0s autopkgtest [14:09:09]: starting date and time: 2026-01-23 14:09:09+0000 0s autopkgtest [14:09:09]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:09:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jupda9ly/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade pyensembl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- 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-2.secgroup --name adt-resolute-s390x-pyensembl-20260123-140909-juju-7f2275-prod-proposed-migration-environment-2-878fd24a-61f7-4af7-8e2e-91afa866a961 --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-20260123-140909-juju-7f2275-prod-proposed-migration-environment-2-878fd24a-61f7-4af7-8e2e-91afa866a961 from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 102s autopkgtest [14:10:51]: testbed dpkg architecture: s390x 103s autopkgtest [14:10:52]: testbed apt version: 3.1.13 103s autopkgtest [14:10:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s autopkgtest [14:10:52]: testbed release detected to be: None 104s autopkgtest [14:10:53]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 104s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [95.0 kB] 104s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 104s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1019 kB] 105s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [117 kB] 105s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [837 kB] 105s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 105s Fetched 2228 kB in 1s (3198 kB/s) 107s Reading package lists... 107s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 108s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 113s Calculating upgrade... 114s The following packages were automatically installed and are no longer required: 114s python3.13 python3.13-minimal 114s Use 'sudo apt autoremove' to remove them. 114s The following NEW packages will be installed: 114s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 114s The following packages will be upgraded: 114s libplymouth5 libpython3-stdlib libtasn1-6 plymouth 114s plymouth-theme-ubuntu-text python3 python3-gdbm python3-jaraco.context 114s python3-minimal 114s 9 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 7066 kB of archives. 114s After this operation, 24.3 MB of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 114s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 114s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 114s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 114s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 115s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 124s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 124s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libtasn1-6 s390x 4.21.0-2 [48.6 kB] 124s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libplymouth5 s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [159 kB] 124s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth-theme-ubuntu-text s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [10.2 kB] 124s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [152 kB] 124s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 124s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x python3-jaraco.context all 6.0.1-2 [8198 B] 125s dpkg-preconfigure: unable to re-open stdin: No such file or directory 125s Fetched 7066 kB in 11s (668 kB/s) 126s Selecting previously unselected package libpython3.14-minimal:s390x. 126s (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 ... 87685 files and directories currently installed.) 126s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 126s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 128s Selecting previously unselected package python3.14-minimal. 128s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 128s Unpacking python3.14-minimal (3.14.2-1) ... 129s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 129s Setting up python3.14-minimal (3.14.2-1) ... 133s (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 ... 88027 files and directories currently installed.) 133s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 134s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 134s Setting up python3-minimal (3.14.2-1) ... 134s (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 ... 88027 files and directories currently installed.) 134s Preparing to unpack .../0-python3_3.14.2-1_s390x.deb ... 135s running python pre-rtupdate hooks for python3.14... 135s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 135s Selecting previously unselected package libpython3.14-stdlib:s390x. 135s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 135s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 136s Selecting previously unselected package python3.14. 136s Preparing to unpack .../2-python3.14_3.14.2-1_s390x.deb ... 136s Unpacking python3.14 (3.14.2-1) ... 136s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_s390x.deb ... 136s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 136s Preparing to unpack .../4-libtasn1-6_4.21.0-2_s390x.deb ... 136s Unpacking libtasn1-6:s390x (4.21.0-2) over (4.20.0-2ubuntu1) ... 137s Preparing to unpack .../5-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 137s Unpacking libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 137s Preparing to unpack .../6-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 137s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 137s Preparing to unpack .../7-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 137s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 139s Preparing to unpack .../8-python3-gdbm_3.14.2-1_s390x.deb ... 139s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 139s Preparing to unpack .../9-python3-jaraco.context_6.0.1-2_all.deb ... 140s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 140s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 140s Setting up libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 140s Setting up libtasn1-6:s390x (4.21.0-2) ... 140s Setting up python3.14 (3.14.2-1) ... 144s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 144s Setting up python3-gdbm (3.14.2-1) ... 144s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 144s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 145s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 146s Setting up python3 (3.14.2-1) ... 146s running python rtupdate hooks for python3.14... 146s running python post-rtupdate hooks for python3.14... 146s Setting up python3-jaraco.context (6.0.1-2) ... 147s Processing triggers for libc-bin (2.42-2ubuntu4) ... 147s Processing triggers for systemd (259-1ubuntu2) ... 147s Processing triggers for man-db (2.13.1-1) ... 152s Processing triggers for initramfs-tools (0.150ubuntu7) ... 152s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 163s Using config file '/etc/zipl.conf' 163s Building bootmap in '/boot' 163s Adding IPL section 'ubuntu' (default) 163s Preparing boot device: vda. 163s Done. 163s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 163s Processing triggers for initramfs-tools (0.150ubuntu7) ... 164s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 175s Using config file '/etc/zipl.conf' 175s Building bootmap in '/boot' 175s Adding IPL section 'ubuntu' (default) 175s Preparing boot device: vda. 175s Done. 176s autopkgtest [14:12:05]: upgrading testbed (apt dist-upgrade and autopurge) 176s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Calculating upgrade... 178s The following packages were automatically installed and are no longer required: 178s python3.13 python3.13-minimal 178s Use 'sudo apt autoremove' to remove them. 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Solving dependencies... 180s The following packages will be REMOVED: 180s python3.13* python3.13-minimal* 180s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 180s After this operation, 8012 kB disk space will be freed. 180s (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 ... 88454 files and directories currently installed.) 180s Removing python3.13 (3.13.11-1) ... 181s Removing python3.13-minimal (3.13.11-1) ... 182s Processing triggers for man-db (2.13.1-1) ... 183s Processing triggers for systemd (259-1ubuntu2) ... 183s (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 ... 88427 files and directories currently installed.) 183s Purging configuration files for python3.13-minimal (3.13.11-1) ... 184s autopkgtest [14:12:13]: rebooting testbed after setup commands that affected boot 226s autopkgtest [14:12:55]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 229s autopkgtest [14:12:58]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 230s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 230s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 230s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 230s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 230s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 230s gpgv: issuer "tchet@debian.org" 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 230s autopkgtest [14:12:59]: testing package pyensembl version 2.3.13-2 231s autopkgtest [14:13:00]: build not needed 231s autopkgtest [14:13:00]: test run-unit-test: preparing testbed 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 232s Solving dependencies... 232s The following NEW packages will be installed: 232s libblas3 libgfortran5 liblapack3 pyensembl pylint python3-all 232s python3-astroid python3-datacache python3-dill python3-gtfparse 232s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 232s python3-memoized-property python3-mypy-extensions python3-numpy 232s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 232s python3-pluggy python3-pytest python3-pytz python3-serializable 232s python3-tomlkit python3-typechecks python3.13 python3.13-minimal 232s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 232s Need to get 24.3 MB of archives. 232s After this operation, 123 MB of additional disk space will be used. 232s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 232s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 232s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 232s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 232s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 232s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 233s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 233s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-astroid all 4.0.2-1ubuntu1 [172 kB] 233s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-isort all 7.0.0-1 [59.7 kB] 233s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mypy-extensions all 1.1.0-1 [6716 B] 233s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-logilab-common all 2.1.0-1build1 [95.9 kB] 233s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-dill all 0.4.0-1 [84.8 kB] 233s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mccabe all 0.7.0-1build1 [8926 B] 233s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x python3-platformdirs all 4.5.1-1 [17.1 kB] 233s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tomlkit all 0.13.3-2 [39.1 kB] 233s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x pylint all 4.0.4-1 [346 kB] 233s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytz all 2025.2-5 [32.4 kB] 233s Get:18 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-3 [7599 kB] 233s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-3 [2948 kB] 233s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-typechecks all 0.1.0+ds-4 [4562 B] 233s Get:21 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-datacache all 1.4.1-2 [13.1 kB] 233s Get:22 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 233s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-memoized-property all 1.0.3-2build1 [5328 B] 233s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-serializable all 0.4.1+ds-2 [8438 B] 233s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x pyensembl all 2.3.13-2 [37.2 kB] 233s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 233s Get:27 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 233s Get:28 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 233s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 234s Fetched 24.3 MB in 1s (18.1 MB/s) 234s Selecting previously unselected package python3.13-minimal. 235s (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 ... 88429 files and directories currently installed.) 235s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_s390x.deb ... 235s Unpacking python3.13-minimal (3.13.11-1) ... 235s Selecting previously unselected package python3-numpy-dev:s390x. 235s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 235s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 235s Selecting previously unselected package libblas3:s390x. 235s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_s390x.deb ... 235s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 235s Selecting previously unselected package libgfortran5:s390x. 235s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_s390x.deb ... 235s Unpacking libgfortran5:s390x (15.2.0-11ubuntu1) ... 235s Selecting previously unselected package liblapack3:s390x. 235s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 235s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 235s Selecting previously unselected package python3-numpy. 235s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 235s Unpacking python3-numpy (1:2.3.5+ds-3) ... 235s Selecting previously unselected package python3.13. 235s Preparing to unpack .../06-python3.13_3.13.11-1_s390x.deb ... 235s Unpacking python3.13 (3.13.11-1) ... 235s Selecting previously unselected package python3-astroid. 235s Preparing to unpack .../07-python3-astroid_4.0.2-1ubuntu1_all.deb ... 235s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 235s Selecting previously unselected package python3-isort. 235s Preparing to unpack .../08-python3-isort_7.0.0-1_all.deb ... 235s Unpacking python3-isort (7.0.0-1) ... 235s Selecting previously unselected package python3-mypy-extensions. 235s Preparing to unpack .../09-python3-mypy-extensions_1.1.0-1_all.deb ... 235s Unpacking python3-mypy-extensions (1.1.0-1) ... 235s Selecting previously unselected package python3-logilab-common. 235s Preparing to unpack .../10-python3-logilab-common_2.1.0-1build1_all.deb ... 235s Unpacking python3-logilab-common (2.1.0-1build1) ... 235s Selecting previously unselected package python3-dill. 235s Preparing to unpack .../11-python3-dill_0.4.0-1_all.deb ... 235s Unpacking python3-dill (0.4.0-1) ... 235s Selecting previously unselected package python3-mccabe. 235s Preparing to unpack .../12-python3-mccabe_0.7.0-1build1_all.deb ... 235s Unpacking python3-mccabe (0.7.0-1build1) ... 235s Selecting previously unselected package python3-platformdirs. 235s Preparing to unpack .../13-python3-platformdirs_4.5.1-1_all.deb ... 235s Unpacking python3-platformdirs (4.5.1-1) ... 235s Selecting previously unselected package python3-tomlkit. 235s Preparing to unpack .../14-python3-tomlkit_0.13.3-2_all.deb ... 235s Unpacking python3-tomlkit (0.13.3-2) ... 235s Selecting previously unselected package pylint. 235s Preparing to unpack .../15-pylint_4.0.4-1_all.deb ... 235s Unpacking pylint (4.0.4-1) ... 235s Selecting previously unselected package python3-pytz. 235s Preparing to unpack .../16-python3-pytz_2025.2-5_all.deb ... 235s Unpacking python3-pytz (2025.2-5) ... 235s Selecting previously unselected package python3-pandas-lib:s390x. 235s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-3_s390x.deb ... 235s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 236s Selecting previously unselected package python3-pandas. 236s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-3_all.deb ... 236s Unpacking python3-pandas (2.3.3+dfsg-3) ... 236s Selecting previously unselected package python3-typechecks. 236s Preparing to unpack .../19-python3-typechecks_0.1.0+ds-4_all.deb ... 236s Unpacking python3-typechecks (0.1.0+ds-4) ... 236s Selecting previously unselected package python3-datacache. 236s Preparing to unpack .../20-python3-datacache_1.4.1-2_all.deb ... 236s Unpacking python3-datacache (1.4.1-2) ... 236s Selecting previously unselected package python3-gtfparse. 236s Preparing to unpack .../21-python3-gtfparse_1.3.0+ds-2_all.deb ... 236s Unpacking python3-gtfparse (1.3.0+ds-2) ... 236s Selecting previously unselected package python3-memoized-property. 236s Preparing to unpack .../22-python3-memoized-property_1.0.3-2build1_all.deb ... 236s Unpacking python3-memoized-property (1.0.3-2build1) ... 236s Selecting previously unselected package python3-serializable. 236s Preparing to unpack .../23-python3-serializable_0.4.1+ds-2_all.deb ... 236s Unpacking python3-serializable (0.4.1+ds-2) ... 236s Selecting previously unselected package pyensembl. 236s Preparing to unpack .../24-pyensembl_2.3.13-2_all.deb ... 236s Unpacking pyensembl (2.3.13-2) ... 236s Selecting previously unselected package python3-all. 236s Preparing to unpack .../25-python3-all_3.14.2-1_s390x.deb ... 236s Unpacking python3-all (3.14.2-1) ... 236s Selecting previously unselected package python3-iniconfig. 236s Preparing to unpack .../26-python3-iniconfig_2.1.0-2_all.deb ... 236s Unpacking python3-iniconfig (2.1.0-2) ... 237s Selecting previously unselected package python3-pluggy. 237s Preparing to unpack .../27-python3-pluggy_1.6.0-2_all.deb ... 237s Unpacking python3-pluggy (1.6.0-2) ... 237s Selecting previously unselected package python3-pytest. 237s Preparing to unpack .../28-python3-pytest_9.0.2-2_all.deb ... 237s Unpacking python3-pytest (9.0.2-2) ... 237s Setting up python3-iniconfig (2.1.0-2) ... 238s Setting up python3-typechecks (0.1.0+ds-4) ... 239s Setting up python3-memoized-property (1.0.3-2build1) ... 239s Setting up python3-mypy-extensions (1.1.0-1) ... 241s Setting up python3-pytz (2025.2-5) ... 241s Setting up python3-serializable (0.4.1+ds-2) ... 241s Setting up python3-platformdirs (4.5.1-1) ... 242s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 242s 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 242s Setting up python3-dill (0.4.0-1) ... 244s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 244s Setting up libgfortran5:s390x (15.2.0-11ubuntu1) ... 244s Setting up python3-isort (7.0.0-1) ... 245s Setting up python3-pluggy (1.6.0-2) ... 246s Setting up python3-astroid (4.0.2-1ubuntu1) ... 248s Setting up python3.13-minimal (3.13.11-1) ... 249s Setting up python3-mccabe (0.7.0-1build1) ... 249s Setting up python3-tomlkit (0.13.3-2) ... 250s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 250s 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 250s Setting up python3-logilab-common (2.1.0-1build1) ... 250s Setting up python3.13 (3.13.11-1) ... 254s Setting up python3-pytest (9.0.2-2) ... 256s Setting up python3-all (3.14.2-1) ... 256s Setting up python3-numpy (1:2.3.5+ds-3) ... 274s Setting up pylint (4.0.4-1) ... 278s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 278s Setting up python3-pandas (2.3.3+dfsg-3) ... 306s Setting up python3-datacache (1.4.1-2) ... 307s Setting up python3-gtfparse (1.3.0+ds-2) ... 307s Setting up pyensembl (2.3.13-2) ... 308s Processing triggers for systemd (259-1ubuntu2) ... 308s Processing triggers for man-db (2.13.1-1) ... 311s Processing triggers for libc-bin (2.42-2ubuntu4) ... 313s autopkgtest [14:14:22]: test run-unit-test: [----------------------- 316s ============================= test session starts ============================== 316s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 316s rootdir: /tmp/autopkgtest.4Uo29Z/autopkgtest_tmp 316s plugins: typeguard-4.4.4 316s collected 15 items 316s 316s tests/test_ensembl_object_properties.py . [ 6%] 316s tests/test_locus.py ...... [ 46%] 316s tests/test_release_versions.py ....... [ 93%] 317s tests/test_shell.py . [100%] 317s 317s =============================== warnings summary =============================== 317s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 317s /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 317s import pkg_resources 317s 317s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 317s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 317s 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 317s declare_namespace(pkg) 317s 317s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 317s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 317s release_group = root_group.add_argument_group() 317s 317s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 317s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 317s path_group = root_group.add_argument_group() 317s 317s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 317s ======================== 15 passed, 4 warnings in 2.24s ======================== 322s ============================= test session starts ============================== 322s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 322s rootdir: /tmp/autopkgtest.4Uo29Z/autopkgtest_tmp 322s plugins: typeguard-4.4.4 322s collected 14 items / 1 error 322s 322s ==================================== ERRORS ==================================== 322s _____________________ ERROR collecting tests/test_shell.py _____________________ 322s tests/test_shell.py:1: in 322s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 322s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 322s release_group = root_group.add_argument_group() 322s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 322s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 322s raise ValueError('argument groups cannot be nested') 322s E ValueError: argument groups cannot be nested 322s =============================== warnings summary =============================== 322s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 322s /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 322s import pkg_resources 322s 322s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 322s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 322s 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 322s declare_namespace(pkg) 322s 322s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 322s =========================== short test summary info ============================ 322s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 322s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 322s ========================= 2 warnings, 1 error in 2.93s ========================= 323s autopkgtest [14:14:32]: test run-unit-test: -----------------------] 324s run-unit-test FAIL non-zero exit status 2 324s autopkgtest [14:14:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 325s autopkgtest [14:14:34]: test pybuild-autopkgtest: preparing testbed 345s Creating nova instance adt-resolute-s390x-pyensembl-20260123-140909-juju-7f2275-prod-proposed-migration-environment-2-878fd24a-61f7-4af7-8e2e-91afa866a961 from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 438s autopkgtest [14:16:27]: testbed dpkg architecture: s390x 439s autopkgtest [14:16:28]: testbed apt version: 3.1.13 439s autopkgtest [14:16:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 439s autopkgtest [14:16:28]: testbed release detected to be: resolute 440s autopkgtest [14:16:29]: updating testbed package index (apt update) 440s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 440s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 440s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 440s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 440s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 440s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1019 kB] 440s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 440s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [95.0 kB] 440s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [117 kB] 441s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [837 kB] 441s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 441s Fetched 2228 kB in 1s (2609 kB/s) 444s Reading package lists... 445s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 445s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 445s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 445s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 448s Reading package lists... 448s Reading package lists... 449s Building dependency tree... 449s Reading state information... 449s Calculating upgrade... 450s The following packages were automatically installed and are no longer required: 450s python3.13 python3.13-minimal 450s Use 'sudo apt autoremove' to remove them. 450s The following NEW packages will be installed: 450s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 450s The following packages will be upgraded: 450s libplymouth5 libpython3-stdlib libtasn1-6 plymouth 450s plymouth-theme-ubuntu-text python3 python3-gdbm python3-jaraco.context 450s python3-minimal 450s 9 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 450s Need to get 7066 kB of archives. 450s After this operation, 24.3 MB of additional disk space will be used. 450s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 450s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 450s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 450s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 450s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 450s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 451s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 451s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libtasn1-6 s390x 4.21.0-2 [48.6 kB] 451s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libplymouth5 s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [159 kB] 451s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth-theme-ubuntu-text s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [10.2 kB] 451s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x plymouth s390x 24.004.60+git20250831.4a3c171d-0ubuntu5 [152 kB] 451s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 451s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x python3-jaraco.context all 6.0.1-2 [8198 B] 452s dpkg-preconfigure: unable to re-open stdin: No such file or directory 452s Fetched 7066 kB in 1s (13.0 MB/s) 453s Selecting previously unselected package libpython3.14-minimal:s390x. 453s (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 ... 87685 files and directories currently installed.) 453s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 453s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 453s Selecting previously unselected package python3.14-minimal. 453s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 453s Unpacking python3.14-minimal (3.14.2-1) ... 454s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 454s Setting up python3.14-minimal (3.14.2-1) ... 459s (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 ... 88027 files and directories currently installed.) 459s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 459s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 459s Setting up python3-minimal (3.14.2-1) ... 460s (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 ... 88027 files and directories currently installed.) 460s Preparing to unpack .../0-python3_3.14.2-1_s390x.deb ... 460s running python pre-rtupdate hooks for python3.14... 460s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 460s Selecting previously unselected package libpython3.14-stdlib:s390x. 460s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 460s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 460s Selecting previously unselected package python3.14. 460s Preparing to unpack .../2-python3.14_3.14.2-1_s390x.deb ... 460s Unpacking python3.14 (3.14.2-1) ... 460s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_s390x.deb ... 460s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 460s Preparing to unpack .../4-libtasn1-6_4.21.0-2_s390x.deb ... 460s Unpacking libtasn1-6:s390x (4.21.0-2) over (4.20.0-2ubuntu1) ... 461s Preparing to unpack .../5-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 461s Unpacking libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 461s Preparing to unpack .../6-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 461s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 461s Preparing to unpack .../7-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu5_s390x.deb ... 461s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) over (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 462s Preparing to unpack .../8-python3-gdbm_3.14.2-1_s390x.deb ... 462s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 462s Preparing to unpack .../9-python3-jaraco.context_6.0.1-2_all.deb ... 462s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 462s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 462s Setting up libplymouth5:s390x (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 462s Setting up libtasn1-6:s390x (4.21.0-2) ... 462s Setting up python3.14 (3.14.2-1) ... 465s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 465s Setting up python3-gdbm (3.14.2-1) ... 465s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 465s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 466s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 468s Setting up python3 (3.14.2-1) ... 468s running python rtupdate hooks for python3.14... 468s running python post-rtupdate hooks for python3.14... 469s Setting up python3-jaraco.context (6.0.1-2) ... 469s Processing triggers for libc-bin (2.42-2ubuntu4) ... 469s Processing triggers for systemd (259-1ubuntu2) ... 470s Processing triggers for man-db (2.13.1-1) ... 475s Processing triggers for initramfs-tools (0.150ubuntu7) ... 476s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 489s Using config file '/etc/zipl.conf' 489s Building bootmap in '/boot' 489s Adding IPL section 'ubuntu' (default) 489s Preparing boot device: vda. 489s Done. 489s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu5) ... 490s Processing triggers for initramfs-tools (0.150ubuntu7) ... 490s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 501s Using config file '/etc/zipl.conf' 501s Building bootmap in '/boot' 501s Adding IPL section 'ubuntu' (default) 501s Preparing boot device: vda. 501s Done. 502s autopkgtest [14:17:31]: upgrading testbed (apt dist-upgrade and autopurge) 502s Reading package lists... 503s Building dependency tree... 503s Reading state information... 504s Calculating upgrade... 504s The following packages were automatically installed and are no longer required: 504s python3.13 python3.13-minimal 504s Use 'sudo apt autoremove' to remove them. 504s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 504s Reading package lists... 505s Building dependency tree... 505s Reading state information... 505s Solving dependencies... 505s The following packages will be REMOVED: 505s python3.13* python3.13-minimal* 506s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 506s After this operation, 8012 kB disk space will be freed. 507s (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 ... 88454 files and directories currently installed.) 507s Removing python3.13 (3.13.11-1) ... 507s Removing python3.13-minimal (3.13.11-1) ... 509s Processing triggers for man-db (2.13.1-1) ... 509s Processing triggers for systemd (259-1ubuntu2) ... 509s (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 ... 88427 files and directories currently installed.) 509s Purging configuration files for python3.13-minimal (3.13.11-1) ... 510s autopkgtest [14:17:39]: rebooting testbed after setup commands that affected boot 552s Reading package lists... 552s Building dependency tree... 552s Reading state information... 552s Solving dependencies... 552s The following NEW packages will be installed: 552s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 552s cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu debhelper debugedit dh-autoreconf 552s dh-python dh-strip-nondeterminism dwz g++ g++-15 g++-15-s390x-linux-gnu 552s g++-s390x-linux-gnu gcc gcc-15 gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu 552s gettext intltool-debian libarchive-zip-perl libasan8 libblas3 libcc1-0 552s libdebhelper-perl libfile-stripnondeterminism-perl libgcc-15-dev 552s libgfortran5 libgomp1 libisl23 libitm1 liblapack3 libmpc3 libstdc++-15-dev 552s libtool libubsan1 m4 po-debconf pybuild-plugin-autopkgtest pyensembl pylint 552s python3-all python3-astroid python3-datacache python3-dill python3-gtfparse 552s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 552s python3-memoized-property python3-mypy-extensions python3-numpy 552s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 552s python3-pluggy python3-pytest python3-pytz python3-serializable 552s python3-tomlkit python3-typechecks python3.13 python3.13-minimal 552s 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. 552s Need to get 80.3 MB of archives. 552s After this operation, 300 MB of additional disk space will be used. 552s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 553s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 553s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 553s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 553s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 553s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 553s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 553s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x m4 s390x 1.4.20-2 [223 kB] 553s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x autoconf all 2.72-3.1ubuntu1 [384 kB] 553s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x autotools-dev all 20240727.1 [43.4 kB] 553s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x automake all 1:1.18.1-3build1 [582 kB] 553s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x autopoint all 0.23.2-1 [620 kB] 553s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 553s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 554s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [10.2 MB] 554s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-11ubuntu1 [1028 B] 554s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 554s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 554s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-11ubuntu1 [50.0 kB] 554s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-11ubuntu1 [154 kB] 554s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-11ubuntu1 [30.9 kB] 554s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-11ubuntu1 [2968 kB] 554s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-11ubuntu1 [1211 kB] 554s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-11ubuntu1 [1045 kB] 554s Get:25 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [19.9 MB] 554s Get:26 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-11ubuntu1 [517 kB] 554s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 554s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 554s Get:29 http://ftpmaster.internal/ubuntu resolute/main s390x libstdc++-15-dev s390x 15.2.0-11ubuntu1 [2660 kB] 554s Get:30 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [11.7 MB] 555s Get:31 http://ftpmaster.internal/ubuntu resolute/main s390x g++-15 s390x 15.2.0-11ubuntu1 [24.6 kB] 555s Get:32 http://ftpmaster.internal/ubuntu resolute/main s390x g++-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [956 B] 555s Get:33 http://ftpmaster.internal/ubuntu resolute/main s390x g++ s390x 4:15.2.0-4ubuntu1 [1078 B] 555s Get:34 http://ftpmaster.internal/ubuntu resolute/main s390x build-essential s390x 12.12ubuntu2 [5258 B] 555s Get:35 http://ftpmaster.internal/ubuntu resolute/main s390x libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 555s Get:36 http://ftpmaster.internal/ubuntu resolute/main s390x libtool all 2.5.4-9 [169 kB] 555s Get:37 http://ftpmaster.internal/ubuntu resolute/main s390x dh-autoreconf all 21 [12.5 kB] 555s Get:38 http://ftpmaster.internal/ubuntu resolute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] 555s Get:39 http://ftpmaster.internal/ubuntu resolute/main s390x libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 555s Get:40 http://ftpmaster.internal/ubuntu resolute/main s390x dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 555s Get:41 http://ftpmaster.internal/ubuntu resolute/main s390x debugedit s390x 1:5.2-3 [52.8 kB] 555s Get:42 http://ftpmaster.internal/ubuntu resolute/main s390x dwz s390x 0.16-2 [121 kB] 555s Get:43 http://ftpmaster.internal/ubuntu resolute/main s390x gettext s390x 0.23.2-1 [1062 kB] 555s Get:44 http://ftpmaster.internal/ubuntu resolute/main s390x intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 555s Get:45 http://ftpmaster.internal/ubuntu resolute/main s390x po-debconf all 1.0.22 [215 kB] 555s Get:46 http://ftpmaster.internal/ubuntu resolute/main s390x debhelper all 13.28ubuntu1 [916 kB] 555s Get:47 http://ftpmaster.internal/ubuntu resolute/universe s390x dh-python all 7.20251231 [122 kB] 555s Get:48 http://ftpmaster.internal/ubuntu resolute/universe s390x pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 555s Get:49 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-astroid all 4.0.2-1ubuntu1 [172 kB] 555s Get:50 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-isort all 7.0.0-1 [59.7 kB] 555s Get:51 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mypy-extensions all 1.1.0-1 [6716 B] 555s Get:52 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-logilab-common all 2.1.0-1build1 [95.9 kB] 555s Get:53 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-dill all 0.4.0-1 [84.8 kB] 555s Get:54 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-mccabe all 0.7.0-1build1 [8926 B] 555s Get:55 http://ftpmaster.internal/ubuntu resolute/main s390x python3-platformdirs all 4.5.1-1 [17.1 kB] 555s Get:56 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-tomlkit all 0.13.3-2 [39.1 kB] 555s Get:57 http://ftpmaster.internal/ubuntu resolute/universe s390x pylint all 4.0.4-1 [346 kB] 555s Get:58 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytz all 2025.2-5 [32.4 kB] 555s Get:59 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-3 [7599 kB] 555s Get:60 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-3 [2948 kB] 555s Get:61 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-typechecks all 0.1.0+ds-4 [4562 B] 555s Get:62 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-datacache all 1.4.1-2 [13.1 kB] 555s Get:63 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 555s Get:64 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-memoized-property all 1.0.3-2build1 [5328 B] 555s Get:65 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-serializable all 0.4.1+ds-2 [8438 B] 555s Get:66 http://ftpmaster.internal/ubuntu resolute/universe s390x pyensembl all 2.3.13-2 [37.2 kB] 555s Get:67 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 555s Get:68 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 555s Get:69 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 555s Get:70 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 556s Fetched 80.3 MB in 2s (32.2 MB/s) 556s Selecting previously unselected package python3.13-minimal. 557s (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 ... 88429 files and directories currently installed.) 557s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_s390x.deb ... 557s Unpacking python3.13-minimal (3.13.11-1) ... 557s Selecting previously unselected package python3-numpy-dev:s390x. 557s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 557s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 557s Selecting previously unselected package libblas3:s390x. 557s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_s390x.deb ... 557s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 557s Selecting previously unselected package libgfortran5:s390x. 557s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_s390x.deb ... 557s Unpacking libgfortran5:s390x (15.2.0-11ubuntu1) ... 557s Selecting previously unselected package liblapack3:s390x. 557s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 557s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 557s Selecting previously unselected package python3-numpy. 557s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 557s Unpacking python3-numpy (1:2.3.5+ds-3) ... 558s Selecting previously unselected package python3.13. 558s Preparing to unpack .../06-python3.13_3.13.11-1_s390x.deb ... 558s Unpacking python3.13 (3.13.11-1) ... 558s Selecting previously unselected package m4. 558s Preparing to unpack .../07-m4_1.4.20-2_s390x.deb ... 558s Unpacking m4 (1.4.20-2) ... 558s Selecting previously unselected package autoconf. 558s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 558s Unpacking autoconf (2.72-3.1ubuntu1) ... 559s Selecting previously unselected package autotools-dev. 559s Preparing to unpack .../09-autotools-dev_20240727.1_all.deb ... 559s Unpacking autotools-dev (20240727.1) ... 559s Selecting previously unselected package automake. 559s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 559s Unpacking automake (1:1.18.1-3build1) ... 559s Selecting previously unselected package autopoint. 559s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 559s Unpacking autopoint (0.23.2-1) ... 559s Selecting previously unselected package libisl23:s390x. 559s Preparing to unpack .../12-libisl23_0.27-1build1_s390x.deb ... 559s Unpacking libisl23:s390x (0.27-1build1) ... 559s Selecting previously unselected package libmpc3:s390x. 559s Preparing to unpack .../13-libmpc3_1.3.1-2_s390x.deb ... 559s Unpacking libmpc3:s390x (1.3.1-2) ... 559s Selecting previously unselected package cpp-15-s390x-linux-gnu. 559s Preparing to unpack .../14-cpp-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 559s Selecting previously unselected package cpp-15. 559s Preparing to unpack .../15-cpp-15_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 559s Selecting previously unselected package cpp-s390x-linux-gnu. 559s Preparing to unpack .../16-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 559s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 559s Selecting previously unselected package cpp. 559s Preparing to unpack .../17-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 559s Unpacking cpp (4:15.2.0-4ubuntu1) ... 559s Selecting previously unselected package libcc1-0:s390x. 559s Preparing to unpack .../18-libcc1-0_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking libcc1-0:s390x (15.2.0-11ubuntu1) ... 559s Selecting previously unselected package libgomp1:s390x. 559s Preparing to unpack .../19-libgomp1_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking libgomp1:s390x (15.2.0-11ubuntu1) ... 559s Selecting previously unselected package libitm1:s390x. 559s Preparing to unpack .../20-libitm1_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking libitm1:s390x (15.2.0-11ubuntu1) ... 559s Selecting previously unselected package libasan8:s390x. 559s Preparing to unpack .../21-libasan8_15.2.0-11ubuntu1_s390x.deb ... 559s Unpacking libasan8:s390x (15.2.0-11ubuntu1) ... 560s Selecting previously unselected package libubsan1:s390x. 560s Preparing to unpack .../22-libubsan1_15.2.0-11ubuntu1_s390x.deb ... 560s Unpacking libubsan1:s390x (15.2.0-11ubuntu1) ... 560s Selecting previously unselected package libgcc-15-dev:s390x. 560s Preparing to unpack .../23-libgcc-15-dev_15.2.0-11ubuntu1_s390x.deb ... 560s Unpacking libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 560s Selecting previously unselected package gcc-15-s390x-linux-gnu. 560s Preparing to unpack .../24-gcc-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 560s Unpacking gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 562s Selecting previously unselected package gcc-15. 562s Preparing to unpack .../25-gcc-15_15.2.0-11ubuntu1_s390x.deb ... 562s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 562s Selecting previously unselected package gcc-s390x-linux-gnu. 562s Preparing to unpack .../26-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 562s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 562s Selecting previously unselected package gcc. 562s Preparing to unpack .../27-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 562s Unpacking gcc (4:15.2.0-4ubuntu1) ... 562s Selecting previously unselected package libstdc++-15-dev:s390x. 562s Preparing to unpack .../28-libstdc++-15-dev_15.2.0-11ubuntu1_s390x.deb ... 562s Unpacking libstdc++-15-dev:s390x (15.2.0-11ubuntu1) ... 562s Selecting previously unselected package g++-15-s390x-linux-gnu. 562s Preparing to unpack .../29-g++-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 562s Unpacking g++-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 563s Selecting previously unselected package g++-15. 563s Preparing to unpack .../30-g++-15_15.2.0-11ubuntu1_s390x.deb ... 563s Unpacking g++-15 (15.2.0-11ubuntu1) ... 563s Selecting previously unselected package g++-s390x-linux-gnu. 563s Preparing to unpack .../31-g++-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 563s Unpacking g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 563s Selecting previously unselected package g++. 563s Preparing to unpack .../32-g++_4%3a15.2.0-4ubuntu1_s390x.deb ... 563s Unpacking g++ (4:15.2.0-4ubuntu1) ... 563s Selecting previously unselected package build-essential. 563s Preparing to unpack .../33-build-essential_12.12ubuntu2_s390x.deb ... 563s Unpacking build-essential (12.12ubuntu2) ... 563s Selecting previously unselected package libdebhelper-perl. 563s Preparing to unpack .../34-libdebhelper-perl_13.28ubuntu1_all.deb ... 563s Unpacking libdebhelper-perl (13.28ubuntu1) ... 563s Selecting previously unselected package libtool. 563s Preparing to unpack .../35-libtool_2.5.4-9_all.deb ... 563s Unpacking libtool (2.5.4-9) ... 563s Selecting previously unselected package dh-autoreconf. 563s Preparing to unpack .../36-dh-autoreconf_21_all.deb ... 563s Unpacking dh-autoreconf (21) ... 563s Selecting previously unselected package libarchive-zip-perl. 563s Preparing to unpack .../37-libarchive-zip-perl_1.68-1_all.deb ... 563s Unpacking libarchive-zip-perl (1.68-1) ... 563s Selecting previously unselected package libfile-stripnondeterminism-perl. 563s Preparing to unpack .../38-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 563s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 564s Selecting previously unselected package dh-strip-nondeterminism. 564s Preparing to unpack .../39-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 564s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 564s Selecting previously unselected package debugedit. 564s Preparing to unpack .../40-debugedit_1%3a5.2-3_s390x.deb ... 564s Unpacking debugedit (1:5.2-3) ... 564s Selecting previously unselected package dwz. 564s Preparing to unpack .../41-dwz_0.16-2_s390x.deb ... 564s Unpacking dwz (0.16-2) ... 564s Selecting previously unselected package gettext. 564s Preparing to unpack .../42-gettext_0.23.2-1_s390x.deb ... 564s Unpacking gettext (0.23.2-1) ... 564s Selecting previously unselected package intltool-debian. 564s Preparing to unpack .../43-intltool-debian_0.35.0+20060710.6build1_all.deb ... 564s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 564s Selecting previously unselected package po-debconf. 564s Preparing to unpack .../44-po-debconf_1.0.22_all.deb ... 564s Unpacking po-debconf (1.0.22) ... 564s Selecting previously unselected package debhelper. 565s Preparing to unpack .../45-debhelper_13.28ubuntu1_all.deb ... 565s Unpacking debhelper (13.28ubuntu1) ... 565s Selecting previously unselected package dh-python. 565s Preparing to unpack .../46-dh-python_7.20251231_all.deb ... 565s Unpacking dh-python (7.20251231) ... 565s Selecting previously unselected package pybuild-plugin-autopkgtest. 565s Preparing to unpack .../47-pybuild-plugin-autopkgtest_7.20251231_all.deb ... 565s Unpacking pybuild-plugin-autopkgtest (7.20251231) ... 565s Selecting previously unselected package python3-astroid. 565s Preparing to unpack .../48-python3-astroid_4.0.2-1ubuntu1_all.deb ... 565s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 565s Selecting previously unselected package python3-isort. 565s Preparing to unpack .../49-python3-isort_7.0.0-1_all.deb ... 565s Unpacking python3-isort (7.0.0-1) ... 565s Selecting previously unselected package python3-mypy-extensions. 565s Preparing to unpack .../50-python3-mypy-extensions_1.1.0-1_all.deb ... 565s Unpacking python3-mypy-extensions (1.1.0-1) ... 565s Selecting previously unselected package python3-logilab-common. 565s Preparing to unpack .../51-python3-logilab-common_2.1.0-1build1_all.deb ... 565s Unpacking python3-logilab-common (2.1.0-1build1) ... 565s Selecting previously unselected package python3-dill. 565s Preparing to unpack .../52-python3-dill_0.4.0-1_all.deb ... 565s Unpacking python3-dill (0.4.0-1) ... 565s Selecting previously unselected package python3-mccabe. 565s Preparing to unpack .../53-python3-mccabe_0.7.0-1build1_all.deb ... 565s Unpacking python3-mccabe (0.7.0-1build1) ... 565s Selecting previously unselected package python3-platformdirs. 565s Preparing to unpack .../54-python3-platformdirs_4.5.1-1_all.deb ... 565s Unpacking python3-platformdirs (4.5.1-1) ... 565s Selecting previously unselected package python3-tomlkit. 565s Preparing to unpack .../55-python3-tomlkit_0.13.3-2_all.deb ... 565s Unpacking python3-tomlkit (0.13.3-2) ... 565s Selecting previously unselected package pylint. 565s Preparing to unpack .../56-pylint_4.0.4-1_all.deb ... 565s Unpacking pylint (4.0.4-1) ... 565s Selecting previously unselected package python3-pytz. 565s Preparing to unpack .../57-python3-pytz_2025.2-5_all.deb ... 565s Unpacking python3-pytz (2025.2-5) ... 565s Selecting previously unselected package python3-pandas-lib:s390x. 565s Preparing to unpack .../58-python3-pandas-lib_2.3.3+dfsg-3_s390x.deb ... 565s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 566s Selecting previously unselected package python3-pandas. 566s Preparing to unpack .../59-python3-pandas_2.3.3+dfsg-3_all.deb ... 566s Unpacking python3-pandas (2.3.3+dfsg-3) ... 567s Selecting previously unselected package python3-typechecks. 567s Preparing to unpack .../60-python3-typechecks_0.1.0+ds-4_all.deb ... 567s Unpacking python3-typechecks (0.1.0+ds-4) ... 567s Selecting previously unselected package python3-datacache. 567s Preparing to unpack .../61-python3-datacache_1.4.1-2_all.deb ... 567s Unpacking python3-datacache (1.4.1-2) ... 567s Selecting previously unselected package python3-gtfparse. 567s 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Unpacking python3-iniconfig (2.1.0-2) ... 567s Selecting previously unselected package python3-pluggy. 567s Preparing to unpack .../68-python3-pluggy_1.6.0-2_all.deb ... 567s Unpacking python3-pluggy (1.6.0-2) ... 567s Selecting previously unselected package python3-pytest. 567s Preparing to unpack .../69-python3-pytest_9.0.2-2_all.deb ... 567s Unpacking python3-pytest (9.0.2-2) ... 567s Setting up dh-python (7.20251231) ... 568s Setting up python3-iniconfig (2.1.0-2) ... 569s Setting up python3-typechecks (0.1.0+ds-4) ... 569s Setting up python3-memoized-property (1.0.3-2build1) ... 570s Setting up libarchive-zip-perl (1.68-1) ... 570s Setting up python3-mypy-extensions (1.1.0-1) ... 571s Setting up libdebhelper-perl (13.28ubuntu1) ... 571s Setting up m4 (1.4.20-2) ... 571s Setting up python3-pytz (2025.2-5) ... 571s Setting up python3-serializable (0.4.1+ds-2) ... 572s Setting up libgomp1:s390x (15.2.0-11ubuntu1) ... 572s Setting up python3-platformdirs (4.5.1-1) ... 573s Setting up autotools-dev (20240727.1) ... 573s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 573s 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 573s Setting up python3-dill (0.4.0-1) ... 574s Setting up libmpc3:s390x (1.3.1-2) ... 574s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 574s Setting up autopoint (0.23.2-1) ... 574s Setting up libgfortran5:s390x (15.2.0-11ubuntu1) ... 574s Setting up autoconf (2.72-3.1ubuntu1) ... 574s Setting up python3-isort (7.0.0-1) ... 575s Setting up python3-pluggy (1.6.0-2) ... 576s Setting up libubsan1:s390x (15.2.0-11ubuntu1) ... 576s Setting up dwz (0.16-2) ... 576s Setting up python3-astroid (4.0.2-1ubuntu1) ... 578s Setting up libasan8:s390x (15.2.0-11ubuntu1) ... 578s Setting up debugedit (1:5.2-3) ... 578s Setting up python3.13-minimal (3.13.11-1) ... 581s Setting up python3-mccabe (0.7.0-1build1) ... 581s Setting up libisl23:s390x (0.27-1build1) ... 581s Setting up python3-tomlkit (0.13.3-2) ... 583s Setting up libcc1-0:s390x (15.2.0-11ubuntu1) ... 583s Setting up libitm1:s390x (15.2.0-11ubuntu1) ... 583s Setting up automake (1:1.18.1-3build1) ... 583s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 583s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 583s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 583s 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 583s Setting up gettext (0.23.2-1) ... 583s Setting up libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 583s Setting up python3-logilab-common (2.1.0-1build1) ... 584s Setting up python3.13 (3.13.11-1) ... 588s Setting up python3-pytest (9.0.2-2) ... 590s Setting up python3-all (3.14.2-1) ... 590s Setting up intltool-debian (0.35.0+20060710.6build1) ... 590s Setting up libstdc++-15-dev:s390x (15.2.0-11ubuntu1) ... 590s Setting up python3-numpy (1:2.3.5+ds-3) ... 601s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 601s Setting up cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 601s Setting up gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 601s Setting up pylint (4.0.4-1) ... 604s Setting up g++-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 604s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 604s Setting up po-debconf (1.0.22) ... 604s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-3) ... 604s Setting up python3-pandas (2.3.3+dfsg-3) ... 644s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 644s Setting up cpp-15 (15.2.0-11ubuntu1) ... 644s Setting up cpp (4:15.2.0-4ubuntu1) ... 644s Setting up python3-datacache (1.4.1-2) ... 645s Setting up python3-gtfparse (1.3.0+ds-2) ... 645s Setting up g++-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 645s Setting up gcc-15 (15.2.0-11ubuntu1) ... 645s Setting up pyensembl (2.3.13-2) ... 646s Setting up g++-15 (15.2.0-11ubuntu1) ... 646s Setting up libtool (2.5.4-9) ... 646s Setting up gcc (4:15.2.0-4ubuntu1) ... 646s Setting up dh-autoreconf (21) ... 646s Setting up g++ (4:15.2.0-4ubuntu1) ... 646s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 646s Setting up build-essential (12.12ubuntu2) ... 646s Setting up debhelper (13.28ubuntu1) ... 646s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 646s Processing triggers for man-db (2.13.1-1) ... 650s Processing triggers for install-info (7.2-5) ... 650s Processing triggers for libc-bin (2.42-2ubuntu4) ... 650s Processing triggers for systemd (259-1ubuntu2) ... 652s autopkgtest [14:20:01]: test pybuild-autopkgtest: pybuild-autopkgtest 652s autopkgtest [14:20:01]: test pybuild-autopkgtest: [----------------------- 653s pybuild-autopkgtest 653s I: pybuild base:384: cd /tmp/autopkgtest.4Uo29Z/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' 654s ============================= test session starts ============================== 654s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 654s cachedir: .pytest_cache 654s rootdir: /tmp/autopkgtest.4Uo29Z/autopkgtest_tmp/build 654s plugins: typeguard-4.4.4 658s collecting ... collected 126 items / 98 deselected / 28 selected 658s 658s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 658s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 658s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 658s tests/test_locus.py::test_locus_contains PASSED [ 14%] 658s tests/test_locus.py::test_position_offset PASSED [ 17%] 658s tests/test_locus.py::test_range_offset PASSED [ 21%] 658s tests/test_locus.py::test_locus_distance PASSED [ 25%] 658s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 658s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 658s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 658s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 658s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 658s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 658s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 658s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 658s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 658s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 658s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 658s tests/test_release_versions.py::test_int_version PASSED [ 67%] 658s tests/test_release_versions.py::test_str_version PASSED [ 71%] 658s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 658s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 658s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 658s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 658s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 658s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 658s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 659s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 659s 659s =============================== warnings summary =============================== 659s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 659s /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 659s import pkg_resources 659s 659s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 659s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 659s 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 659s declare_namespace(pkg) 659s 659s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 659s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 659s release_group = root_group.add_argument_group() 659s 659s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 659s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 659s path_group = root_group.add_argument_group() 659s 659s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 659s ================ 28 passed, 98 deselected, 4 warnings in 4.16s ================= 659s I: pybuild base:384: cd /tmp/autopkgtest.4Uo29Z/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' 660s ============================= test session starts ============================== 660s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 660s cachedir: .pytest_cache 660s rootdir: /tmp/autopkgtest.4Uo29Z/autopkgtest_tmp/build 660s plugins: typeguard-4.4.4 664s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 664s 664s ==================================== ERRORS ==================================== 664s _____________________ ERROR collecting tests/test_shell.py _____________________ 664s tests/test_shell.py:1: in 664s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 664s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 664s release_group = root_group.add_argument_group() 664s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 664s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 664s raise ValueError('argument groups cannot be nested') 664s E ValueError: argument groups cannot be nested 664s =============================== warnings summary =============================== 664s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 664s /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 664s import pkg_resources 664s 664s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 664s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 664s 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 664s declare_namespace(pkg) 664s 664s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 664s =========================== short test summary info ============================ 664s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 664s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 664s ================= 98 deselected, 2 warnings, 1 error in 3.11s ================== 665s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.4Uo29Z/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' 665s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 665s make: *** [/tmp/XEAtP77ZQg/run:4: pybuild-autopkgtest] Error 25 665s pybuild-autopkgtest: error: /tmp/XEAtP77ZQg/run pybuild-autopkgtest returned exit code 2 665s autopkgtest [14:20:14]: test pybuild-autopkgtest: -----------------------] 665s pybuild-autopkgtest FAIL non-zero exit status 25 665s autopkgtest [14:20:14]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 666s autopkgtest [14:20:15]: @@@@@@@@@@@@@@@@@@@@ summary 666s run-unit-test FAIL non-zero exit status 2 666s pybuild-autopkgtest FAIL non-zero exit status 25