0s autopkgtest [19:59:19]: starting date and time: 2026-01-22 19:59:19+0000 0s autopkgtest [19:59:19]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:59:19]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.unmz1zog/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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-13.secgroup --name adt-resolute-arm64-pyensembl-20260122-195919-juju-7f2275-prod-proposed-migration-environment-20-dcc0db9e-86a9-49d6-8221-0c7e77cb9275 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-pyensembl-20260122-195919-juju-7f2275-prod-proposed-migration-environment-20-dcc0db9e-86a9-49d6-8221-0c7e77cb9275 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 66s autopkgtest [20:00:25]: testbed dpkg architecture: arm64 66s autopkgtest [20:00:25]: testbed apt version: 3.1.12 66s autopkgtest [20:00:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 67s autopkgtest [20:00:26]: testbed release detected to be: None 67s autopkgtest [20:00:26]: updating testbed package index (apt update) 68s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 68s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 68s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 68s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 68s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 68s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 68s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 68s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 68s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [101 kB] 68s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3424 B] 68s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 69s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 69s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 69s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [18.1 kB] 69s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [7156 B] 69s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [332 B] 71s Fetched 2107 kB in 1s (1909 kB/s) 72s Reading package lists... 73s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 73s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 73s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 74s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 75s The following packages were automatically installed and are no longer required: 75s python3.13 python3.13-minimal 75s Use 'sudo apt autoremove' to remove them. 75s The following NEW packages will be installed: 75s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 75s The following packages will be upgraded: 75s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 75s python3-gdbm python3-minimal 75s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 6993 kB of archives. 75s After this operation, 26.0 MB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 76s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 76s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 76s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libplymouth5 arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [141 kB] 76s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 76s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [138 kB] 76s dpkg-preconfigure: unable to re-open stdin: No such file or directory 76s Fetched 6993 kB in 1s (6393 kB/s) 76s Selecting previously unselected package libpython3.14-minimal:arm64. 77s (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 ... 135223 files and directories currently installed.) 77s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 77s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 77s Selecting previously unselected package python3.14-minimal. 77s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 77s Unpacking python3.14-minimal (3.14.2-1) ... 77s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 77s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 77s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 77s Setting up python3.14-minimal (3.14.2-1) ... 78s (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 ... 135565 files and directories currently installed.) 78s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 78s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 78s Setting up python3-minimal (3.14.2-1) ... 79s (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 ... 135565 files and directories currently installed.) 79s Preparing to unpack .../0-python3_3.14.2-1_arm64.deb ... 79s running python pre-rtupdate hooks for python3.14... 79s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 79s Selecting previously unselected package libpython3.14-stdlib:arm64. 79s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 79s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 79s Selecting previously unselected package python3.14. 79s Preparing to unpack .../2-python3.14_3.14.2-1_arm64.deb ... 79s Unpacking python3.14 (3.14.2-1) ... 79s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_arm64.deb ... 79s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 79s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 79s Unpacking libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 79s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 79s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 80s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 80s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 80s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 80s Setting up libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 80s Setting up python3.14 (3.14.2-1) ... 81s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 81s Setting up python3-gdbm (3.14.2-1) ... 81s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 81s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 81s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 82s Setting up python3 (3.14.2-1) ... 82s running python rtupdate hooks for python3.14... 82s running python post-rtupdate hooks for python3.14... 82s Processing triggers for libc-bin (2.42-2ubuntu4) ... 82s Processing triggers for systemd (259-1ubuntu2) ... 82s Processing triggers for man-db (2.13.1-1) ... 83s Processing triggers for initramfs-tools (0.150ubuntu7) ... 83s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 101s System running in EFI mode, skipping. 101s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 101s Processing triggers for initramfs-tools (0.150ubuntu7) ... 101s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 117s System running in EFI mode, skipping. 117s autopkgtest [20:01:16]: upgrading testbed (apt dist-upgrade and autopurge) 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s The following packages were automatically installed and are no longer required: 118s python3.13 python3.13-minimal 118s Use 'sudo apt autoremove' to remove them. 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Solving dependencies... 119s The following packages will be REMOVED: 119s python3.13* python3.13-minimal* 120s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 120s After this operation, 7766 kB disk space will be freed. 120s (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 ... 135995 files and directories currently installed.) 120s Removing python3.13 (3.13.11-1) ... 120s Removing python3.13-minimal (3.13.11-1) ... 121s Processing triggers for man-db (2.13.1-1) ... 121s Processing triggers for systemd (259-1ubuntu2) ... 121s (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 ... 135968 files and directories currently installed.) 121s Purging configuration files for python3.13-minimal (3.13.11-1) ... 122s autopkgtest [20:01:21]: rebooting testbed after setup commands that affected boot 161s autopkgtest [20:02:00]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 163s autopkgtest [20:02:02]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 165s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 165s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 165s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 165s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 165s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 165s gpgv: issuer "tchet@debian.org" 165s gpgv: Can't check signature: No public key 165s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 165s autopkgtest [20:02:04]: testing package pyensembl version 2.3.13-2 166s autopkgtest [20:02:05]: build not needed 166s autopkgtest [20:02:05]: test run-unit-test: preparing testbed 166s Reading package lists... 167s Building dependency tree... 167s Reading state information... 167s Solving dependencies... 167s The following NEW packages will be installed: 167s libblas3 libgfortran5 liblapack3 pyensembl pylint python3-all 167s python3-astroid python3-datacache python3-dill python3-gtfparse 167s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 167s python3-memoized-property python3-mypy-extensions python3-numpy 167s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 167s python3-pluggy python3-pytest python3-pytz python3-serializable 167s python3-tomlkit python3-typechecks python3.13 python3.13-minimal 168s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 21.5 MB of archives. 168s After this operation, 114 MB of additional disk space will be used. 168s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-minimal arm64 3.13.11-1 [2346 kB] 168s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 168s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 168s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-11ubuntu1 [450 kB] 168s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 168s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 169s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13 arm64 3.13.11-1 [758 kB] 169s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 169s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-isort all 7.0.0-1 [59.7 kB] 169s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mypy-extensions all 1.1.0-1 [6716 B] 169s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-logilab-common all 2.1.0-1 [95.7 kB] 169s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dill all 0.4.0-1 [84.8 kB] 169s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mccabe all 0.7.0-1build1 [8926 B] 169s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 169s Get:15 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tomlkit all 0.13.3-2 [39.1 kB] 169s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 pylint all 4.0.4-1 [346 kB] 169s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 169s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 169s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 169s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typechecks all 0.1.0+ds-4 [4562 B] 169s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datacache all 1.4.1-2 [13.1 kB] 169s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 169s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-memoized-property all 1.0.3-2build1 [5328 B] 169s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-serializable all 0.4.1+ds-2 [8438 B] 169s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 pyensembl all 2.3.13-2 [37.2 kB] 169s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.14.2-1 [888 B] 169s Get:27 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 169s Get:28 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 169s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 170s Fetched 21.5 MB in 2s (10.4 MB/s) 170s Selecting previously unselected package python3.13-minimal. 170s (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 ... 135970 files and directories currently installed.) 170s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_arm64.deb ... 170s Unpacking python3.13-minimal (3.13.11-1) ... 170s Selecting previously unselected package python3-numpy-dev:arm64. 170s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 170s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 170s Selecting previously unselected package libblas3:arm64. 170s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_arm64.deb ... 170s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 170s Selecting previously unselected package libgfortran5:arm64. 170s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_arm64.deb ... 170s Unpacking libgfortran5:arm64 (15.2.0-11ubuntu1) ... 170s Selecting previously unselected package liblapack3:arm64. 170s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 170s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 170s Selecting previously unselected package python3-numpy. 170s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 170s Unpacking python3-numpy (1:2.3.5+ds-3) ... 170s Selecting previously unselected package python3.13. 170s Preparing to unpack .../06-python3.13_3.13.11-1_arm64.deb ... 170s Unpacking python3.13 (3.13.11-1) ... 170s Selecting previously unselected package python3-astroid. 171s Preparing to unpack .../07-python3-astroid_4.0.2-1ubuntu1_all.deb ... 171s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 171s Selecting previously unselected package python3-isort. 171s Preparing to unpack .../08-python3-isort_7.0.0-1_all.deb ... 171s Unpacking python3-isort (7.0.0-1) ... 171s Selecting previously unselected package python3-mypy-extensions. 171s Preparing to unpack .../09-python3-mypy-extensions_1.1.0-1_all.deb ... 171s Unpacking python3-mypy-extensions (1.1.0-1) ... 171s Selecting previously unselected package python3-logilab-common. 171s Preparing to unpack .../10-python3-logilab-common_2.1.0-1_all.deb ... 171s Unpacking python3-logilab-common (2.1.0-1) ... 171s Selecting previously unselected package python3-dill. 171s Preparing to unpack .../11-python3-dill_0.4.0-1_all.deb ... 171s Unpacking python3-dill (0.4.0-1) ... 171s Selecting previously unselected package python3-mccabe. 171s Preparing to unpack .../12-python3-mccabe_0.7.0-1build1_all.deb ... 171s Unpacking python3-mccabe (0.7.0-1build1) ... 171s Selecting previously unselected package python3-platformdirs. 171s Preparing to unpack .../13-python3-platformdirs_4.5.1-1_all.deb ... 171s Unpacking python3-platformdirs (4.5.1-1) ... 171s Selecting previously unselected package python3-tomlkit. 171s Preparing to unpack .../14-python3-tomlkit_0.13.3-2_all.deb ... 171s Unpacking python3-tomlkit (0.13.3-2) ... 171s Selecting previously unselected package pylint. 171s Preparing to unpack .../15-pylint_4.0.4-1_all.deb ... 171s Unpacking pylint (4.0.4-1) ... 171s Selecting previously unselected package python3-pytz. 171s Preparing to unpack .../16-python3-pytz_2025.2-5_all.deb ... 171s Unpacking python3-pytz (2025.2-5) ... 171s Selecting previously unselected package python3-pandas-lib:arm64. 171s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 171s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 171s Selecting previously unselected package python3-pandas. 171s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-3_all.deb ... 171s Unpacking python3-pandas (2.3.3+dfsg-3) ... 172s Selecting previously unselected package python3-typechecks. 172s Preparing to unpack .../19-python3-typechecks_0.1.0+ds-4_all.deb ... 172s Unpacking python3-typechecks (0.1.0+ds-4) ... 172s Selecting previously unselected package python3-datacache. 172s Preparing to unpack .../20-python3-datacache_1.4.1-2_all.deb ... 172s Unpacking python3-datacache (1.4.1-2) ... 172s Selecting previously unselected package python3-gtfparse. 172s Preparing to unpack .../21-python3-gtfparse_1.3.0+ds-2_all.deb ... 172s Unpacking python3-gtfparse (1.3.0+ds-2) ... 172s Selecting previously unselected package python3-memoized-property. 172s Preparing to unpack .../22-python3-memoized-property_1.0.3-2build1_all.deb ... 172s Unpacking python3-memoized-property (1.0.3-2build1) ... 172s Selecting previously unselected package python3-serializable. 172s Preparing to unpack .../23-python3-serializable_0.4.1+ds-2_all.deb ... 172s Unpacking python3-serializable (0.4.1+ds-2) ... 172s Selecting previously unselected package pyensembl. 172s Preparing to unpack .../24-pyensembl_2.3.13-2_all.deb ... 172s Unpacking pyensembl (2.3.13-2) ... 172s Selecting previously unselected package python3-all. 172s Preparing to unpack .../25-python3-all_3.14.2-1_arm64.deb ... 172s Unpacking python3-all (3.14.2-1) ... 172s Selecting previously unselected package python3-iniconfig. 172s Preparing to unpack .../26-python3-iniconfig_2.1.0-2_all.deb ... 172s Unpacking python3-iniconfig (2.1.0-2) ... 172s Selecting previously unselected package python3-pluggy. 172s Preparing to unpack .../27-python3-pluggy_1.6.0-2_all.deb ... 172s Unpacking python3-pluggy (1.6.0-2) ... 172s Selecting previously unselected package python3-pytest. 172s Preparing to unpack .../28-python3-pytest_9.0.2-2_all.deb ... 172s Unpacking python3-pytest (9.0.2-2) ... 172s Setting up python3-iniconfig (2.1.0-2) ... 173s Setting up python3-typechecks (0.1.0+ds-4) ... 173s Setting up python3-memoized-property (1.0.3-2build1) ... 173s Setting up python3-mypy-extensions (1.1.0-1) ... 173s Setting up python3-pytz (2025.2-5) ... 174s Setting up python3-serializable (0.4.1+ds-2) ... 174s Setting up python3-platformdirs (4.5.1-1) ... 174s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 174s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 174s Setting up python3-dill (0.4.0-1) ... 175s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 175s Setting up libgfortran5:arm64 (15.2.0-11ubuntu1) ... 175s Setting up python3-isort (7.0.0-1) ... 175s Setting up python3-pluggy (1.6.0-2) ... 175s Setting up python3-astroid (4.0.2-1ubuntu1) ... 176s Setting up python3.13-minimal (3.13.11-1) ... 177s Setting up python3-mccabe (0.7.0-1build1) ... 177s Setting up python3-tomlkit (0.13.3-2) ... 177s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 177s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 177s Setting up python3-logilab-common (2.1.0-1) ... 178s Setting up python3.13 (3.13.11-1) ... 179s Setting up python3-pytest (9.0.2-2) ... 180s Setting up python3-all (3.14.2-1) ... 180s Setting up python3-numpy (1:2.3.5+ds-3) ... 184s Setting up pylint (4.0.4-1) ... 185s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 185s Setting up python3-pandas (2.3.3+dfsg-3) ... 196s Setting up python3-datacache (1.4.1-2) ... 197s Setting up python3-gtfparse (1.3.0+ds-2) ... 197s Setting up pyensembl (2.3.13-2) ... 197s Processing triggers for systemd (259-1ubuntu2) ... 197s Processing triggers for man-db (2.13.1-1) ... 197s Processing triggers for libc-bin (2.42-2ubuntu4) ... 198s autopkgtest [20:02:37]: test run-unit-test: [----------------------- 200s ============================= test session starts ============================== 200s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 200s rootdir: /tmp/autopkgtest.wTUGyl/autopkgtest_tmp 200s plugins: typeguard-4.4.4 200s collected 15 items 200s 200s tests/test_ensembl_object_properties.py . [ 6%] 200s tests/test_locus.py ...... [ 46%] 200s tests/test_release_versions.py ....... [ 93%] 200s tests/test_shell.py . [100%] 200s 200s =============================== warnings summary =============================== 200s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 200s /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 200s import pkg_resources 200s 200s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 200s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 200s 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 200s declare_namespace(pkg) 200s 200s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 200s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 200s release_group = root_group.add_argument_group() 200s 200s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 200s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 200s path_group = root_group.add_argument_group() 200s 200s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 200s ======================== 15 passed, 4 warnings in 1.31s ======================== 202s ============================= test session starts ============================== 202s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 202s rootdir: /tmp/autopkgtest.wTUGyl/autopkgtest_tmp 202s plugins: typeguard-4.4.4 202s collected 14 items / 1 error 202s 202s ==================================== ERRORS ==================================== 202s _____________________ ERROR collecting tests/test_shell.py _____________________ 202s tests/test_shell.py:1: in 202s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 202s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 202s release_group = root_group.add_argument_group() 202s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 202s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 202s raise ValueError('argument groups cannot be nested') 202s E ValueError: argument groups cannot be nested 202s =============================== warnings summary =============================== 202s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 202s /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 202s import pkg_resources 202s 202s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 202s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 202s 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 202s declare_namespace(pkg) 202s 202s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 202s =========================== short test summary info ============================ 202s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 202s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 202s ========================= 2 warnings, 1 error in 0.95s ========================= 203s autopkgtest [20:02:42]: test run-unit-test: -----------------------] 203s autopkgtest [20:02:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 203s run-unit-test FAIL non-zero exit status 2 204s autopkgtest [20:02:43]: test pybuild-autopkgtest: preparing testbed 223s Creating nova instance adt-resolute-arm64-pyensembl-20260122-195919-juju-7f2275-prod-proposed-migration-environment-20-dcc0db9e-86a9-49d6-8221-0c7e77cb9275 from image adt/ubuntu-resolute-arm64-server-20260122.img (UUID ed27afc7-5f46-4e8b-ad73-864280a0ddbb)... 283s autopkgtest [20:04:02]: testbed dpkg architecture: arm64 283s autopkgtest [20:04:02]: testbed apt version: 3.1.12 286s autopkgtest [20:04:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 286s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 286s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 286s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 286s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 286s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 286s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1011 kB] 286s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.6 kB] 286s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.2 kB] 286s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [101 kB] 286s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [3424 B] 286s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [7876 B] 286s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [304 B] 286s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [727 kB] 286s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [18.1 kB] 286s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [7156 B] 286s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [332 B] 286s autopkgtest [20:04:03]: testbed release detected to be: resolute 286s autopkgtest [20:04:04]: updating testbed package index (apt update) 288s Fetched 2107 kB in 1s (3173 kB/s) 289s Reading package lists... 290s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 290s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 290s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 290s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 291s Reading package lists... 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 292s Calculating upgrade... 292s The following packages were automatically installed and are no longer required: 292s python3.13 python3.13-minimal 292s Use 'sudo apt autoremove' to remove them. 292s The following NEW packages will be installed: 292s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 292s The following packages will be upgraded: 292s libplymouth5 libpython3-stdlib plymouth plymouth-theme-ubuntu-text python3 292s python3-gdbm python3-minimal 292s 7 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 292s Need to get 6993 kB of archives. 292s After this operation, 26.0 MB of additional disk space will be used. 292s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 293s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 293s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-gdbm arm64 3.14.2-1 [11.1 kB] 293s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-minimal arm64 3.14.2-1 [28.2 kB] 293s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3 arm64 3.14.2-1 [22.9 kB] 293s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 293s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 293s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libpython3-stdlib arm64 3.14.2-1 [10.9 kB] 293s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 libplymouth5 arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [141 kB] 293s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [10.0 kB] 293s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 plymouth arm64 24.004.60+git20250831.4a3c171d-0ubuntu4 [138 kB] 293s dpkg-preconfigure: unable to re-open stdin: No such file or directory 293s Fetched 6993 kB in 0s (15.6 MB/s) 293s Selecting previously unselected package libpython3.14-minimal:arm64. 294s (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 ... 135223 files and directories currently installed.) 294s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_arm64.deb ... 294s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 294s Selecting previously unselected package python3.14-minimal. 294s Preparing to unpack .../python3.14-minimal_3.14.2-1_arm64.deb ... 294s Unpacking python3.14-minimal (3.14.2-1) ... 294s Preparing to unpack .../python3-gdbm_3.14.2-1_arm64.deb ... 294s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-1) ... 294s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 294s Setting up python3.14-minimal (3.14.2-1) ... 296s (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 ... 135565 files and directories currently installed.) 296s Preparing to unpack .../python3-minimal_3.14.2-1_arm64.deb ... 296s Unpacking python3-minimal (3.14.2-1) over (3.13.7-1) ... 296s Setting up python3-minimal (3.14.2-1) ... 296s (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 ... 135565 files and directories currently installed.) 296s Preparing to unpack .../0-python3_3.14.2-1_arm64.deb ... 296s running python pre-rtupdate hooks for python3.14... 296s Unpacking python3 (3.14.2-1) over (3.13.7-1) ... 296s Selecting previously unselected package libpython3.14-stdlib:arm64. 296s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 296s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 297s Selecting previously unselected package python3.14. 297s Preparing to unpack .../2-python3.14_3.14.2-1_arm64.deb ... 297s Unpacking python3.14 (3.14.2-1) ... 297s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_arm64.deb ... 297s Unpacking libpython3-stdlib:arm64 (3.14.2-1) over (3.13.7-1) ... 297s Preparing to unpack .../4-libplymouth5_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 297s Unpacking libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 297s Preparing to unpack .../5-plymouth-theme-ubuntu-text_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 297s Unpacking plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 297s Preparing to unpack .../6-plymouth_24.004.60+git20250831.4a3c171d-0ubuntu4_arm64.deb ... 297s Unpacking plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) over (24.004.60+git20250831.4a3c171d-0ubuntu3) ... 297s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 297s Setting up libplymouth5:arm64 (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 297s Setting up python3.14 (3.14.2-1) ... 299s Setting up libpython3-stdlib:arm64 (3.14.2-1) ... 299s Setting up python3-gdbm (3.14.2-1) ... 299s Setting up plymouth (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 299s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 299s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 299s Setting up python3 (3.14.2-1) ... 299s running python rtupdate hooks for python3.14... 299s running python post-rtupdate hooks for python3.14... 300s Processing triggers for libc-bin (2.42-2ubuntu4) ... 300s Processing triggers for systemd (259-1ubuntu2) ... 300s Processing triggers for man-db (2.13.1-1) ... 302s Processing triggers for initramfs-tools (0.150ubuntu7) ... 302s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 322s System running in EFI mode, skipping. 322s Setting up plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu4) ... 322s Processing triggers for initramfs-tools (0.150ubuntu7) ... 322s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 340s System running in EFI mode, skipping. 340s autopkgtest [20:04:59]: upgrading testbed (apt dist-upgrade and autopurge) 340s Reading package lists... 340s Building dependency tree... 340s Reading state information... 340s Calculating upgrade... 341s The following packages were automatically installed and are no longer required: 341s python3.13 python3.13-minimal 341s Use 'sudo apt autoremove' to remove them. 341s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 341s Reading package lists... 341s Building dependency tree... 341s Reading state information... 342s Solving dependencies... 342s The following packages will be REMOVED: 342s python3.13* python3.13-minimal* 342s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 342s After this operation, 7766 kB disk space will be freed. 342s (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 ... 135995 files and directories currently installed.) 342s Removing python3.13 (3.13.11-1) ... 343s Removing python3.13-minimal (3.13.11-1) ... 344s Processing triggers for man-db (2.13.1-1) ... 344s Processing triggers for systemd (259-1ubuntu2) ... 344s (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 ... 135968 files and directories currently installed.) 344s Purging configuration files for python3.13-minimal (3.13.11-1) ... 344s autopkgtest [20:05:03]: rebooting testbed after setup commands that affected boot 386s Reading package lists... 386s Building dependency tree... 386s Reading state information... 386s Solving dependencies... 387s The following NEW packages will be installed: 387s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 387s cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 387s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-15 387s g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 387s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 387s libarchive-zip-perl libasan8 libblas3 libcc1-0 libdebhelper-perl 387s libfile-stripnondeterminism-perl libgcc-15-dev libgfortran5 libgomp1 387s libhwasan0 libisl23 libitm1 liblapack3 liblsan0 libmpc3 libstdc++-15-dev 387s libtool libtsan2 libubsan1 m4 po-debconf pybuild-plugin-autopkgtest 387s pyensembl pylint python3-all python3-astroid python3-datacache python3-dill 387s python3-gtfparse python3-iniconfig python3-isort python3-logilab-common 387s python3-mccabe python3-memoized-property python3-mypy-extensions 387s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 387s python3-platformdirs python3-pluggy python3-pytest python3-pytz 387s python3-serializable python3-tomlkit python3-typechecks python3.13 387s python3.13-minimal 387s 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. 387s Need to get 90.6 MB of archives. 387s After this operation, 352 MB of additional disk space will be used. 387s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13-minimal arm64 3.13.11-1 [2346 kB] 387s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 387s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 387s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-11ubuntu1 [450 kB] 387s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 387s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 388s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.13 arm64 3.13.11-1 [758 kB] 388s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 m4 arm64 1.4.20-2 [213 kB] 388s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 388s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 autotools-dev all 20240727.1 [43.4 kB] 388s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 automake all 1:1.18.1-3build1 [582 kB] 388s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 autopoint all 0.23.2-1 [620 kB] 388s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 388s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 388s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [11.7 MB] 388s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-11ubuntu1 [1030 B] 388s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 388s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 388s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-11ubuntu1 [49.0 kB] 388s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-11ubuntu1 [147 kB] 388s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-11ubuntu1 [28.0 kB] 388s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-11ubuntu1 [2920 kB] 388s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-11ubuntu1 [1316 kB] 388s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-11ubuntu1 [2690 kB] 388s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-11ubuntu1 [1176 kB] 388s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-11ubuntu1 [1638 kB] 388s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-11ubuntu1 [2600 kB] 388s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [23.1 MB] 389s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-11ubuntu1 [517 kB] 389s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 389s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 389s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-11ubuntu1 [2547 kB] 389s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-11ubuntu1 [13.2 MB] 389s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-11ubuntu1 [24.6 kB] 389s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 389s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 389s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 389s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 389s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 libtool all 2.5.4-9 [169 kB] 389s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-autoreconf all 21 [12.5 kB] 389s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 389s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 389s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 389s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 debugedit arm64 1:5.2-3 [49.1 kB] 389s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 dwz arm64 0.16-2 [113 kB] 389s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB] 389s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 389s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 po-debconf all 1.0.22 [215 kB] 389s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 debhelper all 13.28ubuntu1 [916 kB] 389s Get:50 http://ftpmaster.internal/ubuntu resolute/universe arm64 dh-python all 7.20251231 [122 kB] 389s Get:51 http://ftpmaster.internal/ubuntu resolute/universe arm64 pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 389s Get:52 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 389s Get:53 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-isort all 7.0.0-1 [59.7 kB] 389s Get:54 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mypy-extensions all 1.1.0-1 [6716 B] 389s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-logilab-common all 2.1.0-1 [95.7 kB] 389s Get:56 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dill all 0.4.0-1 [84.8 kB] 389s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mccabe all 0.7.0-1build1 [8926 B] 389s Get:58 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 389s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tomlkit all 0.13.3-2 [39.1 kB] 389s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 pylint all 4.0.4-1 [346 kB] 389s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 389s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 390s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 390s Get:64 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typechecks all 0.1.0+ds-4 [4562 B] 390s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datacache all 1.4.1-2 [13.1 kB] 390s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 390s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-memoized-property all 1.0.3-2build1 [5328 B] 390s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-serializable all 0.4.1+ds-2 [8438 B] 390s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 pyensembl all 2.3.13-2 [37.2 kB] 390s Get:70 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-all arm64 3.14.2-1 [888 B] 390s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 390s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 390s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 390s Fetched 90.6 MB in 3s (32.9 MB/s) 390s Selecting previously unselected package python3.13-minimal. 391s (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 ... 135970 files and directories currently installed.) 391s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_arm64.deb ... 391s Unpacking python3.13-minimal (3.13.11-1) ... 391s Selecting previously unselected package python3-numpy-dev:arm64. 391s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 391s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 391s Selecting previously unselected package libblas3:arm64. 391s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_arm64.deb ... 391s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 391s Selecting previously unselected package libgfortran5:arm64. 391s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_arm64.deb ... 391s Unpacking libgfortran5:arm64 (15.2.0-11ubuntu1) ... 391s Selecting previously unselected package liblapack3:arm64. 391s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 391s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 391s Selecting previously unselected package python3-numpy. 391s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 391s Unpacking python3-numpy (1:2.3.5+ds-3) ... 391s Selecting previously unselected package python3.13. 391s Preparing to unpack .../06-python3.13_3.13.11-1_arm64.deb ... 391s Unpacking python3.13 (3.13.11-1) ... 391s Selecting previously unselected package m4. 391s Preparing to unpack .../07-m4_1.4.20-2_arm64.deb ... 391s Unpacking m4 (1.4.20-2) ... 391s Selecting previously unselected package autoconf. 391s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 391s Unpacking autoconf (2.72-3.1ubuntu1) ... 391s Selecting previously unselected package autotools-dev. 391s Preparing to unpack .../09-autotools-dev_20240727.1_all.deb ... 391s Unpacking autotools-dev (20240727.1) ... 391s Selecting previously unselected package automake. 391s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 391s Unpacking automake (1:1.18.1-3build1) ... 391s Selecting previously unselected package autopoint. 391s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 391s Unpacking autopoint (0.23.2-1) ... 392s Selecting previously unselected package libisl23:arm64. 392s Preparing to unpack .../12-libisl23_0.27-1build1_arm64.deb ... 392s Unpacking libisl23:arm64 (0.27-1build1) ... 392s Selecting previously unselected package libmpc3:arm64. 392s Preparing to unpack .../13-libmpc3_1.3.1-2_arm64.deb ... 392s Unpacking libmpc3:arm64 (1.3.1-2) ... 392s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 392s Preparing to unpack .../14-cpp-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package cpp-15. 392s Preparing to unpack .../15-cpp-15_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package cpp-aarch64-linux-gnu. 392s Preparing to unpack .../16-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 392s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 392s Selecting previously unselected package cpp. 392s Preparing to unpack .../17-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 392s Unpacking cpp (4:15.2.0-4ubuntu1) ... 392s Selecting previously unselected package libcc1-0:arm64. 392s Preparing to unpack .../18-libcc1-0_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking libcc1-0:arm64 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package libgomp1:arm64. 392s Preparing to unpack .../19-libgomp1_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking libgomp1:arm64 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package libitm1:arm64. 392s Preparing to unpack .../20-libitm1_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking libitm1:arm64 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package libasan8:arm64. 392s Preparing to unpack .../21-libasan8_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking libasan8:arm64 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package liblsan0:arm64. 392s Preparing to unpack .../22-liblsan0_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking liblsan0:arm64 (15.2.0-11ubuntu1) ... 392s Selecting previously unselected package libtsan2:arm64. 392s Preparing to unpack .../23-libtsan2_15.2.0-11ubuntu1_arm64.deb ... 392s Unpacking libtsan2:arm64 (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package libubsan1:arm64. 393s Preparing to unpack .../24-libubsan1_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking libubsan1:arm64 (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package libhwasan0:arm64. 393s Preparing to unpack .../25-libhwasan0_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking libhwasan0:arm64 (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package libgcc-15-dev:arm64. 393s Preparing to unpack .../26-libgcc-15-dev_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking libgcc-15-dev:arm64 (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 393s Preparing to unpack .../27-gcc-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package gcc-15. 393s Preparing to unpack .../28-gcc-15_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 393s Selecting previously unselected package gcc-aarch64-linux-gnu. 393s Preparing to unpack .../29-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 393s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 393s Selecting previously unselected package gcc. 393s Preparing to unpack .../30-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 393s Unpacking gcc (4:15.2.0-4ubuntu1) ... 393s Selecting previously unselected package libstdc++-15-dev:arm64. 393s Preparing to unpack .../31-libstdc++-15-dev_15.2.0-11ubuntu1_arm64.deb ... 393s Unpacking libstdc++-15-dev:arm64 (15.2.0-11ubuntu1) ... 394s Selecting previously unselected package g++-15-aarch64-linux-gnu. 394s Preparing to unpack .../32-g++-15-aarch64-linux-gnu_15.2.0-11ubuntu1_arm64.deb ... 394s Unpacking g++-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 394s Selecting previously unselected package g++-15. 394s Preparing to unpack .../33-g++-15_15.2.0-11ubuntu1_arm64.deb ... 394s Unpacking g++-15 (15.2.0-11ubuntu1) ... 394s Selecting previously unselected package g++-aarch64-linux-gnu. 394s Preparing to unpack .../34-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 394s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 394s Selecting previously unselected package g++. 394s Preparing to unpack .../35-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 394s Unpacking g++ (4:15.2.0-4ubuntu1) ... 394s Selecting previously unselected package build-essential. 394s Preparing to unpack .../36-build-essential_12.12ubuntu2_arm64.deb ... 394s Unpacking build-essential (12.12ubuntu2) ... 394s Selecting previously unselected package libdebhelper-perl. 394s Preparing to unpack .../37-libdebhelper-perl_13.28ubuntu1_all.deb ... 394s Unpacking libdebhelper-perl (13.28ubuntu1) ... 394s Selecting previously unselected package libtool. 394s Preparing to unpack .../38-libtool_2.5.4-9_all.deb ... 394s Unpacking libtool (2.5.4-9) ... 394s Selecting previously unselected package dh-autoreconf. 394s Preparing to unpack .../39-dh-autoreconf_21_all.deb ... 394s Unpacking dh-autoreconf (21) ... 394s Selecting previously unselected package libarchive-zip-perl. 394s Preparing to unpack .../40-libarchive-zip-perl_1.68-1_all.deb ... 394s Unpacking libarchive-zip-perl (1.68-1) ... 394s Selecting previously unselected package libfile-stripnondeterminism-perl. 394s Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 394s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 394s Selecting previously unselected package dh-strip-nondeterminism. 394s Preparing to unpack .../42-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 394s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 394s Selecting previously unselected package debugedit. 394s Preparing to unpack .../43-debugedit_1%3a5.2-3_arm64.deb ... 394s Unpacking debugedit (1:5.2-3) ... 395s Selecting previously unselected package dwz. 395s Preparing to unpack .../44-dwz_0.16-2_arm64.deb ... 395s Unpacking dwz (0.16-2) ... 395s Selecting previously unselected package gettext. 395s Preparing to unpack .../45-gettext_0.23.2-1_arm64.deb ... 395s Unpacking gettext (0.23.2-1) ... 395s Selecting previously unselected package intltool-debian. 395s Preparing to unpack .../46-intltool-debian_0.35.0+20060710.6build1_all.deb ... 395s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 395s Selecting previously unselected package po-debconf. 395s Preparing to unpack .../47-po-debconf_1.0.22_all.deb ... 395s Unpacking po-debconf (1.0.22) ... 395s Selecting previously unselected package debhelper. 395s Preparing to unpack .../48-debhelper_13.28ubuntu1_all.deb ... 395s Unpacking debhelper (13.28ubuntu1) ... 395s Selecting previously unselected package dh-python. 395s Preparing to unpack .../49-dh-python_7.20251231_all.deb ... 395s Unpacking dh-python (7.20251231) ... 395s Selecting previously unselected package pybuild-plugin-autopkgtest. 395s Preparing to unpack .../50-pybuild-plugin-autopkgtest_7.20251231_all.deb ... 395s Unpacking pybuild-plugin-autopkgtest (7.20251231) ... 395s Selecting previously unselected package python3-astroid. 395s Preparing to unpack .../51-python3-astroid_4.0.2-1ubuntu1_all.deb ... 395s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 395s Selecting previously unselected package python3-isort. 395s Preparing to unpack .../52-python3-isort_7.0.0-1_all.deb ... 395s Unpacking python3-isort (7.0.0-1) ... 395s Selecting previously unselected package python3-mypy-extensions. 395s Preparing to unpack .../53-python3-mypy-extensions_1.1.0-1_all.deb ... 395s Unpacking python3-mypy-extensions (1.1.0-1) ... 395s Selecting previously unselected package python3-logilab-common. 395s Preparing to unpack .../54-python3-logilab-common_2.1.0-1_all.deb ... 395s Unpacking python3-logilab-common (2.1.0-1) ... 395s Selecting previously unselected package python3-dill. 395s Preparing to unpack .../55-python3-dill_0.4.0-1_all.deb ... 395s Unpacking python3-dill (0.4.0-1) ... 395s Selecting previously unselected package python3-mccabe. 395s Preparing to unpack .../56-python3-mccabe_0.7.0-1build1_all.deb ... 395s Unpacking python3-mccabe (0.7.0-1build1) ... 395s Selecting previously unselected package python3-platformdirs. 395s Preparing to unpack .../57-python3-platformdirs_4.5.1-1_all.deb ... 395s Unpacking python3-platformdirs (4.5.1-1) ... 395s Selecting previously unselected package python3-tomlkit. 395s Preparing to unpack .../58-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 .../59-pylint_4.0.4-1_all.deb ... 395s Unpacking pylint (4.0.4-1) ... 395s Selecting previously unselected package python3-pytz. 395s Preparing to unpack .../60-python3-pytz_2025.2-5_all.deb ... 395s Unpacking python3-pytz (2025.2-5) ... 396s Selecting previously unselected package python3-pandas-lib:arm64. 396s Preparing to unpack .../61-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 396s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 396s Selecting previously unselected package python3-pandas. 396s Preparing to unpack .../62-python3-pandas_2.3.3+dfsg-3_all.deb ... 396s Unpacking python3-pandas (2.3.3+dfsg-3) ... 396s Selecting previously unselected package python3-typechecks. 396s Preparing to unpack .../63-python3-typechecks_0.1.0+ds-4_all.deb ... 396s Unpacking python3-typechecks (0.1.0+ds-4) ... 396s Selecting previously unselected package python3-datacache. 396s Preparing to unpack .../64-python3-datacache_1.4.1-2_all.deb ... 396s Unpacking python3-datacache (1.4.1-2) ... 396s Selecting previously unselected package python3-gtfparse. 396s Preparing to unpack .../65-python3-gtfparse_1.3.0+ds-2_all.deb ... 396s Unpacking python3-gtfparse (1.3.0+ds-2) ... 396s Selecting previously unselected package python3-memoized-property. 396s Preparing to unpack .../66-python3-memoized-property_1.0.3-2build1_all.deb ... 396s Unpacking python3-memoized-property (1.0.3-2build1) ... 396s Selecting previously unselected package python3-serializable. 396s Preparing to unpack .../67-python3-serializable_0.4.1+ds-2_all.deb ... 396s Unpacking python3-serializable (0.4.1+ds-2) ... 396s Selecting previously unselected package pyensembl. 396s Preparing to unpack .../68-pyensembl_2.3.13-2_all.deb ... 396s Unpacking pyensembl (2.3.13-2) ... 396s Selecting previously unselected package python3-all. 396s Preparing to unpack .../69-python3-all_3.14.2-1_arm64.deb ... 396s Unpacking python3-all (3.14.2-1) ... 396s Selecting previously unselected package python3-iniconfig. 396s Preparing to unpack .../70-python3-iniconfig_2.1.0-2_all.deb ... 396s Unpacking python3-iniconfig (2.1.0-2) ... 396s Selecting previously unselected package python3-pluggy. 396s Preparing to unpack .../71-python3-pluggy_1.6.0-2_all.deb ... 396s Unpacking python3-pluggy (1.6.0-2) ... 397s Selecting previously unselected package python3-pytest. 397s Preparing to unpack .../72-python3-pytest_9.0.2-2_all.deb ... 397s Unpacking python3-pytest (9.0.2-2) ... 397s Setting up dh-python (7.20251231) ... 397s Setting up python3-iniconfig (2.1.0-2) ... 397s Setting up python3-typechecks (0.1.0+ds-4) ... 397s Setting up python3-memoized-property (1.0.3-2build1) ... 398s Setting up libarchive-zip-perl (1.68-1) ... 398s Setting up python3-mypy-extensions (1.1.0-1) ... 398s Setting up libdebhelper-perl (13.28ubuntu1) ... 398s Setting up m4 (1.4.20-2) ... 398s Setting up python3-pytz (2025.2-5) ... 398s Setting up python3-serializable (0.4.1+ds-2) ... 398s Setting up libgomp1:arm64 (15.2.0-11ubuntu1) ... 398s Setting up python3-platformdirs (4.5.1-1) ... 399s Setting up autotools-dev (20240727.1) ... 399s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 399s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 399s Setting up python3-dill (0.4.0-1) ... 399s Setting up libmpc3:arm64 (1.3.1-2) ... 399s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 399s Setting up autopoint (0.23.2-1) ... 399s Setting up libgfortran5:arm64 (15.2.0-11ubuntu1) ... 399s Setting up autoconf (2.72-3.1ubuntu1) ... 399s Setting up python3-isort (7.0.0-1) ... 400s Setting up python3-pluggy (1.6.0-2) ... 400s Setting up libubsan1:arm64 (15.2.0-11ubuntu1) ... 400s Setting up dwz (0.16-2) ... 400s Setting up python3-astroid (4.0.2-1ubuntu1) ... 400s Setting up libhwasan0:arm64 (15.2.0-11ubuntu1) ... 400s Setting up libasan8:arm64 (15.2.0-11ubuntu1) ... 400s Setting up debugedit (1:5.2-3) ... 400s Setting up python3.13-minimal (3.13.11-1) ... 402s Setting up python3-mccabe (0.7.0-1build1) ... 402s Setting up libtsan2:arm64 (15.2.0-11ubuntu1) ... 402s Setting up libisl23:arm64 (0.27-1build1) ... 402s Setting up python3-tomlkit (0.13.3-2) ... 402s Setting up libcc1-0:arm64 (15.2.0-11ubuntu1) ... 402s Setting up liblsan0:arm64 (15.2.0-11ubuntu1) ... 402s Setting up libitm1:arm64 (15.2.0-11ubuntu1) ... 402s Setting up automake (1:1.18.1-3build1) ... 402s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 402s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 402s Setting up cpp-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 402s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 402s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 402s Setting up gettext (0.23.2-1) ... 402s Setting up libgcc-15-dev:arm64 (15.2.0-11ubuntu1) ... 402s Setting up python3-logilab-common (2.1.0-1) ... 403s Setting up python3.13 (3.13.11-1) ... 404s Setting up python3-pytest (9.0.2-2) ... 405s Setting up python3-all (3.14.2-1) ... 405s Setting up intltool-debian (0.35.0+20060710.6build1) ... 405s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 405s Setting up libstdc++-15-dev:arm64 (15.2.0-11ubuntu1) ... 405s Setting up python3-numpy (1:2.3.5+ds-3) ... 409s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 409s Setting up cpp-15 (15.2.0-11ubuntu1) ... 409s Setting up cpp (4:15.2.0-4ubuntu1) ... 409s Setting up pylint (4.0.4-1) ... 410s Setting up gcc-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 410s Setting up po-debconf (1.0.22) ... 410s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 410s Setting up gcc-15 (15.2.0-11ubuntu1) ... 410s Setting up python3-pandas (2.3.3+dfsg-3) ... 422s Setting up g++-15-aarch64-linux-gnu (15.2.0-11ubuntu1) ... 422s Setting up g++-15 (15.2.0-11ubuntu1) ... 422s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 422s Setting up python3-datacache (1.4.1-2) ... 422s Setting up libtool (2.5.4-9) ... 422s Setting up python3-gtfparse (1.3.0+ds-2) ... 422s Setting up gcc (4:15.2.0-4ubuntu1) ... 422s Setting up dh-autoreconf (21) ... 422s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 422s Setting up pyensembl (2.3.13-2) ... 423s Setting up debhelper (13.28ubuntu1) ... 423s Setting up g++ (4:15.2.0-4ubuntu1) ... 423s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 423s Setting up build-essential (12.12ubuntu2) ... 423s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 423s Processing triggers for man-db (2.13.1-1) ... 424s Processing triggers for install-info (7.2-5) ... 424s Processing triggers for libc-bin (2.42-2ubuntu4) ... 424s Processing triggers for systemd (259-1ubuntu2) ... 427s autopkgtest [20:06:26]: test pybuild-autopkgtest: pybuild-autopkgtest 427s autopkgtest [20:06:26]: test pybuild-autopkgtest: [----------------------- 427s pybuild-autopkgtest 428s I: pybuild base:384: cd /tmp/autopkgtest.wTUGyl/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' 428s ============================= test session starts ============================== 428s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 428s cachedir: .pytest_cache 428s rootdir: /tmp/autopkgtest.wTUGyl/autopkgtest_tmp/build 428s plugins: typeguard-4.4.4 429s collecting ... collected 126 items / 98 deselected / 28 selected 429s 429s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 429s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 429s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 429s tests/test_locus.py::test_locus_contains PASSED [ 14%] 430s tests/test_locus.py::test_position_offset PASSED [ 17%] 430s tests/test_locus.py::test_range_offset PASSED [ 21%] 430s tests/test_locus.py::test_locus_distance PASSED [ 25%] 430s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 430s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 430s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 430s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 430s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 430s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 430s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 430s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 430s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 430s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 430s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 430s tests/test_release_versions.py::test_int_version PASSED [ 67%] 430s tests/test_release_versions.py::test_str_version PASSED [ 71%] 430s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 430s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 430s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 430s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 430s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 430s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 430s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 430s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 430s 430s =============================== warnings summary =============================== 430s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 430s /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 430s import pkg_resources 430s 430s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 430s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 430s 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 430s declare_namespace(pkg) 430s 430s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 430s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 430s release_group = root_group.add_argument_group() 430s 430s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 430s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 430s path_group = root_group.add_argument_group() 430s 430s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 430s ================ 28 passed, 98 deselected, 4 warnings in 1.69s ================= 430s I: pybuild base:384: cd /tmp/autopkgtest.wTUGyl/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' 431s ============================= test session starts ============================== 431s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 431s cachedir: .pytest_cache 431s rootdir: /tmp/autopkgtest.wTUGyl/autopkgtest_tmp/build 431s plugins: typeguard-4.4.4 432s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 432s 432s ==================================== ERRORS ==================================== 432s _____________________ ERROR collecting tests/test_shell.py _____________________ 432s tests/test_shell.py:1: in 432s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 432s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 432s release_group = root_group.add_argument_group() 432s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 432s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 432s raise ValueError('argument groups cannot be nested') 432s E ValueError: argument groups cannot be nested 432s =============================== warnings summary =============================== 432s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 432s /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 432s import pkg_resources 432s 432s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 432s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 432s 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 432s declare_namespace(pkg) 432s 432s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 432s =========================== short test summary info ============================ 432s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 432s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 432s ================= 98 deselected, 2 warnings, 1 error in 1.11s ================== 433s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.wTUGyl/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' 433s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 433s make: *** [/tmp/vnZOzYYBnJ/run:4: pybuild-autopkgtest] Error 25 433s pybuild-autopkgtest: error: /tmp/vnZOzYYBnJ/run pybuild-autopkgtest returned exit code 2 433s autopkgtest [20:06:32]: test pybuild-autopkgtest: -----------------------] 434s autopkgtest [20:06:33]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 434s pybuild-autopkgtest FAIL non-zero exit status 25 434s autopkgtest [20:06:33]: @@@@@@@@@@@@@@@@@@@@ summary 434s run-unit-test FAIL non-zero exit status 2 434s pybuild-autopkgtest FAIL non-zero exit status 25