: S > C. ... ok test_fail_empty_entity (test_PDB_SASA.TestShrakeRupley.test_fail_empty_entity) Raise exception on invalid level parameter: S > C. ... ok test_fail_n_points (test_PDB_SASA.TestShrakeRupley.test_fail_n_points) Raise exception on bad n_points parameter. ... ok test_fail_probe_radius (test_PDB_SASA.TestShrakeRupley.test_fail_probe_radius) Raise exception on bad probe_radius parameter. ... ok test_higher_resolution (test_PDB_SASA.TestShrakeRupley.test_higher_resolution) Run Shrake-Rupley with 960 points per sphere. ... ok test_level_C (test_PDB_SASA.TestShrakeRupley.test_level_C) Run Shrake-Rupley with level C. ... ok test_level_R (test_PDB_SASA.TestShrakeRupley.test_level_R) Run Shrake-Rupley with level R. ... ok ---------------------------------------------------------------------- Ran 1 test in 4.326 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_SMCRA.py test_PDB_SMCRA ... ok test_assign_unknown_element (test_PDB_SMCRA.Atom_Element.test_assign_unknown_element) Unknown element is assigned 'X'. ... ok test_atom_element_assignment (test_PDB_SMCRA.Atom_Element.test_atom_element_assignment) Atom Element. ... ok test_hydrogens (test_PDB_SMCRA.Atom_Element.test_hydrogens) ... ok test_ions (test_PDB_SMCRA.Atom_Element.test_ions) Element for magnesium is assigned correctly. ... ok test_chain_cog (test_PDB_SMCRA.CenterOfMassTests.test_chain_cog) Calculate center of geometry of individual chains. ... ok test_com_empty_structure (test_PDB_SMCRA.CenterOfMassTests.test_com_empty_structure) Center of mass of empty structure raises ValueError. ... ok test_structure_cog (test_PDB_SMCRA.CenterOfMassTests.test_structure_cog) Calculate Structure center of geometry. ... ok test_structure_com (test_PDB_SMCRA.CenterOfMassTests.test_structure_com) Calculate Structure center of mass. ... ok test_change_chain_id (test_PDB_SMCRA.ChangingIdTests.test_change_chain_id) Change the id of a model. ... ok test_change_id_to_self (test_PDB_SMCRA.ChangingIdTests.test_change_id_to_self) Changing the id to itself does nothing (does not raise). ... ok test_change_model_id (test_PDB_SMCRA.ChangingIdTests.test_change_model_id) Change the id of a model. ... ok test_change_model_id_raises (test_PDB_SMCRA.ChangingIdTests.test_change_model_id_raises) Cannot change id to a value already in use by another child. ... ok test_change_residue_id (test_PDB_SMCRA.ChangingIdTests.test_change_residue_id) Change the id of a residue. ... ok test_full_id_is_updated_chain (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_chain) Invalidate cached full_ids if an id is changed. ... ok test_full_id_is_updated_residue (test_PDB_SMCRA.ChangingIdTests.test_full_id_is_updated_residue) Invalidate cached full_ids if an id is changed. ... ok test_atom_copy (test_PDB_SMCRA.CopyTests.test_atom_copy) ... ok test_entity_copy (test_PDB_SMCRA.CopyTests.test_entity_copy) Make a copy of a residue. ... ok test_get_atoms (test_PDB_SMCRA.IterationTests.test_get_atoms) Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok test_get_chains (test_PDB_SMCRA.IterationTests.test_get_chains) Yields chains from different models separately. ... ok test_get_residues (test_PDB_SMCRA.IterationTests.test_get_residues) Yields all residues from all models. ... ok test_comparison_entities (test_PDB_SMCRA.SortingTests.test_comparison_entities) Test comparing and sorting the several SMCRA objects. ... ok test_residue_sort (test_PDB_SMCRA.SortingTests.test_residue_sort) Test atoms are sorted correctly in residues. ... ok test_transform (test_PDB_SMCRA.TransformTests.test_transform) Transform entities (rotation and translation). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.439 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Selection.py test_PDB_Selection ... ok test_entities_not_homogenous (test_PDB_Selection.UnfoldEntitiesTests.test_entities_not_homogenous) ... ok test_from_atom_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_atom_level) Unfold from lowest level to all levels. ... ok test_from_chain_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_chain_level) Unfold from chain level to all levels. ... ok test_from_model_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_model_level) Unfold from model to all levels. ... ok test_from_residue_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_residue_level) Unfold from chain level to all levels. ... ok test_from_structure_level (test_PDB_Selection.UnfoldEntitiesTests.test_from_structure_level) Unfold from highest level to all levels. ... ok test_invalid_level (test_PDB_Selection.UnfoldEntitiesTests.test_invalid_level) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_StructureAlignment.py test_PDB_StructureAlignment ... ok test_StructAlign (test_PDB_StructureAlignment.StructureAlignTests.test_StructAlign) Tests on module to align two proteins according to a FASTA alignment file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.301 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_Superimposer.py test_PDB_Superimposer ... ok test_Superimposer (test_PDB_Superimposer.SuperimposerTests.test_Superimposer) Test on module that superimpose two protein structures. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.105 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_internal_coords.py test_PDB_internal_coords ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_parse_pdb_header.py test_PDB_parse_pdb_header ... ok test_1 (test_PDB_parse_pdb_header.ParseReal.test_1) Parse the header of a known PDB file (1A8O). ... ok test_2 (test_PDB_parse_pdb_header.ParseReal.test_2) Parse the header of another PDB file (2BEG). ... ok test_parse_header_line (test_PDB_parse_pdb_header.ParseReal.test_parse_header_line) Unit test for parsing and converting fields in HEADER record. ... ok test_parse_no_title (test_PDB_parse_pdb_header.ParseReal.test_parse_no_title) Unit test for sensible result with no TITLE line. ... ok test_parse_pdb_with_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_465) Tests that parse_pdb_header now can identify some REMARK 465 entries. ... ok test_parse_pdb_with_remark_99 (test_PDB_parse_pdb_header.ParseReal.test_parse_pdb_with_remark_99) Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries. ... ok test_parse_remark_465 (test_PDB_parse_pdb_header.ParseReal.test_parse_remark_465) A UNIT-test for the private function _parse_remark_465. ... ok test_parse_title_line (test_PDB_parse_pdb_header.ParseReal.test_parse_title_line) Unit test for correct parsing of multiline title records. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.124 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PDB_vectors.py test_PDB_vectors ... ok test_Vector (test_PDB_vectors.VectorTests.test_Vector) Test Vector object. ... ok test_Vector_angles (test_PDB_vectors.VectorTests.test_Vector_angles) Test Vector angles. ... ok test_coord_space (test_PDB_vectors.VectorTests.test_coord_space) Confirm can generate coordinate space transform for 3 points. ... ok test_division (test_PDB_vectors.VectorTests.test_division) Confirm division works. ... ok test_get_spherical_coordinates (test_PDB_vectors.VectorTests.test_get_spherical_coordinates) Test spherical coordinates. ... ok test_m2rotaxis_0 (test_PDB_vectors.VectorTests.test_m2rotaxis_0) Test 0 deg rotation. Axis must be [1, 0, 0] as per Vector docs. ... ok test_m2rotaxis_180 (test_PDB_vectors.VectorTests.test_m2rotaxis_180) Test 180 deg rotation. ... ok test_m2rotaxis_90 (test_PDB_vectors.VectorTests.test_m2rotaxis_90) Test 90 deg rotation. ... ok test_multi_coord_space (test_PDB_vectors.VectorTests.test_multi_coord_space) Confirm multi_coord_space computes forward, reverse transforms. ... ok test_normalization (test_PDB_vectors.VectorTests.test_normalization) Test Vector normalization. ... ok test_refmat (test_PDB_vectors.VectorTests.test_refmat) Test refmat can mirror one matrix to another. ... ok test_rotmat_0 (test_PDB_vectors.VectorTests.test_rotmat_0) Test rotmat when the rotation is 0 deg (singularity). ... ok test_rotmat_180 (test_PDB_vectors.VectorTests.test_rotmat_180) Test rotmat when the rotation is 180 deg (singularity). ... ok test_rotmat_90 (test_PDB_vectors.VectorTests.test_rotmat_90) Test regular 90 deg rotation. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.079 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PQR.py test_PQR ... ok test_bad_charge (test_PQR.ParseSimplePQR.test_bad_charge) Test if missing or malformed charge case is handled correctly. ... ok test_bad_radius (test_PQR.ParseSimplePQR.test_bad_radius) Test if missing, malformed or negative radius case is handled correctly. ... ok test_bad_xyz (test_PQR.ParseSimplePQR.test_bad_xyz) Test if bad coordinates exception is raised. ... ok test_single_input (test_PQR.ParseSimplePQR.test_single_input) Test if a single ATOM entry correctly parsed. ... ok test_pdbio_write_pqr_structure (test_PQR.WriteTest.test_pdbio_write_pqr_structure) Write a full structure using PDBIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Pathway.py test_Pathway ... ok testAdditionalFunctions (test_Pathway.GraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.GraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.GraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.GraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.GraphTestCase.test_RemoveNode) ... ok testAdditionalFunctions (test_Pathway.MultiGraphTestCase.testAdditionalFunctions) ... ok test_Edges (test_Pathway.MultiGraphTestCase.test_Edges) ... ok test_Equals (test_Pathway.MultiGraphTestCase.test_Equals) ... ok test_Nodes (test_Pathway.MultiGraphTestCase.test_Nodes) ... ok test_RemoveNode (test_Pathway.MultiGraphTestCase.test_RemoveNode) ... ok test_eq (test_Pathway.ReactionTestCase.test_eq) ... ok test_rev (test_Pathway.ReactionTestCase.test_rev) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Phd.py test_Phd ... ok test_check_SeqIO (test_Phd.PhdTest454.test_check_SeqIO) Test phd_454 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestOne.test_check_SeqIO) Test phd1 using parser via SeqIO. ... ok test_check_record_parser (test_Phd.PhdTestOne.test_check_record_parser) Test phd1 file in detail. ... ok test_check_SeqIO (test_Phd.PhdTestSolexa.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok test_check_SeqIO (test_Phd.PhdTestTwo.test_check_SeqIO) Test phd2 using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.101 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop.py test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.010 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop. ---------------------------------------------------------------------- Ran 1 test in 0.011 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py test_PopGen_GenePop_nodepend ... ok test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_file_record_parser) Basic operation of the File Record Parser. ... ok test_remove_features (test_PopGen_GenePop_nodepend.FileParserTest.test_remove_features) Testing the ability to remove population/loci via class methods. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_parser (test_PopGen_GenePop_nodepend.ParserTest.test_record_parser) Basic operation of the Record Parser. ... ok test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest.test_wrong_file_parser) Testing the ability to deal with wrongly formatted files. ... ok test_record_basic (test_PopGen_GenePop_nodepend.RecordTest.test_record_basic) Basic test on Record. ... ok test_utils (test_PopGen_GenePop_nodepend.UtilsTest.test_utils) Basic operation of GenePop Utils. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.022 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Prank_tool.py test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.100 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Probcons_tool.py test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.125 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_ProtParam.py test_ProtParam ... ok test_aromaticity (test_ProtParam.ProtParamTest.test_aromaticity) Calculate protein aromaticity. ... ok test_charge_at_pH (test_ProtParam.ProtParamTest.test_charge_at_pH) Test charge_at_pH function. ... ok test_count_amino_acids (test_ProtParam.ProtParamTest.test_count_amino_acids) Calculate amino acid counts. ... ok test_flexibility (test_ProtParam.ProtParamTest.test_flexibility) Calculate protein flexibility. ... ok test_get_amino_acids_percent (test_ProtParam.ProtParamTest.test_get_amino_acids_percent) Calculate amino acid percentages. ... ok test_get_molecular_weight (test_ProtParam.ProtParamTest.test_get_molecular_weight) Calculate protein molecular weight. ... ok test_get_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight) Calculate monoisotopic molecular weight. ... ok test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest.test_get_monoisotopic_molecular_weight_identical) Confirm protein molecular weight agrees with calculation from Bio.SeqUtils. ... ok test_gravy (test_ProtParam.ProtParamTest.test_gravy) Calculate gravy. Tests all pre-defined scales. ... ok test_instability_index (test_ProtParam.ProtParamTest.test_instability_index) Calculate protein instability index. ... ok test_isoelectric_point (test_ProtParam.ProtParamTest.test_isoelectric_point) Calculate the isoelectric point. ... ok test_molar_extinction_coefficient (test_ProtParam.ProtParamTest.test_molar_extinction_coefficient) Molar extinction coefficient. ... ok test_protein_scale (test_ProtParam.ProtParamTest.test_protein_scale) Calculate the Kite Doolittle scale. ... ok test_secondary_structure_fraction (test_ProtParam.ProtParamTest.test_secondary_structure_fraction) Calculate secondary structure fractions. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.115 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_RCSBFormats.py test_RCSBFormats ... ok test_compare_chains (test_RCSBFormats.CompareStructures.test_compare_chains) Compare parsed chains. ... ok test_compare_models (test_RCSBFormats.CompareStructures.test_compare_models) Compared parsed models. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.642 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.268 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Astral.py test_SCOP_Astral ... ok testConstructWithCustomFile (test_SCOP_Astral.AstralTests.testConstructWithCustomFile) ... ok testGetDomainsClustered (test_SCOP_Astral.AstralTests.testGetDomainsClustered) ... ok testGetDomainsFromFile (test_SCOP_Astral.AstralTests.testGetDomainsFromFile) ... ok testGetSeq (test_SCOP_Astral.AstralTests.testGetSeq) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.095 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Cla.py test_SCOP_Cla ... ok testError (test_SCOP_Cla.ClaTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testIndex (test_SCOP_Cla.ClaTests.testIndex) Test CLA file indexing. ... ok testParse (test_SCOP_Cla.ClaTests.testParse) Test if all records in a CLA file are being read. ... ok testRecord (test_SCOP_Cla.ClaTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Cla.ClaTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.084 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Des.py test_SCOP_Des ... ok testError (test_SCOP_Des.DesTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Des.DesTests.testParse) Test if all records in a DES file are being read. ... ok testRecord (test_SCOP_Des.DesTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Des.DesTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Dom.py test_SCOP_Dom ... ok testError (test_SCOP_Dom.DomTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Dom.DomTests.testParse) Test if all records in a DOM file are being read. ... ok testRecord (test_SCOP_Dom.DomTests.testRecord) Test one record in detail. ... ok testStr (test_SCOP_Dom.DomTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.083 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Hie.py test_SCOP_Hie ... ok testError (test_SCOP_Hie.HieTests.testError) Test if a corrupt record raises the appropriate exception. ... ok testParse (test_SCOP_Hie.HieTests.testParse) Test if all records in a HIE file are being read. ... ok testStr (test_SCOP_Hie.HieTests.testStr) Test if we can convert each record to a string correctly. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.085 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Raf.py test_SCOP_Raf ... ok testParse (test_SCOP_Raf.RafTests.testParse) Parse a RAF record. ... ok testSeqMapAdd (test_SCOP_Raf.RafTests.testSeqMapAdd) ... ok testSeqMapIndex (test_SCOP_Raf.RafTests.testSeqMapIndex) ... ok testSeqMapSlice (test_SCOP_Raf.RafTests.testSeqMapSlice) ... ok test_SeqMap_getAtoms_err (test_SCOP_Raf.RafTests.test_SeqMap_getAtoms_err) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Residues.py test_SCOP_Residues ... ok testAstralParse (test_SCOP_Residues.ResiduesTests.testAstralParse) Test if we can parse residue subsets enclosed in brackets. ... ok testJustPdbId (test_SCOP_Residues.ResiduesTests.testJustPdbId) ... ok testParse (test_SCOP_Residues.ResiduesTests.testParse) ... ok testParseError (test_SCOP_Residues.ResiduesTests.testParseError) ... ok testPdbId (test_SCOP_Residues.ResiduesTests.testPdbId) ... ok testStr (test_SCOP_Residues.ResiduesTests.testStr) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.086 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_Scop.py test_SCOP_Scop ... ok testConstructFromDirectory (test_SCOP_Scop.ScopTests.testConstructFromDirectory) ... ok testGetAscendent (test_SCOP_Scop.ScopTests.testGetAscendent) ... ok testParse (test_SCOP_Scop.ScopTests.testParse) ... ok testParseDomain (test_SCOP_Scop.ScopTests.testParseDomain) ... ok testSccsOrder (test_SCOP_Scop.ScopTests.testSccsOrder) ... ok test_get_descendents (test_SCOP_Scop.ScopTests.test_get_descendents) Test getDescendents method. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.099 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SCOP_online.py test_SCOP_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.080 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SVDSuperimposer.py test_SVDSuperimposer ... ok test_get_init_rms (test_SVDSuperimposer.SVDSuperimposerTest.test_get_init_rms) ... ok test_oldTest (test_SVDSuperimposer.SVDSuperimposerTest.test_oldTest) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.012 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl.py test_SearchIO_blat_psl ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_001) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_002) Test parsing blat output (psl_34_001.psl). ... ok test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_003) Test parsing blat output (psl_34_003.psl). ... ok test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_004) Test parsing blat output (psl_34_004.psl). ... ok test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_34_005) Test parsing blat output (psl_34_005.psl). ... ok test_psl_35_001 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_001) Test parsing blat output (psl_35_001.psl). ... ok test_psl_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_psl_35_002) Test parsing blat output (psl_35_002.psl). ... ok test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_001) Test parsing blat output (pslx_34_001.pslx). ... ok test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_002) Test parsing blat output (pslx_34_002.pslx). ... ok test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_003) Test parsing blat output (pslx_34_003.pslx). ... ok test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_004) Test parsing blat output (pslx_34_004.pslx). ... ok test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_34_005) Test parsing blat output (pslx_34_005.pslx). ... ok test_pslx_35_002 (test_SearchIO_blat_psl.BlatPslxCases.test_pslx_35_002) Test parsing blat output (pslx_35_002.pslx). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.120 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_blat_psl_index.py test_SearchIO_blat_psl_index ... ok test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_001) Test blat-psl indexing, multiple queries. ... ok test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_002) Test blat-psl indexing, single query, no hits. ... ok test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_003) Test blat-psl indexing, single query, single hit. ... ok test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_004) Test blat-psl indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_005) Test blat-psl indexing, multiple queries, no header. ... ok test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_006) Test blat-pslx indexing, multiple queries. ... ok test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_007) Test blat-pslx indexing, single query, no hits. ... ok test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_008) Test blat-pslx indexing, single query, single hit. ... ok test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_009) Test blat-pslx indexing, single query, multiple hits with multiple hsps. ... ok test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases.test_psl_34_010) Test blat-pslx indexing, multiple queries, no header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.158 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.186 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_text_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_m_est2genome) Test exonerate-text indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases.test_exn_22_q_multiple) Test exonerate-text indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.093 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py test_SearchIO_exonerate_vulgar_index ... ok test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_m_est2genome) Test exonerate-vulgar indexing, single. ... ok test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases.test_exn_22_q_multiple) Test exonerate-vulgar indexing, single. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.076 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10 ... ok test_output002 (test_SearchIO_fasta_m10.Fasta34Cases.test_output002) Test parsing fasta34 output (output002.m10). ... ok test_output003 (test_SearchIO_fasta_m10.Fasta34Cases.test_output003) Test parsing fasta34 output (output003.m10). ... ok test_output001 (test_SearchIO_fasta_m10.Fasta35Cases.test_output001) Test parsing fasta35 output (output001.m10). ... ok test_output004 (test_SearchIO_fasta_m10.Fasta35Cases.test_output004) Test parsing fasta35 output (output004.m10). ... ok test_output005 (test_SearchIO_fasta_m10.Fasta35Cases.test_output005) Test parsing ssearch35 output (output005.m10). ... ok test_output006 (test_SearchIO_fasta_m10.Fasta35Cases.test_output006) Test parsing fasta35 output (output006.m10). ... ok test_output007 (test_SearchIO_fasta_m10.Fasta36Cases.test_output007) Test parsing fasta36 output (output007.m10). ... ok test_output008 (test_SearchIO_fasta_m10.Fasta36Cases.test_output008) Test parsing tfastx36 output (output008.m10). ... ok test_output009 (test_SearchIO_fasta_m10.Fasta36Cases.test_output009) Test parsing fasta36 output (output009.m10). ... ok test_output010 (test_SearchIO_fasta_m10.Fasta36Cases.test_output010) Test parsing fasta36 output (output010.m10). ... ok test_output011 (test_SearchIO_fasta_m10.Fasta36Cases.test_output011) Test parsing fasta36 output (output011.m10). ... ok test_output012 (test_SearchIO_fasta_m10.Fasta36Cases.test_output012) Test parsing fasta36 output (output012.m10). ... ok test_output013 (test_SearchIO_fasta_m10.Fasta36Cases.test_output013) Test parsing fasta36 output (output013.m10). ... ok test_output014 (test_SearchIO_fasta_m10.Fasta36Cases.test_output014) Test parsing fasta36 output (output014.m10). ... ok test_output015 (test_SearchIO_fasta_m10.Fasta36Cases.test_output015) Test parsing fasta36 output (output015.m10). ... ok test_output016 (test_SearchIO_fasta_m10.Fasta36Cases.test_output016) Test parsing fasta36 output (output016.m10). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.136 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py test_SearchIO_fasta_m10_index ... ok test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_001) Test fasta-m10 indexing, fasta35, multiple queries. ... ok test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_002) Test fasta-m10 indexing, fasta34, multiple queries. ... ok test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_005) Test fasta-m10 indexing, ssearch35, multiple queries. ... ok test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_008) Test fasta-m10 indexing, tfastx36, multiple queries. ... ok test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_009) Test fasta-m10 indexing, fasta36, multiple queries. ... ok test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_010) Test fasta-m10 indexing, fasta36, single query, no hits. ... ok test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_011) Test fasta-m10 indexing, fasta36, single query, hits with single hsp. ... ok test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases.test_output_012) Test fasta-m10 indexing, fasta36, single query with multiple hsps. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.130 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hhsuite2_text.py test_SearchIO_hhsuite2_text ... ok test_2uvo (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo) Parsing 2uvo. ... ok test_2uvo_emptytable (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_emptytable) Parsing 4uvo with empty results table. ... ok test_2uvo_onlyheader (test_SearchIO_hhsuite2_text.HhsuiteCases.test_2uvo_onlyheader) Parsing 4uvo with only header present. ... ok test_4p79 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4p79) Parsing 4p79_hhsearch_server_NOssm.hhr file. ... ok test_4y9h_nossm (test_SearchIO_hhsuite2_text.HhsuiteCases.test_4y9h_nossm) Parsing 4y9h_hhsearch_server_NOssm.hhr file. ... ok test_9590198 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_9590198) Parsing hhpred_9590198.hhr file. ... ok test_allx (test_SearchIO_hhsuite2_text.HhsuiteCases.test_allx) Parsing allx.hhr file. ... ok test_q9bsu1 (test_SearchIO_hhsuite2_text.HhsuiteCases.test_q9bsu1) Parsing hhsearch_q9bsu1_uniclust_w_ss_pfamA_30.hhr file. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.138 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text ... ok test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_21) Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out). ... ok test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_22) Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out). ... ok test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out). ... ok test_hmmpfam_23_break_in_end_of_seq (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_break_in_end_of_seq) Test parsing hmmpfam 2.3 file with a line break in the end of seq marker. ... ok test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_missing_consensus) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out). ... ok test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_23_no_match) Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out). ... ok test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests.test_hmmpfam_24) Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out). ... ok test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_20) Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out). ... ok test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests.test_hmmsearch_22) Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.190 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer2_text_index ... ok test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_21_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.1. ... ok test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_22_hmmsearch_001) Test hmmer2-text indexing, HMMER 2.2. ... ok test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_23_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.3. ... ok test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases.test_hmmertext_text_24_hmmpfam_001) Test hmmer2-text indexing, HMMER 2.4. ... ok test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_first_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_last_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_multiple_middle_hmmpfam) Test hmmer2-text raw string retrieval, multiple queries, hmmpfam. ... ok test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmpfam) Test hmmer2-text raw string retrieval, single query, hmmpfam. ... ok test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases.test_hmmer2text_22_single_hmmsearch) Test hmmer2-text raw string retrieval, single query, hmmsearch. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.142 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab ... ok test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_30_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001). ... ok test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases.test_domtab_31b1_hmmsearch_001) Parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001). ... ok test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001). ... ok test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_002) Parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002). ... ok test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_003) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003). ... ok test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_30_hmmscan_004) Parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004). ... ok test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases.test_domtab_31b1_hmmscan_001) Parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_domtab_index ... ok test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_001) Test hmmscan-domtab indexing, HMMER 3.0, multiple queries. ... ok test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_002) Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_003) Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmscan_004) Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases.test_hmmerdomtab_30_hmmsearch_001) Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_first) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_last) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_multiple_middle) Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out). ... ok test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases.test_hmmerdomtab_30_single) Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.089 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_002) Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_003) Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases.test_30_hmmscan_004) Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004). ... ok test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases.test_31b1_hmmscan_001) Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases.test_31b1_hmmsearch_001) Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_tab_index ... ok test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_001) Test hmmer3-tab indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_002) Test hmmer3-tab indexing, HMMER 3.0, single query, no hits. ... ok test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_003) Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases.test_hmmer3tab_30_hmmscan_004) Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_first) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_last) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_multiple_middle) Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out). ... ok test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases.test_hmmer3tab_30_single) Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.089 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text ... ok test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_001) Parsing hmmersearch 3.0 (text_30_hmmsearch_001). ... ok test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_002) Parsing hmmersearch 3.0 (text_30_hmmsearch_002). ... ok test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_003) Parsing hmmersearch 3.0 (text_30_hmmsearch_003). ... ok test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_004) Parsing hmmersearch 3.0 (text_30_hmmsearch_004). ... ok test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases.test_30_hmmsearch_005) Parsing hmmersearch 3.0 (text_30_hmmsearch_005). ... ok test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b1_hmmsearch_001) Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001). ... ok test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmscan_001) Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001). ... ok test_31b2_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_001) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_001). ... ok test_31b2_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases.test_31b2_hmmsearch_002) Test parsing hmmsearch 3.1b2 (text_31b2_hmmsearch_002). ... ok test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_001) Parsing hmmscan 3.0 (text_30_hmmscan_001). ... ok test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_002) Parsing hmmscan 3.0 (text_30_hmmscan_002). ... ok test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_003) Parsing hmmscan 3.0 (text_30_hmmscan_003). ... ok test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_004) Parsing hmmscan 3.0 (text_30_hmmscan_004). ... ok test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_005) Parsing hmmscan 3.0 (text_30_hmmscan_005). ... ok test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_006) Parsing hmmscan 3.0 (text_30_hmmscan_006). ... ok test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_007) Parsing hmmscan 3.0 (text_30_hmmscan_007). ... ok test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_008) Parsing hmmscan 3.0 (text_30_hmmscan_008). ... ok test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_009) Parsing hmmscan 3.0 (text_30_hmmscan_009). ... ok test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases.test_30_hmmscan_010) Parsing hmmscan 3.0 (text_30_hmmscan_010). ... ok test_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 0.190 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py test_SearchIO_hmmer3_text_index ... ok test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_001) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_002) Test hmmer3-text indexing, HMMER 3.0, single query, no hits. ... ok test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_006) Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits. ... ok test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_007) Test hmmer3-text indexing, HMMER 3.0, single query, no alignments. ... ok test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmscan_008) Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width. ... ok test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases.test_hmmertext_text_30_hmmsearch_005) Test hmmer3-text indexing, HMMER 3.0, multiple queries. ... ok test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_first) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_last) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_multiple_middle) Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out). ... ok test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases.test_hmmer3text_30_single) Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out). ... ok ---------------------------------------------------------------------- Ran 1 test in 0.114 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_interproscan_xml.py test_SearchIO_interproscan_xml ... ok test_xml_001 (test_SearchIO_interproscan_xml.InterproscanXmlCases.test_xml_001) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.068 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.128 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SearchIO_write.py test_SearchIO_write ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.337 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.094 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO.py test_SeqIO ... ok test_abi1 (test_SeqIO.TestSeqIO.test_abi1) ... ok test_abi2 (test_SeqIO.TestSeqIO.test_abi2) ... ok test_abi3 (test_SeqIO.TestSeqIO.test_abi3) ... ok test_ace1 (test_SeqIO.TestSeqIO.test_ace1) ... ok test_ace2 (test_SeqIO.TestSeqIO.test_ace2) ... ok test_ace3 (test_SeqIO.TestSeqIO.test_ace3) ... ok test_cif_atom1 (test_SeqIO.TestSeqIO.test_cif_atom1) ... ok test_cif_atom2 (test_SeqIO.TestSeqIO.test_cif_atom2) ... ok test_cif_seqres1 (test_SeqIO.TestSeqIO.test_cif_seqres1) ... ok test_cif_seqres2 (test_SeqIO.TestSeqIO.test_cif_seqres2) ... ok test_clustal1 (test_SeqIO.TestSeqIO.test_clustal1) ... ok test_clustal2 (test_SeqIO.TestSeqIO.test_clustal2) ... ok test_clustal3 (test_SeqIO.TestSeqIO.test_clustal3) ... ok test_clustal4 (test_SeqIO.TestSeqIO.test_clustal4) ... ok test_clustal_to_nexus_with_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_with_mol_type) Convert Clustal to NEXUS with molecule type. ... ok test_clustal_to_nexus_without_mol_type (test_SeqIO.TestSeqIO.test_clustal_to_nexus_without_mol_type) Convert Clustal to NEXUS without molecule type. ... ok test_embl1 (test_SeqIO.TestSeqIO.test_embl1) ... ok test_embl10 (test_SeqIO.TestSeqIO.test_embl10) ... ok test_embl11 (test_SeqIO.TestSeqIO.test_embl11) ... ok test_embl12 (test_SeqIO.TestSeqIO.test_embl12) ... ok test_embl13 (test_SeqIO.TestSeqIO.test_embl13) Test parsing embl file with wrapped locations and unspecified type. ... ok test_embl14 (test_SeqIO.TestSeqIO.test_embl14) Test parsing file with features over-indented for EMBL. ... ok test_embl2 (test_SeqIO.TestSeqIO.test_embl2) ... ok test_embl3 (test_SeqIO.TestSeqIO.test_embl3) ... ok test_embl4 (test_SeqIO.TestSeqIO.test_embl4) ... ok test_embl5 (test_SeqIO.TestSeqIO.test_embl5) ... ok test_embl6 (test_SeqIO.TestSeqIO.test_embl6) ... ok test_embl7 (test_SeqIO.TestSeqIO.test_embl7) ... ok test_embl8 (test_SeqIO.TestSeqIO.test_embl8) ... ok test_embl9 (test_SeqIO.TestSeqIO.test_embl9) ... ok test_emboss1 (test_SeqIO.TestSeqIO.test_emboss1) ... ok test_emboss2 (test_SeqIO.TestSeqIO.test_emboss2) ... ok test_emboss3 (test_SeqIO.TestSeqIO.test_emboss3) ... ok test_empty_file (test_SeqIO.TestSeqIO.test_empty_file) Check parsers can cope with an empty file. ... ok test_fasta1 (test_SeqIO.TestSeqIO.test_fasta1) ... ok test_fasta10 (test_SeqIO.TestSeqIO.test_fasta10) ... ok test_fasta11 (test_SeqIO.TestSeqIO.test_fasta11) ... ok test_fasta12 (test_SeqIO.TestSeqIO.test_fasta12) ... ok test_fasta13 (test_SeqIO.TestSeqIO.test_fasta13) ... ok test_fasta14 (test_SeqIO.TestSeqIO.test_fasta14) ... ok test_fasta15 (test_SeqIO.TestSeqIO.test_fasta15) ... ok test_fasta16 (test_SeqIO.TestSeqIO.test_fasta16) ... ok test_fasta17 (test_SeqIO.TestSeqIO.test_fasta17) ... ok test_fasta18 (test_SeqIO.TestSeqIO.test_fasta18) ... ok test_fasta19 (test_SeqIO.TestSeqIO.test_fasta19) ... ok test_fasta2 (test_SeqIO.TestSeqIO.test_fasta2) ... ok test_fasta20 (test_SeqIO.TestSeqIO.test_fasta20) ... ok test_fasta21 (test_SeqIO.TestSeqIO.test_fasta21) ... ok test_fasta22 (test_SeqIO.TestSeqIO.test_fasta22) ... ok test_fasta23 (test_SeqIO.TestSeqIO.test_fasta23) ... ok test_fasta24 (test_SeqIO.TestSeqIO.test_fasta24) ... ok test_fasta3 (test_SeqIO.TestSeqIO.test_fasta3) ... ok test_fasta4 (test_SeqIO.TestSeqIO.test_fasta4) ... ok test_fasta5 (test_SeqIO.TestSeqIO.test_fasta5) ... ok test_fasta6 (test_SeqIO.TestSeqIO.test_fasta6) ... ok test_fasta7 (test_SeqIO.TestSeqIO.test_fasta7) ... ok test_fasta8 (test_SeqIO.TestSeqIO.test_fasta8) ... ok test_fasta9 (test_SeqIO.TestSeqIO.test_fasta9) ... ok test_fasta_2line1 (test_SeqIO.TestSeqIO.test_fasta_2line1) ... ok test_fasta_to_seqxml_with_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_with_mol_type) Convert FASTA to SeqXML with molecule type. ... ok test_fasta_to_seqxml_without_mol_type (test_SeqIO.TestSeqIO.test_fasta_to_seqxml_without_mol_type) Convert FASTA to SeqXML without molecule type. ... ok test_fastq1 (test_SeqIO.TestSeqIO.test_fastq1) ... ok test_fastq2 (test_SeqIO.TestSeqIO.test_fastq2) ... ok test_fastq3 (test_SeqIO.TestSeqIO.test_fastq3) ... ok test_fastq4 (test_SeqIO.TestSeqIO.test_fastq4) ... ok test_fastq5 (test_SeqIO.TestSeqIO.test_fastq5) ... ok test_fastq_illumina1 (test_SeqIO.TestSeqIO.test_fastq_illumina1) ... ok test_fastq_solexa1 (test_SeqIO.TestSeqIO.test_fastq_solexa1) ... ok test_fastq_solexa2 (test_SeqIO.TestSeqIO.test_fastq_solexa2) ... ok test_genbank1 (test_SeqIO.TestSeqIO.test_genbank1) ... ok test_genbank10 (test_SeqIO.TestSeqIO.test_genbank10) ... ok test_genbank11 (test_SeqIO.TestSeqIO.test_genbank11) ... ok test_genbank12 (test_SeqIO.TestSeqIO.test_genbank12) ... ok test_genbank13 (test_SeqIO.TestSeqIO.test_genbank13) ... ok test_genbank14 (test_SeqIO.TestSeqIO.test_genbank14) ... ok test_genbank15 (test_SeqIO.TestSeqIO.test_genbank15) ... ok test_genbank16 (test_SeqIO.TestSeqIO.test_genbank16) Test parsing Genbank file from Vector NTI with an odd LOCUS line. ... ok test_genbank17 (test_SeqIO.TestSeqIO.test_genbank17) ... ok test_genbank18 (test_SeqIO.TestSeqIO.test_genbank18) ... ok test_genbank19 (test_SeqIO.TestSeqIO.test_genbank19) ... ok test_genbank2 (test_SeqIO.TestSeqIO.test_genbank2) ... ok test_genbank20 (test_SeqIO.TestSeqIO.test_genbank20) Test parsing GenPept file with nasty bond locations. ... ok test_genbank21 (test_SeqIO.TestSeqIO.test_genbank21) ... ok test_genbank22 (test_SeqIO.TestSeqIO.test_genbank22) Test that genbank format write doesn't destroy db_source in annotations. ... ok test_genbank23 (test_SeqIO.TestSeqIO.test_genbank23) Test that peptide genbank files can be written with long names. ... ok test_genbank3 (test_SeqIO.TestSeqIO.test_genbank3) ... ok test_genbank4 (test_SeqIO.TestSeqIO.test_genbank4) ... ok test_genbank5 (test_SeqIO.TestSeqIO.test_genbank5) ... ok test_genbank6 (test_SeqIO.TestSeqIO.test_genbank6) ... ok test_genbank7 (test_SeqIO.TestSeqIO.test_genbank7) ... ok test_genbank8 (test_SeqIO.TestSeqIO.test_genbank8) ... ok test_genbank9 (test_SeqIO.TestSeqIO.test_genbank9) ... ok test_ig1 (test_SeqIO.TestSeqIO.test_ig1) ... ok test_ig2 (test_SeqIO.TestSeqIO.test_ig2) ... ok test_ig3 (test_SeqIO.TestSeqIO.test_ig3) Test parsing a MASE alignment with sequence O_ANT70 being shorter. ... ok test_imgt1 (test_SeqIO.TestSeqIO.test_imgt1) Test parsing file with features over-indented for EMBL. ... ok test_imgt2 (test_SeqIO.TestSeqIO.test_imgt2) ... ok test_nexus1 (test_SeqIO.TestSeqIO.test_nexus1) ... ok test_pdb_atom1 (test_SeqIO.TestSeqIO.test_pdb_atom1) ... ok test_pdb_atom2 (test_SeqIO.TestSeqIO.test_pdb_atom2) ... ok test_pdb_atom3 (test_SeqIO.TestSeqIO.test_pdb_atom3) ... ok test_pdb_seqres1 (test_SeqIO.TestSeqIO.test_pdb_seqres1) ... ok test_pdb_seqres2 (test_SeqIO.TestSeqIO.test_pdb_seqres2) ... ok test_pdb_seqres3 (test_SeqIO.TestSeqIO.test_pdb_seqres3) ... ok test_phd1 (test_SeqIO.TestSeqIO.test_phd1) ... ok test_phd2 (test_SeqIO.TestSeqIO.test_phd2) ... ok test_phd3 (test_SeqIO.TestSeqIO.test_phd3) ... ok test_phd4 (test_SeqIO.TestSeqIO.test_phd4) ... ok test_phylip1 (test_SeqIO.TestSeqIO.test_phylip1) ... ok test_phylip2 (test_SeqIO.TestSeqIO.test_phylip2) ... ok test_phylip3 (test_SeqIO.TestSeqIO.test_phylip3) ... ok test_phylip4 (test_SeqIO.TestSeqIO.test_phylip4) ... ok test_phylip5 (test_SeqIO.TestSeqIO.test_phylip5) ... ok test_phylip6 (test_SeqIO.TestSeqIO.test_phylip6) ... ok test_phylip7 (test_SeqIO.TestSeqIO.test_phylip7) ... ok test_pir1 (test_SeqIO.TestSeqIO.test_pir1) ... ok test_pir2 (test_SeqIO.TestSeqIO.test_pir2) ... ok test_pir3 (test_SeqIO.TestSeqIO.test_pir3) ... ok test_pir4 (test_SeqIO.TestSeqIO.test_pir4) ... ok test_pir5 (test_SeqIO.TestSeqIO.test_pir5) ... ok test_qual1 (test_SeqIO.TestSeqIO.test_qual1) ... ok test_seqxml1 (test_SeqIO.TestSeqIO.test_seqxml1) ... ok test_seqxml2 (test_SeqIO.TestSeqIO.test_seqxml2) ... ok test_seqxml3 (test_SeqIO.TestSeqIO.test_seqxml3) ... ok test_sff1 (test_SeqIO.TestSeqIO.test_sff1) ... ok test_snapgene1 (test_SeqIO.TestSeqIO.test_snapgene1) ... ok test_stockholm1 (test_SeqIO.TestSeqIO.test_stockholm1) ... ok test_stockholm2 (test_SeqIO.TestSeqIO.test_stockholm2) ... ok test_swiss1 (test_SeqIO.TestSeqIO.test_swiss1) ... ok test_swiss11 (test_SeqIO.TestSeqIO.test_swiss11) ... ok test_swiss12 (test_SeqIO.TestSeqIO.test_swiss12) ... ok test_swiss13 (test_SeqIO.TestSeqIO.test_swiss13) ... ok test_swiss14 (test_SeqIO.TestSeqIO.test_swiss14) ... ok test_swiss15 (test_SeqIO.TestSeqIO.test_swiss15) ... ok test_swiss16 (test_SeqIO.TestSeqIO.test_swiss16) ... ok test_swiss17 (test_SeqIO.TestSeqIO.test_swiss17) ... ok test_swiss18 (test_SeqIO.TestSeqIO.test_swiss18) ... ok test_swiss19 (test_SeqIO.TestSeqIO.test_swiss19) ... ok test_swiss2 (test_SeqIO.TestSeqIO.test_swiss2) ... ok test_swiss20 (test_SeqIO.TestSeqIO.test_swiss20) ... ok test_swiss3 (test_SeqIO.TestSeqIO.test_swiss3) ... ok test_swiss4 (test_SeqIO.TestSeqIO.test_swiss4) ... ok test_swiss5 (test_SeqIO.TestSeqIO.test_swiss5) ... ok test_swiss6 (test_SeqIO.TestSeqIO.test_swiss6) ... ok test_swiss7 (test_SeqIO.TestSeqIO.test_swiss7) ... ok test_swiss8 (test_SeqIO.TestSeqIO.test_swiss8) ... ok test_swiss9 (test_SeqIO.TestSeqIO.test_swiss9) ... ok test_tab1 (test_SeqIO.TestSeqIO.test_tab1) ... ok test_uniprot_xml1 (test_SeqIO.TestSeqIO.test_uniprot_xml1) ... ok test_uniprot_xml2 (test_SeqIO.TestSeqIO.test_uniprot_xml2) ... ok test_uniprot_xml3 (test_SeqIO.TestSeqIO.test_uniprot_xml3) ... ok test_uniprot_xml4 (test_SeqIO.TestSeqIO.test_uniprot_xml4) ... ok test_uniprot_xml5 (test_SeqIO.TestSeqIO.test_uniprot_xml5) ... ok test_xdna1 (test_SeqIO.TestSeqIO.test_xdna1) ... ok test_gzip_fasta (test_SeqIO.TestZipped.test_gzip_fasta) Testing FASTA with gzip. ... ok test_gzip_fastq (test_SeqIO.TestZipped.test_gzip_fastq) Testing FASTQ with gzip. ... ok test_gzip_genbank (test_SeqIO.TestZipped.test_gzip_genbank) Testing GenBank with gzip. ... ok ---------------------------------------------------------------------- Ran 1 test in 20.958 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_AbiIO.py test_SeqIO_AbiIO ... ok test_file_type (test_SeqIO_AbiIO.TestAbi.test_file_type) Test if filetype is ABIF. ... ok test_no_smpl1 (test_SeqIO_AbiIO.TestAbi.test_no_smpl1) Test parsing of ABIF file without the normally expected SMPL1 tag. ... ok test_raw (test_SeqIO_AbiIO.TestAbi.test_raw) Test access to raw ABIF tags. ... ok test_seqrecord (test_SeqIO_AbiIO.TestAbi.test_seqrecord) Test if the extracted seqrecords data are equal to expected values. ... ok test_trim (test_SeqIO_AbiIO.TestAbi.test_trim) Test if trim works. ... ok test_file_type (test_SeqIO_AbiIO.TestAbiFake.test_file_type) Test if error is raised if filetype is not ABIF. ... ok test_nonascii_tag (test_SeqIO_AbiIO.TestAbiNonAscii.test_nonascii_tag) Test that we can handle non-ascii tags. ... ok test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode.test_file_mode) Test if exception is raised if file is not opened in 'rb' mode. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.491 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_FastaIO.py test_SeqIO_FastaIO ... ok test_edgecases_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_FastaTwoLineParser) Test FastaTwoLineParser edge-cases. ... ok test_edgecases_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_edgecases_SimpleFastaParser) Test SimpleFastaParser edge-cases. ... ok test_exceptions_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_exceptions_FastaTwoLineParser) Test FastaTwoLineParser exceptions. ... ok test_regular_FastaTwoLineParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_FastaTwoLineParser) Test regular FastaTwoLineParser cases. ... ok test_regular_SimpleFastaParser (test_SeqIO_FastaIO.TestSimpleFastaParsers.test_regular_SimpleFastaParser) Test regular SimpleFastaParser cases. ... ok test_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 0.094 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Gck.py test_SeqIO_Gck ... ok test_conflicting_lengths (test_SeqIO_Gck.TestGckWithArtificialData.test_conflicting_lengths) Read a file with incorrect length. ... ok test_read (test_SeqIO_Gck.TestGckWithArtificialData.test_read) Read an artificial sample file. ... ok test_read (test_SeqIO_Gck.TestGckWithImproperHeader.test_read) Read a file with an incomplete header. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Insdc.py test_SeqIO_Insdc ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: 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 0.134 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_NibIO.py test_SeqIO_NibIO ... ok test_read_even (test_SeqIO_NibIO.TestNibReaderWriter.test_read_even) ... ok test_read_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_read_odd) ... ok test_write_even (test_SeqIO_NibIO.TestNibReaderWriter.test_write_even) ... ok test_write_odd (test_SeqIO_NibIO.TestNibReaderWriter.test_write_odd) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.119 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_PdbIO.py test_SeqIO_PdbIO ... ok test_atom_parse (test_SeqIO_PdbIO.TestCifAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestCifAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestCifAtom.test_atom_read_noheader) Read a single-chain CIF without a header by ATOM entries. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestCifSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_noheader) Parse a PDB with no HEADER line. ... ok test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom.test_atom_parse) Parse a multi-chain structure by ATOM entries. ... ok test_atom_read (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read) Read a single-chain structure by ATOM entries. ... ok test_atom_read_noheader (test_SeqIO_PdbIO.TestPdbAtom.test_atom_read_noheader) Read a single-chain PDB without a header by ATOM entries. ... ok test_atom_with_insertion (test_SeqIO_PdbIO.TestPdbAtom.test_atom_with_insertion) Read a PDB with residue insertion code. ... ok test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_missing) Parse a PDB with no SEQRES entries. ... ok test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_parse) Parse a multi-chain PDB by SEQRES entries. ... ok test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres.test_seqres_read) Read a single-chain structure by sequence entries. ... ok ---------------------------------------------------------------------- Ran 1 test in 2.842 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_QualityIO.py test_SeqIO_QualityIO ... ok test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests.test_illumina_to_sanger) Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62). ... ok test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests.test_phred_quality_from_solexa) Mapping check for function phred_quality_from_solexa. ... ok test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests.test_sanger_to_illumina) Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62). ... ok test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests.test_sanger_to_solexa) Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62). ... ok test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests.test_solexa_quality_from_phred) Mapping check for function solexa_quality_from_phred. ... ok test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests.test_solexa_to_sanger) Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62). ... ok test_fasta_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_fasta_as_fastq) ... ok test_sff_as_fastq (test_SeqIO_QualityIO.NonFastqTests.test_sff_as_fastq) ... ok test_reject_high_and_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_and_low) ... ok test_reject_high_but_not_low (test_SeqIO_QualityIO.TestFastqErrors.test_reject_high_but_not_low) ... ok test_fasta (test_SeqIO_QualityIO.TestQual.test_fasta) Check FASTQ parsing matches FASTA parsing. ... ok test_fasta_out (test_SeqIO_QualityIO.TestQual.test_fasta_out) Check FASTQ to FASTA output. ... ok test_paired (test_SeqIO_QualityIO.TestQual.test_paired) Check FASTQ parsing matches FASTA+QUAL parsing. ... ok test_qual (test_SeqIO_QualityIO.TestQual.test_qual) Check FASTQ parsing matches QUAL parsing. ... ok test_qual_negative (test_SeqIO_QualityIO.TestQual.test_qual_negative) Check QUAL negative scores mapped to PHRED zero. ... ok test_qual_out (test_SeqIO_QualityIO.TestQual.test_qual_out) Check FASTQ to QUAL output. ... ok test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_1000) Read and write back simple example with mixed case 1000bp read. ... ok test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite.test_fastq_2000) Read and write back simple example with upper case 2000bp read. ... ok test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_dna) Read and write back simple example with ambiguous DNA. ... ok test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite.test_fastq_rna) Read and write back simple example with ambiguous RNA. ... ok test_reference_conversion (test_SeqIO_QualityIO.TestReferenceFastqConversions.test_reference_conversion) ... ok test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_end) Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL. ... ok test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_at_start) Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL. ... ok test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions.test_alt_index_in_middle) Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL. ... ok test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_end) Test converting E3MFGYR02_index_in_middle into FASTA+QUAL. ... ok test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions.test_index_at_start) Test converting E3MFGYR02_index_at_start into FASTA+QUAL. ... ok test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions.test_no_manifest) Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL. ... ok test_original (test_SeqIO_QualityIO.TestReferenceSffConversions.test_original) Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL. ... ok test_negative_clip (test_SeqIO_QualityIO.TestSFF.test_negative_clip) ... ok test_overlapping_clip (test_SeqIO_QualityIO.TestSFF.test_overlapping_clip) ... ok test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02) Write and read back E3MFGYR02_random_10_reads.sff. ... ok test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_end) Write and read back E3MFGYR02_alt_index_at_end.sff. ... ok test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_at_start) Write and read back E3MFGYR02_alt_index_at_start.sff. ... ok test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_alt_index_in_middle) Write and read back E3MFGYR02_alt_index_in_middle.sff. ... ok test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_at_start) Write and read back E3MFGYR02_index_at_start.sff. ... ok test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_index_in_middle) Write and read back E3MFGYR02_index_in_middle.sff. ... ok test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_no_manifest) Write and read back E3MFGYR02_no_manifest.sff. ... ok test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead.test_E3MFGYR02_trimmed) Write and read back E3MFGYR02_random_10_reads.sff (trimmed). ... ok test_example_fasta (test_SeqIO_QualityIO.TestWriteRead.test_example_fasta) Write and read back example.fasta. ... ok test_example_fastq (test_SeqIO_QualityIO.TestWriteRead.test_example_fastq) Write and read back example.fastq. ... ok test_example_qual (test_SeqIO_QualityIO.TestWriteRead.test_example_qual) Write and read back example.qual. ... ok test_generated (test_SeqIO_QualityIO.TestWriteRead.test_generated) Write and read back odd SeqRecord objects. ... ok test_greek_sff (test_SeqIO_QualityIO.TestWriteRead.test_greek_sff) Write and read back greek.sff. ... ok test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead.test_illumina_faked) Write and read back illumina_faked.fastq. ... ok test_paired_sff (test_SeqIO_QualityIO.TestWriteRead.test_paired_sff) Write and read back paired.sff. ... ok test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead.test_sanger_93) Write and read back sanger_93.fastq. ... ok test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead.test_sanger_faked) Write and read back sanger_faked.fastq. ... ok test_solexa_example (test_SeqIO_QualityIO.TestWriteRead.test_solexa_example) Write and read back solexa_example.fastq. ... ok test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead.test_solexa_faked) Write and read back solexa_faked.fastq. ... ok test_tricky (test_SeqIO_QualityIO.TestWriteRead.test_tricky) Write and read back tricky.fastq. ... ok test_conversion (test_SeqIO_QualityIO.TestsConverter.test_conversion) ... ok test_failure_detection (test_SeqIO_QualityIO.TestsConverter.test_failure_detection) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.613 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SeqXML.py test_SeqIO_SeqXML ... ok test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_dbxref) Read multiple cross references to a single source. ... ok test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead.test_duplicated_property) Read property with multiple values. ... ok test_empty_description (test_SeqIO_SeqXML.TestDetailedRead.test_empty_description) Check empty description. ... ok test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead.test_full_characters_set_read) Read full characters set for each type. ... ok test_global_species (test_SeqIO_SeqXML.TestDetailedRead.test_global_species) Check global species. ... ok test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead.test_local_source_definition) Check local source. ... ok test_local_species (test_SeqIO_SeqXML.TestDetailedRead.test_local_species) Check local species. ... ok test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead.test_read_minimal_required) Check minimal record. ... ok test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_special_characters_desc) Read special XML characters in description. ... ok test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead.test_unicode_characters_desc) Test special unicode characters in the description. ... ok test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_dna) Read and write DNA. ... ok test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_globalSpecies) Read and write global species. ... ok test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_protein) Read and write protein. ... ok test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite.test_read_write_rna) Read and write RNA. ... ok test_write_species (test_SeqIO_SeqXML.TestReadAndWrite.test_write_species) Test writing species from annotation tags. ... ok test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles.test_for_errors) Handling of corrupt files. ... ok test_check_dna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_dna_header) Check if the header information is parsed. ... ok test_check_global_species_example_header (test_SeqIO_SeqXML.TestReadHeader.test_check_global_species_example_header) Check if the header information is parsed. ... ok test_check_protein_header (test_SeqIO_SeqXML.TestReadHeader.test_check_protein_header) Check if the header information is parsed. ... ok test_check_rna_header (test_SeqIO_SeqXML.TestReadHeader.test_check_rna_header) Check if the header information is parsed. ... ok test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead.test_check_SeqIO) Files readable using parser via SeqIO. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.122 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_SnapGene.py test_SeqIO_SnapGene ... ok test_extra_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_extra_dna) Read a file with supernumerary DNA packet. ... ok test_invalid_cookie (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_invalid_cookie) Read a file with missing or invalid cookie packet. ... ok test_missing_dna (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_missing_dna) Read a file without a DNA packet. ... ok test_truncated_packet (test_SeqIO_SnapGene.TestCorruptedSnapGene.test_truncated_packet) Read a file with incomplete packet. ... ok test_read (test_SeqIO_SnapGene.TestSnapGene.test_read) Read sample files. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.097 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 1.026 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_Xdna.py test_SeqIO_Xdna ... ok test_corrupted_length (test_SeqIO_Xdna.TestInvalidXdna.test_corrupted_length) Read a file with incorrect length. ... ok test_invalid_sequence_type (test_SeqIO_Xdna.TestInvalidXdna.test_invalid_sequence_type) Read a file with an unknown sequence type. ... ok test_missing_features (test_SeqIO_Xdna.TestInvalidXdna.test_missing_features) Read a file with an incorrect number of features. ... ok test_unsupported_version (test_SeqIO_Xdna.TestInvalidXdna.test_unsupported_version) Read a file with unexpected version number. ... ok test_read (test_SeqIO_Xdna.TestXdna.test_read) Read sample files. ... ok test_warnings_on_data_loss (test_SeqIO_Xdna.TestXdnaWriter.test_warnings_on_data_loss) Emit warnings when dropping data on write. ... ok test_write_sequence_type (test_SeqIO_Xdna.TestXdnaWriter.test_write_sequence_type) Write correct sequence type. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_features.py test_SeqIO_features ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: unassigned DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: genomic DNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:1241: BiopythonWarning: Non-standard molecule type: mRNA warnings.warn(f"Non-standard molecule type: {mol_type}", BiopythonWarning) /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/SeqIO/InsdcIO.py:549: BiopythonWarning: Annotation 'swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505' too long for 'DBSOURCE' line warnings.warn( ok test_after (test_SeqIO_features.FeatureWriting.test_after) Features: write/read simple after locations. ... ok test_before (test_SeqIO_features.FeatureWriting.test_before) Features: write/read simple before locations. ... ok test_between (test_SeqIO_features.FeatureWriting.test_between) GenBank/EMBL write/read simple between locations. ... ok test_exact (test_SeqIO_features.FeatureWriting.test_exact) GenBank/EMBL write/read simple exact locations. ... ok test_fuzzy_join (test_SeqIO_features.FeatureWriting.test_fuzzy_join) Features: write/read fuzzy join locations. ... ok test_join (test_SeqIO_features.FeatureWriting.test_join) GenBank/EMBL write/read simple join locations. ... ok test_oneof (test_SeqIO_features.FeatureWriting.test_oneof) Features: write/read simple one-of locations. ... ok test_unknown (test_SeqIO_features.FeatureWriting.test_unknown) GenBank/EMBL write/read with unknown end points. ... ok test_within (test_SeqIO_features.FeatureWriting.test_within) Features: write/read simple within locations. ... ok test_mixed_strand (test_SeqIO_features.GenBankLocations.test_mixed_strand) ... ok test_rev_comp_styles (test_SeqIO_features.GenBankLocations.test_rev_comp_styles) ... ok test_CDS (test_SeqIO_features.NC_000932.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_CDS (test_SeqIO_features.NC_005816.test_CDS) Checking GenBank CDS translations vs FASTA faa file. ... ok test_Features (test_SeqIO_features.NC_005816.test_Features) Checking GenBank features sequences vs FASTA ffn file. ... ok test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816.test_GenBank_vs_EMBL) ... ok test_Genome (test_SeqIO_features.NC_005816.test_Genome) Checking GenBank sequence vs FASTA fna file. ... ok test_Translations (test_SeqIO_features.NC_005816.test_Translations) Checking translation of FASTA features (faa vs ffn). ... ok test_qualifiers (test_SeqIO_features.SeqFeatureCreation.test_qualifiers) Pass in qualifiers to SeqFeatures. ... ok test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_join) Feature on DNA (join, mixed strand). ... ok test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_mixed_strand_dna_multi_join) Feature on DNA (multi-join, mixed strand). ... ok test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_between) Feature on protein (between location, zero length). ... ok test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join) Feature on protein (join). ... ok test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_join_fuzzy) Feature on protein (fuzzy join). ... ok test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_multi_join) Feature on protein (multi-join). ... ok test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_oneof) Feature on protein (one-of positions). ... ok test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_protein_simple) Feature on protein (simple). ... ok test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna) Feature on DNA (simple, default strand). ... ok test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join) Feature on DNA (join, strand +1). ... ok test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_after) Feature on DNA (join, strand -1, after position). ... ok test_simple_dna_join_before (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_before) Feature on DNA (join, strand -1, before position). ... ok test_simple_dna_join_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_join_strand_minus) Feature on DNA (join, strand -1). ... ok test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand0) Feature on DNA (simple, strand 0). ... ok test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand1) Feature on DNA (simple, strand +1). ... ok test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_minus) Feature on DNA (simple, strand -1). ... ok test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_dna_strand_none) Feature on DNA (simple, strand None). ... ok test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_simple_rna) Feature on RNA (simple, default strand). ... ok test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_single_letter_dna) Feature on DNA (single letter, default strand). ... ok test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna) Feature on DNA (between location, zero length, default strand). ... ok test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading.test_zero_len_dna_end) Feature on DNA (between location at end, zero length, default strand). ... ok test_AAA03323 (test_SeqIO_features.TestWriteRead.test_AAA03323) Write and read back AAA03323.embl. ... ok test_AE017046 (test_SeqIO_features.TestWriteRead.test_AE017046) Write and read back AE017046.embl. ... ok test_DD231055_edited (test_SeqIO_features.TestWriteRead.test_DD231055_edited) Write and read back DD231055_edited.embl. ... ok test_Human_contigs (test_SeqIO_features.TestWriteRead.test_Human_contigs) Write and read back Human_contigs.embl. ... ok test_NC_000932 (test_SeqIO_features.TestWriteRead.test_NC_000932) Write and read back NC_000932.gb. ... ok test_NC_005816 (test_SeqIO_features.TestWriteRead.test_NC_005816) Write and read back NC_005816.gb. ... ok test_NT_019265 (test_SeqIO_features.TestWriteRead.test_NT_019265) Write and read back NT_019265.gb. ... ok test_SC10H5 (test_SeqIO_features.TestWriteRead.test_SC10H5) Write and read back SC10H5.embl. ... ok test_TRBG361 (test_SeqIO_features.TestWriteRead.test_TRBG361) Write and read back TRBG361.embl. ... ok test_U87107 (test_SeqIO_features.TestWriteRead.test_U87107) Write and read back U87107.embl. ... ok test_arab1 (test_SeqIO_features.TestWriteRead.test_arab1) Write and read back arab1.gb. ... ok test_blank_seq (test_SeqIO_features.TestWriteRead.test_blank_seq) Write and read back blank_seq.gb. ... ok test_cor6 (test_SeqIO_features.TestWriteRead.test_cor6) Write and read back cor6_6.gb. ... ok test_dbsource_wrap (test_SeqIO_features.TestWriteRead.test_dbsource_wrap) Write and read back dbsource_wrap.gb. ... ok test_extra_keywords (test_SeqIO_features.TestWriteRead.test_extra_keywords) Write and read back extra_keywords.gb. ... ok test_gbvrl1_start (test_SeqIO_features.TestWriteRead.test_gbvrl1_start) Write and read back gbvrl1_start.seq. ... ok test_noref (test_SeqIO_features.TestWriteRead.test_noref) Write and read back noref.gb. ... ok test_one_of (test_SeqIO_features.TestWriteRead.test_one_of) Write and read back of_one.gb. ... ok test_origin_line (test_SeqIO_features.TestWriteRead.test_origin_line) Write and read back origin_line.gb. ... ok test_pri1 (test_SeqIO_features.TestWriteRead.test_pri1) Write and read back pri1.gb. ... ok test_protein_refseq (test_SeqIO_features.TestWriteRead.test_protein_refseq) Write and read back protein_refseq.gb. ... ok test_protein_refseq2 (test_SeqIO_features.TestWriteRead.test_protein_refseq2) Write and read back protein_refseq2.gb. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.703 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_index.py test_SeqIO_index ... ok test_alpha_fails (test_SeqIO_index.IndexDictTests.test_alpha_fails) Reject alphabet argument in Bio.SeqIO.index(). ... ok test_alpha_fails_db (test_SeqIO_index.IndexDictTests.test_alpha_fails_db) Reject alphabet argument in Bio.SeqIO.index_db(). ... ok test_duplicates_index (test_SeqIO_index.IndexDictTests.test_duplicates_index) Index file with duplicate identifiers with Bio.SeqIO.index(). ... ok test_duplicates_index_db (test_SeqIO_index.IndexDictTests.test_duplicates_index_db) Index file with duplicate identifiers with Bio.SeqIO.index_db(). ... ok test_duplicates_to_dict (test_SeqIO_index.IndexDictTests.test_duplicates_to_dict) Index file with duplicate identifiers with Bio.SeqIO.to_dict(). ... ok test_key_checks (test_SeqIO_index.IndexDictTests.test_key_checks) ... ok test_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 10.124 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.082 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqIO_write.py test_SeqIO_write ... ok test_alignment_formats (test_SeqIO_write.WriterTests.test_alignment_formats) ... ok test_bad_handle (test_SeqIO_write.WriterTests.test_bad_handle) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqRecord.py test_SeqRecord ... ok test_annotations (test_SeqRecord.SeqRecordCreation.test_annotations) Pass in annotations to SeqRecords. ... ok test_letter_annotations (test_SeqRecord.SeqRecordCreation.test_letter_annotations) Pass in letter annotations to SeqRecords. ... ok test_replacing_seq (test_SeqRecord.SeqRecordCreation.test_replacing_seq) Replacing .seq if .letter_annotation present. ... ok test_valid_annotations (test_SeqRecord.SeqRecordCreation.test_valid_annotations) ... ok test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation.test_valid_dbxrefs) ... ok test_valid_description (test_SeqRecord.SeqRecordCreation.test_valid_description) ... ok test_valid_features (test_SeqRecord.SeqRecordCreation.test_valid_features) ... ok test_valid_id (test_SeqRecord.SeqRecordCreation.test_valid_id) ... ok test_valid_name (test_SeqRecord.SeqRecordCreation.test_valid_name) ... ok test_add_seq (test_SeqRecord.SeqRecordMethods.test_add_seq) Simple addition of Seq or string. ... ok test_add_seq_left (test_SeqRecord.SeqRecordMethods.test_add_seq_left) Simple left addition of Seq or string. ... ok test_add_seqrecord (test_SeqRecord.SeqRecordMethods.test_add_seqrecord) Simple left addition of SeqRecord from genbank file. ... ok test_add_simple (test_SeqRecord.SeqRecordMethods.test_add_simple) Simple addition. ... ok test_bytes (test_SeqRecord.SeqRecordMethods.test_bytes) ... ok test_contains (test_SeqRecord.SeqRecordMethods.test_contains) ... ok test_count (test_SeqRecord.SeqRecordMethods.test_count) ... ok test_format (test_SeqRecord.SeqRecordMethods.test_format) ... ok test_format_spaces (test_SeqRecord.SeqRecordMethods.test_format_spaces) ... ok test_format_str (test_SeqRecord.SeqRecordMethods.test_format_str) ... ok test_format_str_binary (test_SeqRecord.SeqRecordMethods.test_format_str_binary) ... ok test_islower (test_SeqRecord.SeqRecordMethods.test_islower) ... ok test_isupper (test_SeqRecord.SeqRecordMethods.test_isupper) ... ok test_iter (test_SeqRecord.SeqRecordMethods.test_iter) ... ok test_lower (test_SeqRecord.SeqRecordMethods.test_lower) ... ok test_repr (test_SeqRecord.SeqRecordMethods.test_repr) ... ok test_slice_add_shift (test_SeqRecord.SeqRecordMethods.test_slice_add_shift) Simple slice and add to shift. ... ok test_slice_add_simple (test_SeqRecord.SeqRecordMethods.test_slice_add_simple) Simple slice and add. ... ok test_slice_simple (test_SeqRecord.SeqRecordMethods.test_slice_simple) Simple slice. ... ok test_slice_variants (test_SeqRecord.SeqRecordMethods.test_slice_variants) Simple slices using different start/end values. ... ok test_slice_zero (test_SeqRecord.SeqRecordMethods.test_slice_zero) Zero slice. ... ok test_slicing (test_SeqRecord.SeqRecordMethods.test_slicing) ... ok test_str (test_SeqRecord.SeqRecordMethods.test_str) ... ok test_upper (test_SeqRecord.SeqRecordMethods.test_upper) ... ok test_eq_exception (test_SeqRecord.SeqRecordMethodsMore.test_eq_exception) ... ok test_ge_exception (test_SeqRecord.SeqRecordMethodsMore.test_ge_exception) ... ok test_gt_exception (test_SeqRecord.SeqRecordMethodsMore.test_gt_exception) ... ok test_hash_exception (test_SeqRecord.SeqRecordMethodsMore.test_hash_exception) ... ok test_le_exception (test_SeqRecord.SeqRecordMethodsMore.test_le_exception) ... ok test_lt_exception (test_SeqRecord.SeqRecordMethodsMore.test_lt_exception) ... ok test_ne_exception (test_SeqRecord.SeqRecordMethodsMore.test_ne_exception) ... ok test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_mutable_seq) ... ok test_reverse_complement_seq (test_SeqRecord.SeqRecordMethodsMore.test_reverse_complement_seq) ... ok test_translate (test_SeqRecord.SeqRecordMethodsMore.test_translate) ... ok test_defaults (test_SeqRecord.TestTranslation.test_defaults) ... ok test_new_annot (test_SeqRecord.TestTranslation.test_new_annot) ... ok test_preserve (test_SeqRecord.TestTranslation.test_preserve) ... ok Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.211 seconds 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SeqUtils.py test_SeqUtils ... ok test_GC_skew (test_SeqUtils.SeqUtilsTests.test_GC_skew) ... ok test_checksum1 (test_SeqUtils.SeqUtilsTests.test_checksum1) ... ok test_checksum2 (test_SeqUtils.SeqUtilsTests.test_checksum2) ... ok test_checksum3 (test_SeqUtils.SeqUtilsTests.test_checksum3) ... ok test_codon_adaptation_index (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 0.243 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Seq_objs.py test_Seq_objs ... ok test_eq (test_Seq_objs.ComparisonTests.test_eq) ... ok test_ge (test_Seq_objs.ComparisonTests.test_ge) ... ok test_gt (test_Seq_objs.ComparisonTests.test_gt) ... ok test_le (test_Seq_objs.ComparisonTests.test_le) ... ok test_lt (test_Seq_objs.ComparisonTests.test_lt) ... ok test_ne (test_Seq_objs.ComparisonTests.test_ne) ... ok test_unknown_seq (test_Seq_objs.FileBasedTests.test_unknown_seq) Test if feature extraction works properly for unknown sequences. ... ok test_addition (test_Seq_objs.PartialSequenceTests.test_addition) ... ok test_complement (test_Seq_objs.PartialSequenceTests.test_complement) ... ok test_getitem (test_Seq_objs.PartialSequenceTests.test_getitem) ... ok test_init (test_Seq_objs.PartialSequenceTests.test_init) ... ok test_lower_upper (test_Seq_objs.PartialSequenceTests.test_lower_upper) ... ok test_multiplication (test_Seq_objs.PartialSequenceTests.test_multiplication) ... ok test_replace (test_Seq_objs.PartialSequenceTests.test_replace) ... ok test_repr (test_Seq_objs.PartialSequenceTests.test_repr) ... ok test_transcribe (test_Seq_objs.PartialSequenceTests.test_transcribe) ... ok test_MutableSeq_extend (test_Seq_objs.StringMethodTests.test_MutableSeq_extend) Check extending a MutableSeq object. ... ok test_MutableSeq_init_error (test_Seq_objs.StringMethodTests.test_MutableSeq_init_error) Check MutableSeq __init__ raises the appropriate exceptions. ... ok test_MutableSeq_setitem (test_Seq_objs.StringMethodTests.test_MutableSeq_setitem) Check setting sequence contents of a MutableSeq object. ... ok test_Seq_init_error (test_Seq_objs.StringMethodTests.test_Seq_init_error) Check Seq __init__ raises the appropriate exceptions. ... ok test_count_overlap (test_Seq_objs.StringMethodTests.test_count_overlap) Check count_overlap exception matches python string count method. ... ok test_count_overlap_start_end_GG (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_GG) Check our count_overlap method using GG with variable ends and starts. ... ok test_count_overlap_start_end_NN (test_Seq_objs.StringMethodTests.test_count_overlap_start_end_NN) Check our count_overlap method using NN with variable ends and starts. ... ok test_equality (test_Seq_objs.StringMethodTests.test_equality) Test equality when mixing types. ... ok test_join_MutableSeq (test_Seq_objs.StringMethodTests.test_join_MutableSeq) Checks if MutableSeq join correctly concatenates sequence with the spacer. ... ok test_join_MutableSeq_TypeError_iter (test_Seq_objs.StringMethodTests.test_join_MutableSeq_TypeError_iter) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_MutableSeq_mixed (test_Seq_objs.StringMethodTests.test_join_MutableSeq_mixed) Check MutableSeq objects can be joined. ... ok test_join_MutableSeq_with_file (test_Seq_objs.StringMethodTests.test_join_MutableSeq_with_file) Checks if MutableSeq join correctly concatenates sequence from a file with the spacer. ... ok test_join_Seq (test_Seq_objs.StringMethodTests.test_join_Seq) Checks if Seq join correctly concatenates sequence with the spacer. ... ok test_join_Seq_TypeError (test_Seq_objs.StringMethodTests.test_join_Seq_TypeError) Checks that a TypeError is thrown for all non-iterable types. ... ok test_join_Seq_with_file (test_Seq_objs.StringMethodTests.test_join_Seq_with_file) Checks if Seq join correctly concatenates sequence from a file with the spacer. ... ok test_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 2.776 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SffIO.py test_SffIO ... ok test_alt_index_at_end (test_SffIO.TestAlternativeIndexes.test_alt_index_at_end) ... ok test_alt_index_at_start (test_SffIO.TestAlternativeIndexes.test_alt_index_at_start) ... ok test_alt_index_in_middle (test_SffIO.TestAlternativeIndexes.test_alt_index_in_middle) ... ok test_index_at_start (test_SffIO.TestAlternativeIndexes.test_index_at_start) ... ok test_index_in_middle (test_SffIO.TestAlternativeIndexes.test_index_in_middle) ... ok test_trim (test_SffIO.TestAlternativeIndexes.test_trim) ... ok test_index1 (test_SffIO.TestConcatenated.test_index1) ... ok test_index2 (test_SffIO.TestConcatenated.test_index2) ... ok test_parse1 (test_SffIO.TestConcatenated.test_parse1) ... ok test_parse2 (test_SffIO.TestConcatenated.test_parse2) ... ok test_parses_gzipped_stream (test_SffIO.TestConcatenated.test_parses_gzipped_stream) ... ok test_30bytes (test_SffIO.TestErrors.test_30bytes) ... ok test_31bytes (test_SffIO.TestErrors.test_31bytes) ... ok test_31bytes_bad_flowgram (test_SffIO.TestErrors.test_31bytes_bad_flowgram) ... ok test_31bytes_bad_ver (test_SffIO.TestErrors.test_31bytes_bad_ver) ... ok test_31bytes_index_header (test_SffIO.TestErrors.test_31bytes_index_header) ... ok test_bad_index_eof (test_SffIO.TestErrors.test_bad_index_eof) ... ok test_bad_index_length (test_SffIO.TestErrors.test_bad_index_length) ... ok test_bad_index_offset (test_SffIO.TestErrors.test_bad_index_offset) ... ok test_empty (test_SffIO.TestErrors.test_empty) ... ok test_index_lengths (test_SffIO.TestErrors.test_index_lengths) ... ok test_index_mft_data_size (test_SffIO.TestErrors.test_index_mft_data_size) ... ok test_index_mft_version (test_SffIO.TestErrors.test_index_mft_version) ... ok test_index_name_no_null (test_SffIO.TestErrors.test_index_name_no_null) ... ok test_no_index (test_SffIO.TestErrors.test_no_index) ... ok test_no_manifest_xml (test_SffIO.TestErrors.test_no_manifest_xml) ... ok test_premature_end_of_index (test_SffIO.TestErrors.test_premature_end_of_index) ... ok test_unknown_index (test_SffIO.TestErrors.test_unknown_index) ... ok test_both_ways (test_SffIO.TestIndex.test_both_ways) ... ok test_manifest (test_SffIO.TestIndex.test_manifest) ... ok test_index (test_SffIO.TestSelf.test_index) ... ok test_read (test_SffIO.TestSelf.test_read) ... ok test_read_wrong (test_SffIO.TestSelf.test_read_wrong) ... ok test_write (test_SffIO.TestSelf.test_write) ... ok test_coords (test_SffIO.TestUAN.test_coords) ... ok test_region (test_SffIO.TestUAN.test_region) ... ok test_time (test_SffIO.TestUAN.test_time) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.115 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_SwissProt.py test_SwissProt ... ok test_O23729 (test_SwissProt.TestSwissProt.test_O23729) Parsing SwissProt file O23729.txt. ... ok test_O95832 (test_SwissProt.TestSwissProt.test_O95832) Parsing SwissProt file O95832.txt. ... ok test_P04439 (test_SwissProt.TestSwissProt.test_P04439) Parsing SwissProt file P04439.txt. ... ok test_P0A186 (test_SwissProt.TestSwissProt.test_P0A186) Parsing SwissProt file P0A186.txt. ... ok test_P0CK95 (test_SwissProt.TestSwissProt.test_P0CK95) Parsing SwissProt file P0CK95.txt. ... ok test_P16235 (test_SwissProt.TestSwissProt.test_P16235) Parsing SwissProt file P16235.txt. ... ok test_P39896 (test_SwissProt.TestSwissProt.test_P39896) Parsing SwissProt file P39896.txt. ... ok test_P60137 (test_SwissProt.TestSwissProt.test_P60137) Parsing SwissProt file P60137.txt. ... ok test_P60904 (test_SwissProt.TestSwissProt.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P62258 (test_SwissProt.TestSwissProt.test_P62258) Parsing SwissProt file P62258. ... ok test_P68308 (test_SwissProt.TestSwissProt.test_P68308) Parsing SwissProt file P68308.txt. ... ok test_Q13454 (test_SwissProt.TestSwissProt.test_Q13454) Parsing SwissProt file Q13454.txt. ... ok test_Q13639 (test_SwissProt.TestSwissProt.test_Q13639) Parsing SwissProt file Q13639. ... ok test_Q7Z739 (test_SwissProt.TestSwissProt.test_Q7Z739) Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03. ... ok test_ft_line (test_SwissProt.TestSwissProt.test_ft_line) Parsing SwissProt file O23729, which has a new-style FT line. ... ok test_sp012 (test_SwissProt.TestSwissProt.test_sp012) Parsing SwissProt file sp012. ... ok test_sp013 (test_SwissProt.TestSwissProt.test_sp013) Parsing SwissProt file sp013. ... ok test_sp015 (test_SwissProt.TestSwissProt.test_sp015) Parsing SwissProt file sp015. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.250 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TCoffee_tool.py test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.095 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TogoWS.py test_TogoWS ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_TreeConstruction.py test_TreeConstruction ... ok test_known_matrices (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices) ... ok test_known_matrices_msa (test_TreeConstruction.DistanceCalculatorTest.test_known_matrices_msa) ... ok test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs) ... ok test_nonmatching_seqs_msa (test_TreeConstruction.DistanceCalculatorTest.test_nonmatching_seqs_msa) ... ok test_bad_construction (test_TreeConstruction.DistanceMatrixTest.test_bad_construction) ... ok test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest.test_bad_manipulation) ... ok test_format_phylip (test_TreeConstruction.DistanceMatrixTest.test_format_phylip) ... ok test_good_construction (test_TreeConstruction.DistanceMatrixTest.test_good_construction) ... ok test_good_manipulation (test_TreeConstruction.DistanceMatrixTest.test_good_manipulation) ... ok test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree) ... ok test_built_tree_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_built_tree_msa) ... ok test_nj (test_TreeConstruction.DistanceTreeConstructorTest.test_nj) ... ok test_nj_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_nj_msa) ... ok test_upgma (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma) ... ok test_upgma_msa (test_TreeConstruction.DistanceTreeConstructorTest.test_upgma_msa) ... ok test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest.test_get_neighbors) ... ok test_get_score (test_TreeConstruction.ParsimonyScorerTest.test_get_score) ... ok test_get_score_msa (test_TreeConstruction.ParsimonyScorerTest.test_get_score_msa) ... ok test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree) ... ok test_build_tree_msa (test_TreeConstruction.ParsimonyTreeConstructorTest.test_build_tree_msa) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.752 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_UniGene.py test_UniGene ... ok test_parse (test_UniGene.TestUniGene.test_parse) ... ok test_read (test_UniGene.TestUniGene.test_read) ... ok test_read_value_error (test_UniGene.TestUniGene.test_read_value_error) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.033 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.027 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_Uniprot.py test_Uniprot ... ok test_F2CXE6 (test_Uniprot.TestUniprot.test_F2CXE6) Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok test_H2CNN8 (test_Uniprot.TestUniprot.test_H2CNN8) Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok test_P60904 (test_Uniprot.TestUniprot.test_P60904) Parsing SwissProt file P60904.txt. ... ok test_P84001 (test_Uniprot.TestUniprot.test_P84001) Parse mass spec structured comment with unknown loc. ... ok test_Q13639 (test_Uniprot.TestUniprot.test_Q13639) Compare SwissProt text and uniprot XML versions of Q13639. ... ok test_multi_ex (test_Uniprot.TestUniprot.test_multi_ex) Compare SwissProt text and uniprot XML versions of several examples. ... ok test_multi_ex_index (test_Uniprot.TestUniprot.test_multi_ex_index) Index SwissProt text and uniprot XML versions of several examples. ... ok test_sp016 (test_Uniprot.TestUniprot.test_sp016) Parsing SwissProt file sp016. ... ok test_submittedName_allowed (test_Uniprot.TestUniprot.test_submittedName_allowed) Checks if parser supports new XML Element (submittedName). ... ok test_uni001 (test_Uniprot.TestUniprot.test_uni001) Parsing Uniprot file uni001. ... ok test_uni003 (test_Uniprot.TestUniprot.test_uni003) Parsing Uniprot file uni003. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.270 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.016 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_XXmotif_tool.py test_XXmotif_tool ... skipping. Install XXmotif if you want to use XXmotif from Biopython. ---------------------------------------------------------------------- Ran 1 test in 0.096 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.144 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.544 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.009 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_codonalign.py test_codonalign ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/Seq.py:2779: 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-1.81-4.fc39.s390x/usr/lib64/python3.12/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-1.81-4.fc39.s390x/usr/lib64/python3.12/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 6.783 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_geo.py test_geo ... ok test_GSE16 (test_geo.TestGeo.test_GSE16) ... ok test_GSM645 (test_geo.TestGeo.test_GSM645) ... ok test_GSM691 (test_geo.TestGeo.test_GSM691) ... ok test_GSM700 (test_geo.TestGeo.test_GSM700) ... ok test_GSM804 (test_geo.TestGeo.test_GSM804) ... ok test_record_str (test_geo.TestGeo.test_record_str) ... ok test_soft_ex_affy (test_geo.TestGeo.test_soft_ex_affy) ... ok test_soft_ex_affy_chp (test_geo.TestGeo.test_soft_ex_affy_chp) ... ok test_soft_ex_dual (test_geo.TestGeo.test_soft_ex_dual) ... ok test_soft_ex_family (test_geo.TestGeo.test_soft_ex_family) ... ok test_soft_ex_platform (test_geo.TestGeo.test_soft_ex_platform) ... ok test_soft_ex_series (test_geo.TestGeo.test_soft_ex_series) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_kNN.py test_kNN ... ok test_calculate_model (test_kNN.TestKNN.test_calculate_model) ... ok test_calculate_probability (test_kNN.TestKNN.test_calculate_probability) ... ok test_classify (test_kNN.TestKNN.test_classify) ... ok test_leave_one_out (test_kNN.TestKNN.test_leave_one_out) ... ok test_model_accuracy (test_kNN.TestKNN.test_model_accuracy) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.013 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf.py test_mmtf ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.077 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_mmtf_online.py test_mmtf_online ... skipping. Error: Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python) ---------------------------------------------------------------------- Ran 1 test in 0.075 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs.py test_motifs ... ok test_calculate_pseudocounts (test_motifs.MotifTestPWM.test_calculate_pseudocounts) ... ok test_getitem (test_motifs.MotifTestPWM.test_getitem) ... ok test_simple (test_motifs.MotifTestPWM.test_simple) Test if Bio.motifs PWM scoring works. ... ok test_with_bad_char (test_motifs.MotifTestPWM.test_with_bad_char) Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok test_with_mixed_case (test_motifs.MotifTestPWM.test_with_mixed_case) Test if Bio.motifs PWM scoring works with mixed case. ... ok test_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 Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] Operating system: posix linux ---------------------------------------------------------------------- Ran 1 test in 0.138 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_motifs_online.py test_motifs_online ... skipping. internet not available ---------------------------------------------------------------------- Ran 1 test in 0.061 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2.py test_pairwise2 ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.123 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise2_no_C.py test_pairwise2_no_C ... /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( ok test_alignments_can_be_pickled (pairwise2_testCases.TestOtherFunctions.test_alignments_can_be_pickled) ... ok test_clean_alignments (pairwise2_testCases.TestOtherFunctions.test_clean_alignments) ``_clean_alignments`` removes redundant and wrong alignments. ... ok test_print_matrix (pairwise2_testCases.TestOtherFunctions.test_print_matrix) ``print_matrix`` prints nested lists as nice matrices. ... ok test_recover_alignments (pairwise2_testCases.TestOtherFunctions.test_recover_alignments) One possible start position in local alignment is not a match. ... ok test_function_name (pairwise2_testCases.TestPairwiseErrorConditions.test_function_name) Test for wrong function names. ... ok test_function_parameters (pairwise2_testCases.TestPairwiseErrorConditions.test_function_parameters) Test for number of parameters. ... ok test_param_names (pairwise2_testCases.TestPairwiseErrorConditions.test_param_names) Test for unknown parameter in parameter names. ... ok test_warnings (pairwise2_testCases.TestPairwiseErrorConditions.test_warnings) Test for warnings. ... ok test_extend_penalty1 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty1) Test 1. ... ok test_extend_penalty2 (pairwise2_testCases.TestPairwiseExtendPenalty.test_extend_penalty2) Test 2. ... ok test_globalxx_simple (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple) Test globalxx. ... ok test_globalxx_simple2 (pairwise2_testCases.TestPairwiseGlobal.test_globalxx_simple2) Do the same test with sequence order reversed. ... ok test_list_input (pairwise2_testCases.TestPairwiseGlobal.test_list_input) Do a global alignment with sequences supplied as lists. ... ok test_one_alignment_only (pairwise2_testCases.TestPairwiseGlobal.test_one_alignment_only) Test one_alignment_only parameter. ... ok test_keywords (pairwise2_testCases.TestPairwiseKeywordUsage.test_keywords) Test equality of calls with and without keywords. ... ok test_blosum62 (pairwise2_testCases.TestPairwiseLocal.test_blosum62) Test localds with blosum62. ... ok test_empty_result (pairwise2_testCases.TestPairwiseLocal.test_empty_result) Return no alignment. ... ok test_localds_zero_score_segments_symmetric (pairwise2_testCases.TestPairwiseLocal.test_localds_zero_score_segments_symmetric) Test if alignment is independent on direction of sequence. ... ok test_localms (pairwise2_testCases.TestPairwiseLocal.test_localms) Two different local alignments. ... ok test_localxs_1 (pairwise2_testCases.TestPairwiseLocal.test_localxs_1) Test localxx. ... ok test_localxs_2 (pairwise2_testCases.TestPairwiseLocal.test_localxs_2) Test localxx with ``full_sequences=True``. ... ok test_localxs_generic (pairwise2_testCases.TestPairwiseLocal.test_localxs_generic) Test the generic method with local alignments. ... ok test_match_dictionary1 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary1) Test 1. ... ok test_match_dictionary2 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary2) Test 2. ... ok test_match_dictionary3 (pairwise2_testCases.TestPairwiseMatchDictionary.test_match_dictionary3) Test 3. ... ok test_align_one_char1 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char1) Test sequence with only one match. ... ok test_align_one_char2 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char2) Test sequences with two possible match positions. ... ok test_align_one_char3 (pairwise2_testCases.TestPairwiseOneCharacter.test_align_one_char3) Like test 1, but global alignment. ... ok test_match_score_open_penalty1 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty1) Test 1. ... ok test_match_score_open_penalty2 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty2) Test 2. ... ok test_match_score_open_penalty3 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty3) Test 3. ... ok test_match_score_open_penalty4 (pairwise2_testCases.TestPairwiseOpenPenalty.test_match_score_open_penalty4) Test 4. ... ok test_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps) Turn off end-gap penalties. ... ok test_penalize_end_gaps2 (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_penalize_end_gaps2) Do the same, but use the generic method (with the same result). ... ok test_separate_penalize_end_gaps (pairwise2_testCases.TestPairwisePenalizeEndgaps.test_separate_penalize_end_gaps) Test alignment where end-gaps are differently penalized. ... ok test_penalize_extend_when_opening (pairwise2_testCases.TestPairwisePenalizeExtendWhenOpening.test_penalize_extend_when_opening) Add gap-extend penalty to gap-opening penalty. ... ok test_separate_gap_penalties1 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties1) Test 1. ... ok test_separate_gap_penalties2 (pairwise2_testCases.TestPairwiseSeparateGapPenalties.test_separate_gap_penalties2) Test 2. ... ok test_separate_gap_penalties_with_extension (pairwise2_testCases.TestPairwiseSeparateGapPenaltiesWithExtension.test_separate_gap_penalties_with_extension) Test separate gap-extension penalties and list input. ... ok test_gap_here_only_1 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_1) Open a gap in second sequence only. ... ok test_gap_here_only_2 (pairwise2_testCases.TestPersiteGapPenalties.test_gap_here_only_2) Force a bad alignment. ... ok test_score_only_global (pairwise2_testCases.TestScoreOnly.test_score_only_global) Test ``score_only`` in a global alignment. ... ok test_score_only_local (pairwise2_testCases.TestScoreOnly.test_score_only_local) Test ``score_only`` in a local alignment. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.113 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_pairwise_alignment_map.py test_pairwise_alignment_map ... ok test1 (test_pairwise_alignment_map.TestComplex.test1) ... ok test2 (test_pairwise_alignment_map.TestComplex.test2) ... ok test_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 0.092 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype.py test_phenotype ... ok test_CsvIterator (test_phenotype.TestPhenoMicro.test_CsvIterator) Test basic functionalities of CsvIterator file parser. ... ok test_JsonIterator (test_phenotype.TestPhenoMicro.test_JsonIterator) Test basic functionalities of JsonIterator file parser. ... ok test_PlateRecord (test_phenotype.TestPhenoMicro.test_PlateRecord) Test basic functionalities of PlateRecord objects. ... ok test_PlateRecord_errors (test_phenotype.TestPhenoMicro.test_PlateRecord_errors) Test bad arguments with PlateRecord objects. ... ok test_WellRecord (test_phenotype.TestPhenoMicro.test_WellRecord) Test basic functionalities of WellRecord objects. ... ok test_bad_fit_args (test_phenotype.TestPhenoMicro.test_bad_fit_args) Test error handling of the fit method. ... ok test_phenotype_IO (test_phenotype.TestPhenoMicro.test_phenotype_IO) Test basic functionalities of phenotype IO methods. ... ok test_phenotype_IO_errors (test_phenotype.TestPhenoMicro.test_phenotype_IO_errors) Test bad arguments to phenotype IO methods. ... ok ---------------------------------------------------------------------- Ran 1 test in 8.339 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phenotype_fit.py test_phenotype_fit ... skipping. Install SciPy if you want to use Bio.phenotype fit functionality. ---------------------------------------------------------------------- Ran 1 test in 0.007 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_phyml_tool.py test_phyml_tool ... skipping. Couldn't find the PhyML software. Install PhyML 3.0 or later if you want to use the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.147 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 0.015 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_prosite.py test_prosite ... ok test_read1 (test_prosite.TestPrositeRead.test_read1) Parsing Prosite record ps00107.txt. ... ok test_read2 (test_prosite.TestPrositeRead.test_read2) Parsing Prosite record ps00159.txt. ... ok test_read3 (test_prosite.TestPrositeRead.test_read3) Parsing Prosite record ps00165.txt. ... ok test_read4 (test_prosite.TestPrositeRead.test_read4) Parsing Prosite record ps00432.txt. ... ok test_read5 (test_prosite.TestPrositeRead.test_read5) Parsing Prosite record ps00488.txt. ... ok test_read6 (test_prosite.TestPrositeRead.test_read6) Parsing Prosite record ps00546.txt. ... ok ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_raxml_tool.py test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper. ---------------------------------------------------------------------- Ran 1 test in 0.121 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_samtools_tool.py test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program if you want to use it from Biopython ---------------------------------------------------------------------- Ran 1 test in 0.016 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/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 ---------------------------------------------------------------------- Ran 1 test in 0.102 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] 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-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + PYTHONPATH=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/lib64/python3.12/site-packages + /usr/bin/python3 run_tests.py --offline -v test_translate.py test_translate ... ok test_ambiguous (test_translate.TestTranscriptionTranslation.test_ambiguous) ... ok test_dna_rna_translation (test_translate.TestTranscriptionTranslation.test_dna_rna_translation) ... ok test_transcription (test_translate.TestTranscriptionTranslation.test_transcription) ... ok test_translation (test_translate.TestTranscriptionTranslation.test_translation) ... ok ---------------------------------------------------------------------- Ran 1 test in 0.090 seconds Skipping any tests requiring internet access Python version: 3.12.0b4 (main, Jul 21 2023, 00:00:00) [GCC 13.1.1 20230614 (Red Hat 13.1.1-4)] Operating system: posix linux + popd ~/build/BUILD/python-biopython-1.81 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: python3-biopython-1.81-4.fc39.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2nMihr + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.81 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/Scripts /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/CONTRIB.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/DEPRECATED.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/NEWS.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/README.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.H3abGW + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.81 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python3-biopython + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python3-biopython + cp -pr /builddir/build/BUILD/python-biopython-1.81/python3/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python3-biopython + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython = 1.81-4.fc39 python3-biopython = 1.81-4.fc39 python3-biopython(s390-64) = 1.81-4.fc39 python3.12-biopython = 1.81-4.fc39 python3.12dist(biopython) = 1.81 python3dist(biopython) = 1.81 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_2.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) python(abi) = 3.12 python3.12dist(numpy) rtld(GNU_HASH) Processing files: python-biopython-doc-1.81-4.fc39.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.GkenbU + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.81 + DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python-biopython-doc + cp -pr /builddir/build/BUILD/python-biopython-1.81/biopython-1.81/Doc /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/doc/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Qj9btw + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.81 + LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python-biopython-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python-biopython-doc + cp -pr /builddir/build/BUILD/python-biopython-1.81/biopython-1.81/LICENSE.rst /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x/usr/share/licenses/python-biopython-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-biopython-doc = 1.81-4.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-biopython-debugsource-1.81-4.fc39.s390x Provides: python-biopython-debugsource = 1.81-4.fc39 python-biopython-debugsource(s390-64) = 1.81-4.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-biopython-debuginfo-1.81-4.fc39.s390x Provides: debuginfo(build-id) = 0a397a82a1973f82a2ca8f5b954e936d6082a8c3 debuginfo(build-id) = 0eb586080d9bc25ea5d0250040cdc2e946f5ea64 debuginfo(build-id) = 3c6a8057303f4a8a892fd5ab355e30708413d519 debuginfo(build-id) = 6a9881e6d67c231902493d28135f17166a119e72 debuginfo(build-id) = 73052bdb6baa757753ef54e9ec1e85b22077cc8a debuginfo(build-id) = 8c86c7908339b2cebfea1f923957861e689a4aa7 debuginfo(build-id) = a6db60b8c28b6afbd1de113a4c26b1c52e4a83a2 debuginfo(build-id) = ec2d8d5b5d2499e999da35944c1ce15c9479e7f7 debuginfo(build-id) = fb1a92f5430dae1f3d36d30ff6f4e7b8234d3910 python-biopython-debuginfo = 1.81-4.fc39 python3-biopython-debuginfo = 1.81-4.fc39 python3-biopython-debuginfo(s390-64) = 1.81-4.fc39 python3.12-biopython-debuginfo = 1.81-4.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-biopython-debugsource(s390-64) = 1.81-4.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x Wrote: /builddir/build/RPMS/python-biopython-doc-1.81-4.fc39.noarch.rpm Wrote: /builddir/build/RPMS/python3-biopython-debuginfo-1.81-4.fc39.s390x.rpm Wrote: /builddir/build/RPMS/python-biopython-debugsource-1.81-4.fc39.s390x.rpm Wrote: /builddir/build/RPMS/python3-biopython-1.81-4.fc39.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ujPpY8 + umask 022 + cd /builddir/build/BUILD + cd python-biopython-1.81 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.81-4.fc39.s390x + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.D3rnIC + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/python-biopython-1.81-SPECPARTS + rm -rf python-biopython-1.81 python-biopython-1.81.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild python-biopython-1.81-4.fc39.src.rpm Finish: build phase for python-biopython-1.81-4.fc39.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-s390x-1691114939.268004/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-biopython-1.81-4.fc39.src.rpm) Config(child) 4 minutes 18 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool