0s autopkgtest [06:26:56]: starting date and time: 2026-02-07 06:26:56+0000 0s autopkgtest [06:26:56]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:26:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nbs223le/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade pyensembl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.1-0.1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-s390x-30.secgroup --name adt-resolute-s390x-pyensembl-20260207-062656-juju-7f2275-prod-proposed-migration-environment-2-312e57b3-8a84-4d4e-b867-ab5a1f84a344 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-pyensembl-20260207-062656-juju-7f2275-prod-proposed-migration-environment-2-312e57b3-8a84-4d4e-b867-ab5a1f84a344 from image adt/ubuntu-resolute-s390x-server-20260206.img (UUID 49c0a1d9-89cb-4112-bb14-7a2a39e81cac)... 209s autopkgtest [06:30:25]: testbed dpkg architecture: s390x 210s autopkgtest [06:30:26]: testbed apt version: 3.1.15 212s autopkgtest [06:30:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 212s autopkgtest [06:30:28]: testbed release detected to be: None 217s autopkgtest [06:30:33]: updating testbed package index (apt update) 219s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 219s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 219s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 219s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 219s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [204 kB] 219s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [10.7 kB] 220s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [36.7 kB] 220s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1651 kB] 220s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [243 kB] 220s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1442 kB] 220s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [10.2 kB] 224s Fetched 3721 kB in 5s (681 kB/s) 232s Reading package lists... 237s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 237s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 237s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 237s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 246s Reading package lists... 247s Reading package lists... 248s Building dependency tree... 249s Reading state information... 250s Calculating upgrade... 251s The following packages will be upgraded: 251s python3-pkg-resources python3-setuptools 252s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 252s Need to get 805 kB of archives. 252s After this operation, 0 B of additional disk space will be used. 252s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 253s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-setuptools all 78.1.1-0.1build1 [661 kB] 263s dpkg-preconfigure: unable to re-open stdin: No such file or directory 263s Fetched 805 kB in 1s (591 kB/s) 270s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61954 files and directories currently installed.) 270s Preparing to unpack .../python3-pkg-resources_78.1.1-0.1build1_all.deb ... 272s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 281s Preparing to unpack .../python3-setuptools_78.1.1-0.1build1_all.deb ... 283s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 290s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 297s Setting up python3-setuptools (78.1.1-0.1build1) ... 309s autopkgtest [06:32:05]: upgrading testbed (apt dist-upgrade and autopurge) 309s Reading package lists... 312s Building dependency tree... 312s Reading state information... 314s Calculating upgrade... 315s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 316s Reading package lists... 319s Building dependency tree... 319s Reading state information... 320s Solving dependencies... 321s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 334s autopkgtest [06:32:30]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 334s autopkgtest [06:32:30]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 345s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 345s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 345s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 351s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 351s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 351s gpgv: issuer "tchet@debian.org" 351s gpgv: Can't check signature: No public key 351s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 353s autopkgtest [06:32:49]: testing package pyensembl version 2.3.13-2 355s autopkgtest [06:32:51]: build not needed 356s autopkgtest [06:32:52]: test run-unit-test: preparing testbed 358s Reading package lists... 360s Building dependency tree... 360s Reading state information... 361s Solving dependencies... 362s The following NEW packages will be installed: 362s libblas3 libgfortran5 liblapack3 libpython3.14-minimal libpython3.14-stdlib 362s pyensembl pylint python3-all python3-astroid python3-datacache python3-dill 362s python3-gtfparse python3-iniconfig python3-isort python3-logilab-common 362s python3-mccabe python3-memoized-property python3-mypy-extensions 362s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 362s python3-platformdirs python3-pluggy python3-pytest python3-pytz 362s python3-serializable python3-tomlkit python3-typechecks python3.14 362s python3.14-minimal 363s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 363s Need to get 27.7 MB of archives. 363s After this operation, 139 MB of additional disk space will be used. 363s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 363s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 364s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-12ubuntu1 [629 kB] 364s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 364s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 365s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 365s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 365s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 365s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-astroid all 4.0.2-1ubuntu1 [172 kB] 365s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-isort all 7.0.0-1 [59.7 kB] 365s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mypy-extensions all 1.1.0-1 [6716 B] 365s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-logilab-common all 2.1.0-1build1 [95.9 kB] 365s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-dill all 0.4.0-1 [84.8 kB] 365s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mccabe all 0.7.0-1build1 [8926 B] 365s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x python3-platformdirs all 4.5.1-1 [17.1 kB] 365s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tomlkit all 0.13.3-2 [39.1 kB] 365s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x pylint all 4.0.4-1 [346 kB] 365s Get:18 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytz all 2025.2-5 [32.4 kB] 365s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-3 [7599 kB] 366s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-3 [2948 kB] 366s Get:21 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-typechecks all 0.1.0+ds-4 [4562 B] 366s Get:22 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-datacache all 1.4.1-2 [13.1 kB] 366s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 366s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-memoized-property all 1.0.3-2build1 [5328 B] 366s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-serializable all 0.4.1+ds-2 [8438 B] 366s Get:26 http://ftpmaster.internal/ubuntu resolute/universe s390x pyensembl all 2.3.13-2 [37.2 kB] 366s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 366s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.9-3 [890 B] 366s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 366s Get:30 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 366s Get:31 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 372s Fetched 27.7 MB in 4s (6939 kB/s) 373s Selecting previously unselected package python3-numpy-dev:s390x. 373s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61954 files and directories currently installed.) 373s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 373s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 374s Selecting previously unselected package libblas3:s390x. 374s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_s390x.deb ... 374s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 374s Selecting previously unselected package libgfortran5:s390x. 375s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_s390x.deb ... 375s Unpacking libgfortran5:s390x (15.2.0-12ubuntu1) ... 376s Selecting previously unselected package liblapack3:s390x. 376s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 376s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 378s Selecting previously unselected package python3-numpy. 378s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 379s Unpacking python3-numpy (1:2.3.5+ds-3) ... 383s Selecting previously unselected package libpython3.14-minimal:s390x. 383s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_s390x.deb ... 383s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 386s Selecting previously unselected package python3.14-minimal. 386s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_s390x.deb ... 386s Unpacking python3.14-minimal (3.14.2-1) ... 387s Selecting previously unselected package libpython3.14-stdlib:s390x. 387s Preparing to unpack .../07-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 387s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 389s Selecting previously unselected package python3-astroid. 389s Preparing to unpack .../08-python3-astroid_4.0.2-1ubuntu1_all.deb ... 389s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 390s Selecting previously unselected package python3-isort. 390s Preparing to unpack .../09-python3-isort_7.0.0-1_all.deb ... 390s Unpacking python3-isort (7.0.0-1) ... 391s Selecting previously unselected package python3-mypy-extensions. 391s Preparing to unpack .../10-python3-mypy-extensions_1.1.0-1_all.deb ... 391s Unpacking python3-mypy-extensions (1.1.0-1) ... 391s Selecting previously unselected package python3-logilab-common. 391s Preparing to unpack .../11-python3-logilab-common_2.1.0-1build1_all.deb ... 391s Unpacking python3-logilab-common (2.1.0-1build1) ... 393s Selecting previously unselected package python3-dill. 393s Preparing to unpack .../12-python3-dill_0.4.0-1_all.deb ... 393s Unpacking python3-dill (0.4.0-1) ... 393s Selecting previously unselected package python3-mccabe. 393s Preparing to unpack .../13-python3-mccabe_0.7.0-1build1_all.deb ... 393s Unpacking python3-mccabe (0.7.0-1build1) ... 394s Selecting previously unselected package python3-platformdirs. 394s Preparing to unpack .../14-python3-platformdirs_4.5.1-1_all.deb ... 394s Unpacking python3-platformdirs (4.5.1-1) ... 394s Selecting previously unselected package python3-tomlkit. 395s Preparing to unpack .../15-python3-tomlkit_0.13.3-2_all.deb ... 395s Unpacking python3-tomlkit (0.13.3-2) ... 395s Selecting previously unselected package pylint. 395s Preparing to unpack .../16-pylint_4.0.4-1_all.deb ... 395s Unpacking pylint (4.0.4-1) ... 396s Selecting previously unselected package python3-pytz. 397s Preparing to unpack .../17-python3-pytz_2025.2-5_all.deb ... 397s Unpacking python3-pytz (2025.2-5) ... 398s Selecting previously unselected package python3-pandas-lib:s390x. 398s Preparing to unpack .../18-python3-pandas-lib_2.3.3+dfsg-3_s390x.deb ... 398s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 402s Selecting previously unselected package python3-pandas. 402s Preparing to unpack .../19-python3-pandas_2.3.3+dfsg-3_all.deb ... 402s Unpacking python3-pandas (2.3.3+dfsg-3) ... 404s Selecting previously unselected package python3-typechecks. 404s Preparing to unpack .../20-python3-typechecks_0.1.0+ds-4_all.deb ... 404s Unpacking python3-typechecks (0.1.0+ds-4) ... 404s Selecting previously unselected package python3-datacache. 404s Preparing to unpack .../21-python3-datacache_1.4.1-2_all.deb ... 404s Unpacking python3-datacache (1.4.1-2) ... 404s Selecting previously unselected package python3-gtfparse. 404s Preparing to unpack .../22-python3-gtfparse_1.3.0+ds-2_all.deb ... 404s Unpacking python3-gtfparse (1.3.0+ds-2) ... 405s Selecting previously unselected package python3-memoized-property. 405s Preparing to unpack .../23-python3-memoized-property_1.0.3-2build1_all.deb ... 405s Unpacking python3-memoized-property (1.0.3-2build1) ... 405s Selecting previously unselected package python3-serializable. 405s Preparing to unpack .../24-python3-serializable_0.4.1+ds-2_all.deb ... 405s Unpacking python3-serializable (0.4.1+ds-2) ... 405s Selecting previously unselected package pyensembl. 405s Preparing to unpack .../25-pyensembl_2.3.13-2_all.deb ... 405s Unpacking pyensembl (2.3.13-2) ... 405s Selecting previously unselected package python3.14. 405s Preparing to unpack .../26-python3.14_3.14.2-1_s390x.deb ... 405s Unpacking python3.14 (3.14.2-1) ... 407s Selecting previously unselected package python3-all. 407s Preparing to unpack .../27-python3-all_3.13.9-3_s390x.deb ... 407s Unpacking python3-all (3.13.9-3) ... 407s Selecting previously unselected package python3-iniconfig. 407s Preparing to unpack .../28-python3-iniconfig_2.1.0-2_all.deb ... 407s Unpacking python3-iniconfig (2.1.0-2) ... 407s Selecting previously unselected package python3-pluggy. 407s Preparing to unpack .../29-python3-pluggy_1.6.0-2_all.deb ... 407s Unpacking python3-pluggy (1.6.0-2) ... 407s Selecting previously unselected package python3-pytest. 407s Preparing to unpack .../30-python3-pytest_9.0.2-2_all.deb ... 407s Unpacking python3-pytest (9.0.2-2) ... 409s Setting up python3-iniconfig (2.1.0-2) ... 413s Setting up python3-typechecks (0.1.0+ds-4) ... 415s Setting up python3-memoized-property (1.0.3-2build1) ... 417s Setting up python3-mypy-extensions (1.1.0-1) ... 419s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 419s Setting up python3-pytz (2025.2-5) ... 422s Setting up python3-serializable (0.4.1+ds-2) ... 425s Setting up python3-platformdirs (4.5.1-1) ... 427s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 428s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 428s Setting up python3-dill (0.4.0-1) ... 430s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 430s Setting up libgfortran5:s390x (15.2.0-12ubuntu1) ... 430s Setting up python3-isort (7.0.0-1) ... 434s Setting up python3-pluggy (1.6.0-2) ... 436s Setting up python3-astroid (4.0.2-1ubuntu1) ... 444s Setting up python3-mccabe (0.7.0-1build1) ... 445s Setting up python3-tomlkit (0.13.3-2) ... 448s Setting up python3.14-minimal (3.14.2-1) ... 458s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 458s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 458s Setting up python3-logilab-common (2.1.0-1build1) ... 461s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 461s Setting up python3-pytest (9.0.2-2) ... 467s Setting up python3-numpy (1:2.3.5+ds-3) ... 504s Setting up python3.14 (3.14.2-1) ... 514s Setting up pylint (4.0.4-1) ... 523s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 523s Setting up python3-all (3.13.9-3) ... 523s Setting up python3-pandas (2.3.3+dfsg-3) ... 619s Setting up python3-datacache (1.4.1-2) ... 622s Setting up python3-gtfparse (1.3.0+ds-2) ... 623s Setting up pyensembl (2.3.13-2) ... 626s Processing triggers for systemd (259-1ubuntu3) ... 626s Processing triggers for man-db (2.13.1-1) ... 660s Processing triggers for libc-bin (2.42-2ubuntu4) ... 667s autopkgtest [06:38:03]: test run-unit-test: [----------------------- 715s ============================= test session starts ============================== 715s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 715s rootdir: /tmp/autopkgtest.IARefs/autopkgtest_tmp 715s plugins: typeguard-4.4.4 715s collected 14 items / 1 error 715s 715s ==================================== ERRORS ==================================== 715s _____________________ ERROR collecting tests/test_shell.py _____________________ 715s tests/test_shell.py:1: in 715s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 715s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 715s release_group = root_group.add_argument_group() 715s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 715s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 715s raise ValueError('argument groups cannot be nested') 715s E ValueError: argument groups cannot be nested 715s =============================== warnings summary =============================== 715s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 715s /usr/lib/python3/dist-packages/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 715s import pkg_resources 715s 715s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 715s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 715s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 715s declare_namespace(pkg) 715s 715s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 715s =========================== short test summary info ============================ 715s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 715s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 715s ======================== 2 warnings, 1 error in 35.36s ========================= 716s autopkgtest [06:38:52]: test run-unit-test: -----------------------] 718s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 718s autopkgtest [06:38:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 719s autopkgtest [06:38:55]: test pybuild-autopkgtest: preparing testbed 749s Creating nova instance adt-resolute-s390x-pyensembl-20260207-062656-juju-7f2275-prod-proposed-migration-environment-2-312e57b3-8a84-4d4e-b867-ab5a1f84a344 from image adt/ubuntu-resolute-s390x-server-20260206.img (UUID 49c0a1d9-89cb-4112-bb14-7a2a39e81cac)... 850s autopkgtest [06:41:06]: testbed dpkg architecture: s390x 850s autopkgtest [06:41:06]: testbed apt version: 3.1.15 851s autopkgtest [06:41:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 851s autopkgtest [06:41:07]: testbed release detected to be: resolute 852s autopkgtest [06:41:08]: updating testbed package index (apt update) 853s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 853s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 853s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 853s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 853s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1651 kB] 854s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [10.7 kB] 854s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [36.7 kB] 854s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [204 kB] 854s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [243 kB] 854s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1442 kB] 854s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [10.2 kB] 857s Fetched 3721 kB in 4s (968 kB/s) 861s Reading package lists... 862s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 862s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 862s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 862s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 868s Reading package lists... 869s Reading package lists... 870s Building dependency tree... 870s Reading state information... 871s Calculating upgrade... 872s The following packages will be upgraded: 872s python3-pkg-resources python3-setuptools 873s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 873s Need to get 805 kB of archives. 873s After this operation, 0 B of additional disk space will be used. 873s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 873s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-setuptools all 78.1.1-0.1build1 [661 kB] 876s dpkg-preconfigure: unable to re-open stdin: No such file or directory 876s Fetched 805 kB in 1s (1050 kB/s) 884s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61954 files and directories currently installed.) 884s Preparing to unpack .../python3-pkg-resources_78.1.1-0.1build1_all.deb ... 886s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 887s Preparing to unpack .../python3-setuptools_78.1.1-0.1build1_all.deb ... 890s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 894s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 897s Setting up python3-setuptools (78.1.1-0.1build1) ... 904s autopkgtest [06:42:00]: upgrading testbed (apt dist-upgrade and autopurge) 905s Reading package lists... 907s Building dependency tree... 907s Reading state information... 907s Calculating upgrade... 908s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 909s Reading package lists... 911s Building dependency tree... 911s Reading state information... 911s Solving dependencies... 912s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 921s Reading package lists... 922s Building dependency tree... 922s Reading state information... 923s Solving dependencies... 924s The following NEW packages will be installed: 924s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 924s cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf 924s dh-python dh-strip-nondeterminism dwz g++ g++-15 g++-15-s390x-linux-gnu 924s g++-s390x-linux-gnu gcc gcc-15 gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu 924s gettext intltool-debian libarchive-zip-perl libasan8 libblas3 libc-dev-bin 924s libc6-dev libcc1-0 libcrypt-dev libdebhelper-perl 924s libfile-stripnondeterminism-perl libgcc-15-dev libgfortran5 libgomp1 924s libisl23 libitm1 liblapack3 liblsan0 libmpc3 libpython3.14-minimal 924s libpython3.14-stdlib libstdc++-15-dev libtool libtsan2 libubsan1 924s linux-libc-dev m4 po-debconf pybuild-plugin-autopkgtest pyensembl pylint 924s python3-all python3-astroid python3-datacache python3-dill python3-gtfparse 924s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 924s python3-memoized-property python3-mypy-extensions python3-numpy 924s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 924s python3-pluggy python3-pytest python3-pytz python3-serializable 924s python3-tomlkit python3-typechecks python3.14 python3.14-minimal 924s rpcsvc-proto 924s 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 924s Need to get 91.8 MB of archives. 924s After this operation, 352 MB of additional disk space will be used. 924s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 924s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 924s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-12ubuntu1 [629 kB] 925s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 925s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 925s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 925s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 925s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 925s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 925s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1build1 [43.4 kB] 925s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.18.1-3build1 [582 kB] 925s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.2-1 [620 kB] 925s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libc-dev-bin s390x 2.42-2ubuntu4 [22.9 kB] 925s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x linux-libc-dev s390x 6.18.0-9.9 [1854 kB] 926s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libcrypt-dev s390x 1:4.5.1-1 [127 kB] 926s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x rpcsvc-proto s390x 1.4.3-1build1 [67.1 kB] 926s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libc6-dev s390x 2.42-2ubuntu4 [1696 kB] 926s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 926s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 926s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [10.2 MB] 926s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-12ubuntu1 [1028 B] 926s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 926s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 926s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-12ubuntu1 [50.0 kB] 926s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-12ubuntu1 [154 kB] 926s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-12ubuntu1 [30.9 kB] 926s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-12ubuntu1 [2968 kB] 926s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x liblsan0 s390x 15.2.0-12ubuntu1 [1354 kB] 926s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libtsan2 s390x 15.2.0-12ubuntu1 [2685 kB] 926s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-12ubuntu1 [1211 kB] 927s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-12ubuntu1 [1294 kB] 927s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [19.9 MB] 927s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-12ubuntu1 [519 kB] 927s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 927s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 927s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-12ubuntu1 [2660 kB] 928s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [11.7 MB] 928s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-12ubuntu1 [25.3 kB] 928s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 928s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 928s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu2 [5258 B] 928s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 928s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-9 [169 kB] 928s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21+nmu1 [11.9 kB] 928s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 928s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 928s Get:47 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 928s Get:48 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3build1 [52.7 kB] 928s Get:49 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2build1 [121 kB] 928s Get:50 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.2-1 [1062 kB] 928s Get:51 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 928s Get:52 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.22 [215 kB] 928s Get:53 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.28ubuntu1 [916 kB] 928s Get:54 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 7.20260125 [122 kB] 928s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 928s Get:56 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 929s Get:57 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-astroid all 4.0.2-1ubuntu1 [172 kB] 929s Get:58 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-isort all 7.0.0-1 [59.7 kB] 929s Get:59 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mypy-extensions all 1.1.0-1 [6716 B] 929s Get:60 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-logilab-common all 2.1.0-1build1 [95.9 kB] 929s Get:61 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-dill all 0.4.0-1 [84.8 kB] 929s Get:62 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mccabe all 0.7.0-1build1 [8926 B] 929s Get:63 http://ftpmaster.internal/ubuntu resolute/main s390x python3-platformdirs all 4.5.1-1 [17.1 kB] 929s Get:64 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tomlkit all 0.13.3-2 [39.1 kB] 929s Get:65 http://ftpmaster.internal/ubuntu resolute/universe s390x pylint all 4.0.4-1 [346 kB] 929s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytz all 2025.2-5 [32.4 kB] 929s Get:67 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-3 [7599 kB] 929s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-3 [2948 kB] 930s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-typechecks all 0.1.0+ds-4 [4562 B] 930s Get:70 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-datacache all 1.4.1-2 [13.1 kB] 930s Get:71 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 930s Get:72 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-memoized-property all 1.0.3-2build1 [5328 B] 930s Get:73 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-serializable all 0.4.1+ds-2 [8438 B] 930s Get:74 http://ftpmaster.internal/ubuntu resolute/universe s390x pyensembl all 2.3.13-2 [37.2 kB] 930s Get:75 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 930s Get:76 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.9-3 [890 B] 930s Get:77 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 930s Get:78 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 930s Get:79 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 932s Fetched 91.8 MB in 6s (15.8 MB/s) 933s Selecting previously unselected package python3-numpy-dev:s390x. 933s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61954 files and directories currently installed.) 933s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 933s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 933s Selecting previously unselected package libblas3:s390x. 933s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_s390x.deb ... 933s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 934s Selecting previously unselected package libgfortran5:s390x. 934s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_s390x.deb ... 934s Unpacking libgfortran5:s390x (15.2.0-12ubuntu1) ... 934s Selecting previously unselected package liblapack3:s390x. 934s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 934s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 936s Selecting previously unselected package python3-numpy. 936s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 936s Unpacking python3-numpy (1:2.3.5+ds-3) ... 938s Selecting previously unselected package libpython3.14-minimal:s390x. 938s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_s390x.deb ... 938s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 939s Selecting previously unselected package python3.14-minimal. 939s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_s390x.deb ... 939s Unpacking python3.14-minimal (3.14.2-1) ... 939s Selecting previously unselected package m4. 939s Preparing to unpack .../07-m4_1.4.20-2_s390x.deb ... 939s Unpacking m4 (1.4.20-2) ... 939s Selecting previously unselected package autoconf. 939s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 939s Unpacking autoconf (2.72-3.1ubuntu1) ... 940s Selecting previously unselected package autotools-dev. 940s Preparing to unpack .../09-autotools-dev_20240727.1build1_all.deb ... 940s Unpacking autotools-dev (20240727.1build1) ... 940s Selecting previously unselected package automake. 940s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 940s Unpacking automake (1:1.18.1-3build1) ... 940s Selecting previously unselected package autopoint. 940s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 940s Unpacking autopoint (0.23.2-1) ... 940s Selecting previously unselected package libc-dev-bin. 940s Preparing to unpack .../12-libc-dev-bin_2.42-2ubuntu4_s390x.deb ... 940s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 940s Selecting previously unselected package linux-libc-dev:s390x. 940s Preparing to unpack .../13-linux-libc-dev_6.18.0-9.9_s390x.deb ... 940s Unpacking linux-libc-dev:s390x (6.18.0-9.9) ... 941s Selecting previously unselected package libcrypt-dev:s390x. 941s Preparing to unpack .../14-libcrypt-dev_1%3a4.5.1-1_s390x.deb ... 941s Unpacking libcrypt-dev:s390x (1:4.5.1-1) ... 941s Selecting previously unselected package rpcsvc-proto. 941s Preparing to unpack .../15-rpcsvc-proto_1.4.3-1build1_s390x.deb ... 941s Unpacking rpcsvc-proto (1.4.3-1build1) ... 941s Selecting previously unselected package libc6-dev:s390x. 941s Preparing to unpack .../16-libc6-dev_2.42-2ubuntu4_s390x.deb ... 941s Unpacking libc6-dev:s390x (2.42-2ubuntu4) ... 941s Selecting previously unselected package libisl23:s390x. 941s Preparing to unpack .../17-libisl23_0.27-1build1_s390x.deb ... 941s Unpacking libisl23:s390x (0.27-1build1) ... 942s Selecting previously unselected package libmpc3:s390x. 942s Preparing to unpack .../18-libmpc3_1.3.1-2_s390x.deb ... 942s Unpacking libmpc3:s390x (1.3.1-2) ... 942s Selecting previously unselected package cpp-15-s390x-linux-gnu. 942s Preparing to unpack .../19-cpp-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 942s Unpacking cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 944s Selecting previously unselected package cpp-15. 944s Preparing to unpack .../20-cpp-15_15.2.0-12ubuntu1_s390x.deb ... 944s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 944s Selecting previously unselected package cpp-s390x-linux-gnu. 944s Preparing to unpack .../21-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 944s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 944s Selecting previously unselected package cpp. 944s Preparing to unpack .../22-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 944s Unpacking cpp (4:15.2.0-4ubuntu1) ... 944s Selecting previously unselected package libcc1-0:s390x. 944s Preparing to unpack .../23-libcc1-0_15.2.0-12ubuntu1_s390x.deb ... 944s Unpacking libcc1-0:s390x (15.2.0-12ubuntu1) ... 944s Selecting previously unselected package libgomp1:s390x. 944s Preparing to unpack .../24-libgomp1_15.2.0-12ubuntu1_s390x.deb ... 944s Unpacking libgomp1:s390x (15.2.0-12ubuntu1) ... 944s Selecting previously unselected package libitm1:s390x. 944s Preparing to unpack .../25-libitm1_15.2.0-12ubuntu1_s390x.deb ... 944s Unpacking libitm1:s390x (15.2.0-12ubuntu1) ... 944s Selecting previously unselected package libasan8:s390x. 944s Preparing to unpack .../26-libasan8_15.2.0-12ubuntu1_s390x.deb ... 944s Unpacking libasan8:s390x (15.2.0-12ubuntu1) ... 945s Selecting previously unselected package liblsan0:s390x. 945s Preparing to unpack .../27-liblsan0_15.2.0-12ubuntu1_s390x.deb ... 945s Unpacking liblsan0:s390x (15.2.0-12ubuntu1) ... 946s Selecting previously unselected package libtsan2:s390x. 946s Preparing to unpack .../28-libtsan2_15.2.0-12ubuntu1_s390x.deb ... 946s Unpacking libtsan2:s390x (15.2.0-12ubuntu1) ... 946s Selecting previously unselected package libubsan1:s390x. 946s Preparing to unpack .../29-libubsan1_15.2.0-12ubuntu1_s390x.deb ... 946s Unpacking libubsan1:s390x (15.2.0-12ubuntu1) ... 946s Selecting previously unselected package libgcc-15-dev:s390x. 946s Preparing to unpack .../30-libgcc-15-dev_15.2.0-12ubuntu1_s390x.deb ... 946s Unpacking libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 947s Selecting previously unselected package gcc-15-s390x-linux-gnu. 947s Preparing to unpack .../31-gcc-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 947s Unpacking gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 950s Selecting previously unselected package gcc-15. 950s Preparing to unpack .../32-gcc-15_15.2.0-12ubuntu1_s390x.deb ... 950s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 950s Selecting previously unselected package gcc-s390x-linux-gnu. 950s Preparing to unpack .../33-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 950s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 950s Selecting previously unselected package gcc. 950s Preparing to unpack .../34-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 950s Unpacking gcc (4:15.2.0-4ubuntu1) ... 950s Selecting previously unselected package libstdc++-15-dev:s390x. 951s Preparing to unpack .../35-libstdc++-15-dev_15.2.0-12ubuntu1_s390x.deb ... 951s Unpacking libstdc++-15-dev:s390x (15.2.0-12ubuntu1) ... 952s Selecting previously unselected package g++-15-s390x-linux-gnu. 952s Preparing to unpack .../36-g++-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 952s Unpacking g++-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 954s Selecting previously unselected package g++-15. 954s Preparing to unpack .../37-g++-15_15.2.0-12ubuntu1_s390x.deb ... 954s Unpacking g++-15 (15.2.0-12ubuntu1) ... 955s Selecting previously unselected package g++-s390x-linux-gnu. 955s Preparing to unpack .../38-g++-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 955s Unpacking g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 955s Selecting previously unselected package g++. 955s Preparing to unpack .../39-g++_4%3a15.2.0-4ubuntu1_s390x.deb ... 955s Unpacking g++ (4:15.2.0-4ubuntu1) ... 955s Selecting previously unselected package build-essential. 955s Preparing to unpack .../40-build-essential_12.12ubuntu2_s390x.deb ... 955s Unpacking build-essential (12.12ubuntu2) ... 955s Selecting previously unselected package libdebhelper-perl. 955s Preparing to unpack .../41-libdebhelper-perl_13.28ubuntu1_all.deb ... 955s Unpacking libdebhelper-perl (13.28ubuntu1) ... 955s Selecting previously unselected package libtool. 955s Preparing to unpack .../42-libtool_2.5.4-9_all.deb ... 955s Unpacking libtool (2.5.4-9) ... 955s Selecting previously unselected package dh-autoreconf. 955s Preparing to unpack .../43-dh-autoreconf_21+nmu1_all.deb ... 955s Unpacking dh-autoreconf (21+nmu1) ... 955s Selecting previously unselected package libarchive-zip-perl. 955s Preparing to unpack .../44-libarchive-zip-perl_1.68-1_all.deb ... 955s Unpacking libarchive-zip-perl (1.68-1) ... 955s Selecting previously unselected package libfile-stripnondeterminism-perl. 955s Preparing to unpack .../45-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 955s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 955s Selecting previously unselected package dh-strip-nondeterminism. 955s Preparing to unpack .../46-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 955s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 955s Selecting previously unselected package debugedit. 955s Preparing to unpack .../47-debugedit_1%3a5.2-3build1_s390x.deb ... 955s Unpacking debugedit (1:5.2-3build1) ... 956s Selecting previously unselected package dwz. 956s Preparing to unpack .../48-dwz_0.16-2build1_s390x.deb ... 956s Unpacking dwz (0.16-2build1) ... 956s Selecting previously unselected package gettext. 956s Preparing to unpack .../49-gettext_0.23.2-1_s390x.deb ... 956s Unpacking gettext (0.23.2-1) ... 956s Selecting previously unselected package intltool-debian. 956s Preparing to unpack .../50-intltool-debian_0.35.0+20060710.6build1_all.deb ... 956s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 956s Selecting previously unselected package po-debconf. 956s Preparing to unpack .../51-po-debconf_1.0.22_all.deb ... 956s Unpacking po-debconf (1.0.22) ... 957s Selecting previously unselected package debhelper. 957s Preparing to unpack .../52-debhelper_13.28ubuntu1_all.deb ... 957s Unpacking debhelper (13.28ubuntu1) ... 958s Selecting previously unselected package dh-python. 958s Preparing to unpack .../53-dh-python_7.20260125_all.deb ... 958s Unpacking dh-python (7.20260125) ... 958s Selecting previously unselected package libpython3.14-stdlib:s390x. 958s Preparing to unpack .../54-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 958s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 959s Selecting previously unselected package pybuild-plugin-autopkgtest. 959s Preparing to unpack .../55-pybuild-plugin-autopkgtest_7.20260125_all.deb ... 959s Unpacking pybuild-plugin-autopkgtest (7.20260125) ... 959s Selecting previously unselected package python3-astroid. 959s Preparing to unpack .../56-python3-astroid_4.0.2-1ubuntu1_all.deb ... 959s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 959s Selecting previously unselected package python3-isort. 959s Preparing to unpack .../57-python3-isort_7.0.0-1_all.deb ... 959s Unpacking python3-isort (7.0.0-1) ... 959s Selecting previously unselected package python3-mypy-extensions. 959s Preparing to unpack .../58-python3-mypy-extensions_1.1.0-1_all.deb ... 959s Unpacking python3-mypy-extensions (1.1.0-1) ... 960s Selecting previously unselected package python3-logilab-common. 960s Preparing to unpack .../59-python3-logilab-common_2.1.0-1build1_all.deb ... 960s Unpacking python3-logilab-common (2.1.0-1build1) ... 960s Selecting previously unselected package python3-dill. 960s Preparing to unpack .../60-python3-dill_0.4.0-1_all.deb ... 960s Unpacking python3-dill (0.4.0-1) ... 960s Selecting previously unselected package python3-mccabe. 960s Preparing to unpack .../61-python3-mccabe_0.7.0-1build1_all.deb ... 960s Unpacking python3-mccabe (0.7.0-1build1) ... 960s Selecting previously unselected package python3-platformdirs. 960s Preparing to unpack .../62-python3-platformdirs_4.5.1-1_all.deb ... 960s Unpacking python3-platformdirs (4.5.1-1) ... 960s Selecting previously unselected package python3-tomlkit. 960s Preparing to unpack .../63-python3-tomlkit_0.13.3-2_all.deb ... 960s Unpacking python3-tomlkit (0.13.3-2) ... 960s Selecting previously unselected package pylint. 960s Preparing to unpack .../64-pylint_4.0.4-1_all.deb ... 960s Unpacking pylint (4.0.4-1) ... 960s Selecting previously unselected package python3-pytz. 960s Preparing to unpack .../65-python3-pytz_2025.2-5_all.deb ... 960s Unpacking python3-pytz (2025.2-5) ... 960s Selecting previously unselected package python3-pandas-lib:s390x. 960s Preparing to unpack .../66-python3-pandas-lib_2.3.3+dfsg-3_s390x.deb ... 960s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 962s Selecting previously unselected package python3-pandas. 962s Preparing to unpack .../67-python3-pandas_2.3.3+dfsg-3_all.deb ... 962s Unpacking python3-pandas (2.3.3+dfsg-3) ... 964s Selecting previously unselected package python3-typechecks. 964s Preparing to unpack .../68-python3-typechecks_0.1.0+ds-4_all.deb ... 964s Unpacking python3-typechecks (0.1.0+ds-4) ... 964s Selecting previously unselected package python3-datacache. 964s Preparing to unpack .../69-python3-datacache_1.4.1-2_all.deb ... 964s Unpacking python3-datacache (1.4.1-2) ... 964s Selecting previously unselected package python3-gtfparse. 964s Preparing to unpack .../70-python3-gtfparse_1.3.0+ds-2_all.deb ... 964s Unpacking python3-gtfparse (1.3.0+ds-2) ... 964s Selecting previously unselected package python3-memoized-property. 964s Preparing to unpack .../71-python3-memoized-property_1.0.3-2build1_all.deb ... 964s Unpacking python3-memoized-property (1.0.3-2build1) ... 964s Selecting previously unselected package python3-serializable. 964s Preparing to unpack .../72-python3-serializable_0.4.1+ds-2_all.deb ... 964s Unpacking python3-serializable (0.4.1+ds-2) ... 964s Selecting previously unselected package pyensembl. 964s Preparing to unpack .../73-pyensembl_2.3.13-2_all.deb ... 964s Unpacking pyensembl (2.3.13-2) ... 965s Selecting previously unselected package python3.14. 965s Preparing to unpack .../74-python3.14_3.14.2-1_s390x.deb ... 965s Unpacking python3.14 (3.14.2-1) ... 965s Selecting previously unselected package python3-all. 965s Preparing to unpack .../75-python3-all_3.13.9-3_s390x.deb ... 965s Unpacking python3-all (3.13.9-3) ... 965s Selecting previously unselected package python3-iniconfig. 965s Preparing to unpack .../76-python3-iniconfig_2.1.0-2_all.deb ... 965s Unpacking python3-iniconfig (2.1.0-2) ... 965s Selecting previously unselected package python3-pluggy. 965s Preparing to unpack .../77-python3-pluggy_1.6.0-2_all.deb ... 965s Unpacking python3-pluggy (1.6.0-2) ... 965s Selecting previously unselected package python3-pytest. 965s Preparing to unpack .../78-python3-pytest_9.0.2-2_all.deb ... 965s Unpacking python3-pytest (9.0.2-2) ... 966s Setting up dh-python (7.20260125) ... 967s Setting up python3-iniconfig (2.1.0-2) ... 968s Setting up python3-typechecks (0.1.0+ds-4) ... 969s Setting up python3-memoized-property (1.0.3-2build1) ... 970s Setting up libarchive-zip-perl (1.68-1) ... 970s Setting up python3-mypy-extensions (1.1.0-1) ... 971s Setting up libdebhelper-perl (13.28ubuntu1) ... 971s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 971s Setting up linux-libc-dev:s390x (6.18.0-9.9) ... 971s Setting up m4 (1.4.20-2) ... 971s Setting up python3-pytz (2025.2-5) ... 972s Setting up python3-serializable (0.4.1+ds-2) ... 973s Setting up libgomp1:s390x (15.2.0-12ubuntu1) ... 973s Setting up python3-platformdirs (4.5.1-1) ... 973s Setting up autotools-dev (20240727.1build1) ... 973s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 974s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 974s Setting up rpcsvc-proto (1.4.3-1build1) ... 974s Setting up python3-dill (0.4.0-1) ... 976s Setting up libmpc3:s390x (1.3.1-2) ... 976s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 976s Setting up autopoint (0.23.2-1) ... 976s Setting up libgfortran5:s390x (15.2.0-12ubuntu1) ... 976s Setting up autoconf (2.72-3.1ubuntu1) ... 976s Setting up python3-isort (7.0.0-1) ... 979s Setting up python3-pluggy (1.6.0-2) ... 980s Setting up libubsan1:s390x (15.2.0-12ubuntu1) ... 980s Setting up dwz (0.16-2build1) ... 980s Setting up python3-astroid (4.0.2-1ubuntu1) ... 985s Setting up libcrypt-dev:s390x (1:4.5.1-1) ... 985s Setting up libasan8:s390x (15.2.0-12ubuntu1) ... 985s Setting up debugedit (1:5.2-3build1) ... 985s Setting up python3-mccabe (0.7.0-1build1) ... 987s Setting up libtsan2:s390x (15.2.0-12ubuntu1) ... 987s Setting up libisl23:s390x (0.27-1build1) ... 987s Setting up libc-dev-bin (2.42-2ubuntu4) ... 987s Setting up python3-tomlkit (0.13.3-2) ... 988s Setting up python3.14-minimal (3.14.2-1) ... 996s Setting up libcc1-0:s390x (15.2.0-12ubuntu1) ... 996s Setting up liblsan0:s390x (15.2.0-12ubuntu1) ... 996s Setting up libitm1:s390x (15.2.0-12ubuntu1) ... 996s Setting up automake (1:1.18.1-3build1) ... 996s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 996s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 996s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 996s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 996s Setting up gettext (0.23.2-1) ... 996s Setting up libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 996s Setting up python3-logilab-common (2.1.0-1build1) ... 999s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 999s Setting up python3-pytest (9.0.2-2) ... 1003s Setting up intltool-debian (0.35.0+20060710.6build1) ... 1003s Setting up python3-numpy (1:2.3.5+ds-3) ... 1031s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 1031s Setting up cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 1031s Setting up libc6-dev:s390x (2.42-2ubuntu4) ... 1031s Setting up python3.14 (3.14.2-1) ... 1038s Setting up gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 1038s Setting up pylint (4.0.4-1) ... 1045s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1045s Setting up po-debconf (1.0.22) ... 1045s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 1045s Setting up python3-all (3.13.9-3) ... 1045s Setting up libstdc++-15-dev:s390x (15.2.0-12ubuntu1) ... 1045s Setting up python3-pandas (2.3.3+dfsg-3) ... 1112s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1112s Setting up cpp-15 (15.2.0-12ubuntu1) ... 1112s Setting up cpp (4:15.2.0-4ubuntu1) ... 1112s Setting up g++-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 1112s Setting up python3-datacache (1.4.1-2) ... 1113s Setting up python3-gtfparse (1.3.0+ds-2) ... 1114s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 1114s Setting up gcc-15 (15.2.0-12ubuntu1) ... 1114s Setting up pyensembl (2.3.13-2) ... 1115s Setting up g++-15 (15.2.0-12ubuntu1) ... 1115s Setting up libtool (2.5.4-9) ... 1115s Setting up gcc (4:15.2.0-4ubuntu1) ... 1115s Setting up dh-autoreconf (21+nmu1) ... 1115s Setting up g++ (4:15.2.0-4ubuntu1) ... 1115s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1115s Setting up build-essential (12.12ubuntu2) ... 1115s Setting up debhelper (13.28ubuntu1) ... 1115s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 1115s Processing triggers for man-db (2.13.1-1) ... 1136s Processing triggers for install-info (7.2-5) ... 1137s Processing triggers for libc-bin (2.42-2ubuntu4) ... 1137s Processing triggers for systemd (259-1ubuntu3) ... 1143s autopkgtest [06:45:59]: test pybuild-autopkgtest: pybuild-autopkgtest 1143s autopkgtest [06:45:59]: test pybuild-autopkgtest: [----------------------- 1145s pybuild-autopkgtest 1148s I: pybuild base:384: cd /tmp/autopkgtest.IARefs/autopkgtest_tmp/build; python3.14 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' 1154s ============================= test session starts ============================== 1154s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 1154s cachedir: .pytest_cache 1154s rootdir: /tmp/autopkgtest.IARefs/autopkgtest_tmp/build 1154s plugins: typeguard-4.4.4 1170s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 1170s 1170s ==================================== ERRORS ==================================== 1170s _____________________ ERROR collecting tests/test_shell.py _____________________ 1170s tests/test_shell.py:1: in 1170s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 1170s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 1170s release_group = root_group.add_argument_group() 1170s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1170s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 1170s raise ValueError('argument groups cannot be nested') 1170s E ValueError: argument groups cannot be nested 1170s =============================== warnings summary =============================== 1170s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 1170s /usr/lib/python3/dist-packages/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 1170s import pkg_resources 1170s 1170s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 1170s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 1170s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 1170s declare_namespace(pkg) 1170s 1170s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1170s =========================== short test summary info ============================ 1170s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 1170s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 1170s ================= 98 deselected, 2 warnings, 1 error in 14.04s ================= 1171s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.IARefs/autopkgtest_tmp/build; python3.14 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' 1171s I: pybuild base:384: cd /tmp/autopkgtest.IARefs/autopkgtest_tmp/build; python3.13 -m pytest -v -k 'not test_download_cache.py and not test_gene_ids.py and not test_gene_names.py and not test_gene_objects.py and not test_id_length.py and not test_search.py and not test_serialization.py and not test_transcript_ids.py and not test_transcript_objects.py and not test_contigs.py and not test_exon_id.py and not test_exon_object.py and not test_string_representation.py and not test_timings.py and not test_transcript_sequences.py and not test_transcript_support_level.py' 1173s ============================= test session starts ============================== 1173s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 1173s cachedir: .pytest_cache 1173s rootdir: /tmp/autopkgtest.IARefs/autopkgtest_tmp/build 1173s plugins: typeguard-4.4.4 1179s collecting ... collected 126 items / 98 deselected / 28 selected 1179s 1179s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 1179s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 1179s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 1179s tests/test_locus.py::test_locus_contains PASSED [ 14%] 1179s tests/test_locus.py::test_position_offset PASSED [ 17%] 1179s tests/test_locus.py::test_range_offset PASSED [ 21%] 1179s tests/test_locus.py::test_locus_distance PASSED [ 25%] 1179s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 1179s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 1180s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 1180s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 1180s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 1180s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 1180s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 1180s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 1180s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 1180s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 1180s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 1180s tests/test_release_versions.py::test_int_version PASSED [ 67%] 1180s tests/test_release_versions.py::test_str_version PASSED [ 71%] 1180s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 1180s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 1180s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 1180s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 1180s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 1180s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 1180s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 1181s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 1181s 1181s =============================== warnings summary =============================== 1181s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 1181s /usr/lib/python3/dist-packages/pyensembl/shell.py:43: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 1181s import pkg_resources 1181s 1181s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 1181s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 1181s Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages 1181s declare_namespace(pkg) 1181s 1181s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 1181s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 1181s release_group = root_group.add_argument_group() 1181s 1181s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 1181s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 1181s path_group = root_group.add_argument_group() 1181s 1181s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1181s ================ 28 passed, 98 deselected, 4 warnings in 7.51s ================= 1182s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 1182s make: *** [/tmp/hlvtVS32qX/run:4: pybuild-autopkgtest] Error 25 1182s pybuild-autopkgtest: error: /tmp/hlvtVS32qX/run pybuild-autopkgtest returned exit code 2 1183s autopkgtest [06:46:39]: test pybuild-autopkgtest: -----------------------] 1184s autopkgtest [06:46:40]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 1184s pybuild-autopkgtest FAIL non-zero exit status 25 1185s autopkgtest [06:46:41]: @@@@@@@@@@@@@@@@@@@@ summary 1185s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 1185s pybuild-autopkgtest FAIL non-zero exit status 25