0s autopkgtest [12:54:11]: starting date and time: 2026-01-24 12:54:11+0000 0s autopkgtest [12:54:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:54:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.y8e26eov/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-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-7.secgroup --name adt-resolute-amd64-pyensembl-20260124-125411-juju-7f2275-prod-proposed-migration-environment-15-ee2f4335-47fc-47d1-9701-cf05207e305b --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-pyensembl-20260124-125411-juju-7f2275-prod-proposed-migration-environment-15-ee2f4335-47fc-47d1-9701-cf05207e305b from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 87s autopkgtest [12:55:38]: testbed dpkg architecture: amd64 88s autopkgtest [12:55:39]: testbed apt version: 3.1.13 88s autopkgtest [12:55:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s autopkgtest [12:55:39]: testbed release detected to be: None 89s autopkgtest [12:55:40]: updating testbed package index (apt update) 89s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 89s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 89s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 89s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 89s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 89s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 89s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 90s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 90s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 90s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 90s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 90s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 90s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 90s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 90s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 90s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 90s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 90s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 91s Fetched 2806 kB in 1s (2875 kB/s) 92s Reading package lists... 93s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 93s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 93s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 93s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 94s Reading package lists... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Calculating upgrade... 94s The following packages were automatically installed and are no longer required: 94s python3.13 python3.13-minimal 94s Use 'sudo apt autoremove' to remove them. 94s The following NEW packages will be installed: 94s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 94s The following packages will be upgraded: 94s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 94s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 10.4 MB of archives. 94s After this operation, 25.2 MB of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 95s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 95s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 95s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 95s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 95s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 95s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 95s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 95s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 95s dpkg-preconfigure: unable to re-open stdin: No such file or directory 95s Fetched 10.4 MB in 1s (15.2 MB/s) 95s Selecting previously unselected package libpython3.14-minimal:amd64. 96s (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 ... 124177 files and directories currently installed.) 96s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 96s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 96s Selecting previously unselected package python3.14-minimal. 96s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 96s Unpacking python3.14-minimal (3.14.2-1) ... 96s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 96s Setting up python3.14-minimal (3.14.2-1) ... 97s (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 ... 124519 files and directories currently installed.) 97s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 97s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 97s Setting up python3-minimal (3.14.2-1) ... 97s (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 ... 124519 files and directories currently installed.) 97s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 97s running python pre-rtupdate hooks for python3.14... 97s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 97s Selecting previously unselected package libpython3.14-stdlib:amd64. 98s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 98s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 98s Selecting previously unselected package python3.14. 98s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 98s Unpacking python3.14 (3.14.2-1) ... 98s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 98s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 98s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 98s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 98s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 98s (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 ... 124980 files and directories currently installed.) 98s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 98s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 98s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 98s Setting up python3.14 (3.14.2-1) ... 99s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 99s Setting up python3-gdbm (3.14.2-1) ... 99s Setting up python3 (3.14.2-1) ... 99s running python rtupdate hooks for python3.14... 99s running python post-rtupdate hooks for python3.14... 99s Processing triggers for man-db (2.13.1-1) ... 100s Processing triggers for systemd (259-1ubuntu2) ... 100s autopkgtest [12:55:51]: upgrading testbed (apt dist-upgrade and autopurge) 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Calculating upgrade... 101s The following packages were automatically installed and are no longer required: 101s python3.13 python3.13-minimal 101s Use 'sudo apt autoremove' to remove them. 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s Solving dependencies... 102s The following packages will be REMOVED: 102s python3.13* python3.13-minimal* 102s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 102s After this operation, 7860 kB disk space will be freed. 102s (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 ... 124978 files and directories currently installed.) 102s Removing python3.13 (3.13.11-1) ... 102s Removing python3.13-minimal (3.13.11-1) ... 103s Processing triggers for man-db (2.13.1-1) ... 103s Processing triggers for systemd (259-1ubuntu2) ... 103s (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 ... 124951 files and directories currently installed.) 103s Purging configuration files for python3.13-minimal (3.13.11-1) ... 106s autopkgtest [12:55:57]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 106s autopkgtest [12:55:57]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 108s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 108s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 108s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 108s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 108s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 108s gpgv: issuer "tchet@debian.org" 108s gpgv: Can't check signature: No public key 108s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 108s autopkgtest [12:55:59]: testing package pyensembl version 2.3.13-2 108s autopkgtest [12:55:59]: build not needed 108s autopkgtest [12:55:59]: test run-unit-test: preparing testbed 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Solving dependencies... 109s The following NEW packages will be installed: 109s libblas3 libgfortran5 liblapack3 pyensembl pylint python3-all 109s python3-astroid python3-datacache python3-dill python3-gtfparse 109s python3-iniconfig python3-isort python3-logilab-common python3-mccabe 109s python3-memoized-property python3-mypy-extensions python3-numpy 109s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 109s python3-pluggy python3-pytest python3-pytz python3-serializable 109s python3-tomlkit python3-typechecks python3.13 python3.13-minimal 109s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 26.5 MB of archives. 109s After this operation, 135 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 109s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 109s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 109s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 109s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 109s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 109s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 109s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 109s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-isort all 7.0.0-1 [59.7 kB] 109s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 109s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 109s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dill all 0.4.0-1 [84.8 kB] 109s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mccabe all 0.7.0-1build1 [8926 B] 109s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.5.1-1 [17.1 kB] 109s Get:15 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tomlkit all 0.13.3-2 [39.1 kB] 109s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 pylint all 4.0.4-1 [346 kB] 109s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 109s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 110s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 110s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typechecks all 0.1.0+ds-4 [4562 B] 110s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-datacache all 1.4.1-2 [13.1 kB] 110s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 110s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-memoized-property all 1.0.3-2build1 [5328 B] 110s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-serializable all 0.4.1+ds-2 [8438 B] 110s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 pyensembl all 2.3.13-2 [37.2 kB] 110s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 110s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 110s Get:28 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 110s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 110s Fetched 26.5 MB in 1s (40.5 MB/s) 110s Selecting previously unselected package python3.13-minimal. 110s (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 ... 124953 files and directories currently installed.) 110s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_amd64.deb ... 110s Unpacking python3.13-minimal (3.13.11-1) ... 110s Selecting previously unselected package python3-numpy-dev:amd64. 110s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 110s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 110s Selecting previously unselected package libblas3:amd64. 110s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_amd64.deb ... 110s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 110s Selecting previously unselected package libgfortran5:amd64. 110s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 110s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 110s Selecting previously unselected package liblapack3:amd64. 110s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 110s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 110s Selecting previously unselected package python3-numpy. 110s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 110s Unpacking python3-numpy (1:2.3.5+ds-3) ... 110s Selecting previously unselected package python3.13. 110s Preparing to unpack .../06-python3.13_3.13.11-1_amd64.deb ... 110s Unpacking python3.13 (3.13.11-1) ... 110s Selecting previously unselected package python3-astroid. 110s Preparing to unpack .../07-python3-astroid_4.0.2-1ubuntu1_all.deb ... 110s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 110s Selecting previously unselected package python3-isort. 110s Preparing to unpack .../08-python3-isort_7.0.0-1_all.deb ... 110s Unpacking python3-isort (7.0.0-1) ... 111s Selecting previously unselected package python3-mypy-extensions. 111s Preparing to unpack .../09-python3-mypy-extensions_1.1.0-1_all.deb ... 111s Unpacking python3-mypy-extensions (1.1.0-1) ... 111s Selecting previously unselected package python3-logilab-common. 111s Preparing to unpack .../10-python3-logilab-common_2.1.0-1build1_all.deb ... 111s Unpacking python3-logilab-common (2.1.0-1build1) ... 111s Selecting previously unselected package python3-dill. 111s Preparing to unpack .../11-python3-dill_0.4.0-1_all.deb ... 111s Unpacking python3-dill (0.4.0-1) ... 111s Selecting previously unselected package python3-mccabe. 111s Preparing to unpack .../12-python3-mccabe_0.7.0-1build1_all.deb ... 111s Unpacking python3-mccabe (0.7.0-1build1) ... 111s Selecting previously unselected package python3-platformdirs. 111s Preparing to unpack .../13-python3-platformdirs_4.5.1-1_all.deb ... 111s Unpacking python3-platformdirs (4.5.1-1) ... 111s Selecting previously unselected package python3-tomlkit. 111s Preparing to unpack .../14-python3-tomlkit_0.13.3-2_all.deb ... 111s Unpacking python3-tomlkit (0.13.3-2) ... 111s Selecting previously unselected package pylint. 111s Preparing to unpack .../15-pylint_4.0.4-1_all.deb ... 111s Unpacking pylint (4.0.4-1) ... 111s Selecting previously unselected package python3-pytz. 111s Preparing to unpack .../16-python3-pytz_2025.2-5_all.deb ... 111s Unpacking python3-pytz (2025.2-5) ... 111s Selecting previously unselected package python3-pandas-lib:amd64. 111s Preparing to unpack .../17-python3-pandas-lib_2.3.3+dfsg-3_amd64.deb ... 111s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 111s Selecting previously unselected package python3-pandas. 111s Preparing to unpack .../18-python3-pandas_2.3.3+dfsg-3_all.deb ... 111s Unpacking python3-pandas (2.3.3+dfsg-3) ... 111s Selecting previously unselected package python3-typechecks. 111s Preparing to unpack .../19-python3-typechecks_0.1.0+ds-4_all.deb ... 111s Unpacking python3-typechecks (0.1.0+ds-4) ... 111s Selecting previously unselected package python3-datacache. 111s Preparing to unpack .../20-python3-datacache_1.4.1-2_all.deb ... 111s Unpacking python3-datacache (1.4.1-2) ... 111s Selecting previously unselected package python3-gtfparse. 111s Preparing to unpack .../21-python3-gtfparse_1.3.0+ds-2_all.deb ... 111s Unpacking python3-gtfparse (1.3.0+ds-2) ... 111s Selecting previously unselected package python3-memoized-property. 111s Preparing to unpack .../22-python3-memoized-property_1.0.3-2build1_all.deb ... 111s Unpacking python3-memoized-property (1.0.3-2build1) ... 111s Selecting previously unselected package python3-serializable. 111s Preparing to unpack .../23-python3-serializable_0.4.1+ds-2_all.deb ... 111s Unpacking python3-serializable (0.4.1+ds-2) ... 111s Selecting previously unselected package pyensembl. 111s Preparing to unpack .../24-pyensembl_2.3.13-2_all.deb ... 111s Unpacking pyensembl (2.3.13-2) ... 111s Selecting previously unselected package python3-all. 111s Preparing to unpack .../25-python3-all_3.14.2-1_amd64.deb ... 111s Unpacking python3-all (3.14.2-1) ... 111s Selecting previously unselected package python3-iniconfig. 111s Preparing to unpack .../26-python3-iniconfig_2.1.0-2_all.deb ... 111s Unpacking python3-iniconfig (2.1.0-2) ... 111s Selecting previously unselected package python3-pluggy. 111s Preparing to unpack .../27-python3-pluggy_1.6.0-2_all.deb ... 111s Unpacking python3-pluggy (1.6.0-2) ... 111s Selecting previously unselected package python3-pytest. 111s Preparing to unpack .../28-python3-pytest_9.0.2-2_all.deb ... 111s Unpacking python3-pytest (9.0.2-2) ... 111s Setting up python3-iniconfig (2.1.0-2) ... 112s Setting up python3-typechecks (0.1.0+ds-4) ... 112s Setting up python3-memoized-property (1.0.3-2build1) ... 112s Setting up python3-mypy-extensions (1.1.0-1) ... 112s Setting up python3-pytz (2025.2-5) ... 112s Setting up python3-serializable (0.4.1+ds-2) ... 113s Setting up python3-platformdirs (4.5.1-1) ... 113s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 113s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 113s Setting up python3-dill (0.4.0-1) ... 113s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 113s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 113s Setting up python3-isort (7.0.0-1) ... 114s Setting up python3-pluggy (1.6.0-2) ... 114s Setting up python3-astroid (4.0.2-1ubuntu1) ... 114s Setting up python3.13-minimal (3.13.11-1) ... 115s Setting up python3-mccabe (0.7.0-1build1) ... 116s Setting up python3-tomlkit (0.13.3-2) ... 116s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 116s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 116s Setting up python3-logilab-common (2.1.0-1build1) ... 116s Setting up python3.13 (3.13.11-1) ... 118s Setting up python3-pytest (9.0.2-2) ... 118s Setting up python3-all (3.14.2-1) ... 118s Setting up python3-numpy (1:2.3.5+ds-3) ... 122s Setting up pylint (4.0.4-1) ... 123s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 123s Setting up python3-pandas (2.3.3+dfsg-3) ... 134s Setting up python3-datacache (1.4.1-2) ... 134s Setting up python3-gtfparse (1.3.0+ds-2) ... 134s Setting up pyensembl (2.3.13-2) ... 134s Processing triggers for systemd (259-1ubuntu2) ... 135s Processing triggers for man-db (2.13.1-1) ... 135s Processing triggers for libc-bin (2.42-2ubuntu4) ... 136s autopkgtest [12:56:27]: test run-unit-test: [----------------------- 137s ============================= test session starts ============================== 137s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 137s rootdir: /tmp/autopkgtest.gyB75a/autopkgtest_tmp 137s plugins: typeguard-4.4.4 137s collected 15 items 137s 137s tests/test_ensembl_object_properties.py . [ 6%] 137s tests/test_locus.py ...... [ 46%] 137s tests/test_release_versions.py ....... [ 93%] 138s tests/test_shell.py . [100%] 138s 138s =============================== warnings summary =============================== 138s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 138s /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 138s import pkg_resources 138s 138s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 138s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 138s 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 138s declare_namespace(pkg) 138s 138s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 138s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 138s release_group = root_group.add_argument_group() 138s 138s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 138s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 138s path_group = root_group.add_argument_group() 138s 138s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 138s ======================== 15 passed, 4 warnings in 1.10s ======================== 139s ============================= test session starts ============================== 139s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 139s rootdir: /tmp/autopkgtest.gyB75a/autopkgtest_tmp 139s plugins: typeguard-4.4.4 139s collected 14 items / 1 error 139s 139s ==================================== ERRORS ==================================== 139s _____________________ ERROR collecting tests/test_shell.py _____________________ 139s tests/test_shell.py:1: in 139s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 139s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 139s release_group = root_group.add_argument_group() 139s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 139s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 139s raise ValueError('argument groups cannot be nested') 139s E ValueError: argument groups cannot be nested 139s =============================== warnings summary =============================== 139s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 139s /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 139s import pkg_resources 139s 139s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 139s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 139s 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 139s declare_namespace(pkg) 139s 139s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 139s =========================== short test summary info ============================ 139s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 139s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 139s ========================= 2 warnings, 1 error in 1.04s ========================= 140s autopkgtest [12:56:31]: test run-unit-test: -----------------------] 140s run-unit-test FAIL non-zero exit status 2 140s autopkgtest [12:56:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 140s autopkgtest [12:56:31]: test pybuild-autopkgtest: preparing testbed 158s Creating nova instance adt-resolute-amd64-pyensembl-20260124-125411-juju-7f2275-prod-proposed-migration-environment-15-ee2f4335-47fc-47d1-9701-cf05207e305b from image adt/ubuntu-resolute-amd64-server-20260124.img (UUID 46811f22-3700-43f4-953b-ee3c613d71bb)... 230s autopkgtest [12:58:01]: testbed dpkg architecture: amd64 230s autopkgtest [12:58:01]: testbed apt version: 3.1.13 231s autopkgtest [12:58:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 231s autopkgtest [12:58:02]: testbed release detected to be: resolute 231s autopkgtest [12:58:02]: updating testbed package index (apt update) 231s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 231s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 232s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 232s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 232s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 232s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [24.3 kB] 232s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [998 kB] 232s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [92.3 kB] 232s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [98.2 kB] 232s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [115 kB] 232s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3712 B] 232s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [12.3 kB] 232s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3696 B] 232s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 232s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [385 kB] 232s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [905 kB] 232s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [24.9 kB] 232s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4704 B] 232s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [12.4 kB] 232s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [824 B] 233s Fetched 2806 kB in 1s (3097 kB/s) 233s Reading package lists... 234s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 234s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 234s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 234s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 235s Reading package lists... 235s Reading package lists... 235s Building dependency tree... 235s Reading state information... 235s Calculating upgrade... 235s The following packages were automatically installed and are no longer required: 235s python3.13 python3.13-minimal 235s Use 'sudo apt autoremove' to remove them. 235s The following NEW packages will be installed: 235s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 235s The following packages will be upgraded: 235s libpython3-stdlib python3 python3-gdbm python3-minimal rust-coreutils 235s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 10.4 MB of archives. 235s After this operation, 25.2 MB of additional disk space will be used. 235s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 235s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 235s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-minimal amd64 3.14.2-1 [28.2 kB] 235s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3 amd64 3.14.2-1 [22.9 kB] 235s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 235s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 235s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libpython3-stdlib amd64 3.14.2-1 [10.9 kB] 236s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 rust-coreutils amd64 0.5.0-0ubuntu1 [3628 kB] 236s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-gdbm amd64 3.14.2-1 [11.1 kB] 236s dpkg-preconfigure: unable to re-open stdin: No such file or directory 236s Fetched 10.4 MB in 1s (13.7 MB/s) 236s Selecting previously unselected package libpython3.14-minimal:amd64. 236s (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 ... 124177 files and directories currently installed.) 236s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_amd64.deb ... 236s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 236s Selecting previously unselected package python3.14-minimal. 236s Preparing to unpack .../python3.14-minimal_3.14.2-1_amd64.deb ... 236s Unpacking python3.14-minimal (3.14.2-1) ... 236s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 236s Setting up python3.14-minimal (3.14.2-1) ... 237s (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 ... 124519 files and directories currently installed.) 237s Preparing to unpack .../python3-minimal_3.14.2-1_amd64.deb ... 237s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 237s Setting up python3-minimal (3.14.2-1) ... 237s (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 ... 124519 files and directories currently installed.) 237s Preparing to unpack .../python3_3.14.2-1_amd64.deb ... 237s running python pre-rtupdate hooks for python3.14... 237s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 237s Selecting previously unselected package libpython3.14-stdlib:amd64. 237s Preparing to unpack .../libpython3.14-stdlib_3.14.2-1_amd64.deb ... 237s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 237s Selecting previously unselected package python3.14. 237s Preparing to unpack .../python3.14_3.14.2-1_amd64.deb ... 237s Unpacking python3.14 (3.14.2-1) ... 237s Preparing to unpack .../libpython3-stdlib_3.14.2-1_amd64.deb ... 237s Unpacking libpython3-stdlib:amd64 (3.14.2-1) over (3.13.9-3) ... 237s Preparing to unpack .../rust-coreutils_0.5.0-0ubuntu1_amd64.deb ... 237s Unpacking rust-coreutils (0.5.0-0ubuntu1) over (0.2.2-0ubuntu2) ... 237s Setting up rust-coreutils (0.5.0-0ubuntu1) ... 237s (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 ... 124980 files and directories currently installed.) 237s Preparing to unpack .../python3-gdbm_3.14.2-1_amd64.deb ... 237s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 237s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 237s Setting up python3.14 (3.14.2-1) ... 238s Setting up libpython3-stdlib:amd64 (3.14.2-1) ... 238s Setting up python3-gdbm (3.14.2-1) ... 238s Setting up python3 (3.14.2-1) ... 238s running python rtupdate hooks for python3.14... 238s running python post-rtupdate hooks for python3.14... 238s Processing triggers for man-db (2.13.1-1) ... 239s Processing triggers for systemd (259-1ubuntu2) ... 239s autopkgtest [12:58:10]: upgrading testbed (apt dist-upgrade and autopurge) 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 239s Calculating upgrade... 239s The following packages were automatically installed and are no longer required: 239s python3.13 python3.13-minimal 239s Use 'sudo apt autoremove' to remove them. 239s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 239s Solving dependencies... 239s The following packages will be REMOVED: 239s python3.13* python3.13-minimal* 240s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 240s After this operation, 7860 kB disk space will be freed. 240s (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 ... 124978 files and directories currently installed.) 240s Removing python3.13 (3.13.11-1) ... 240s Removing python3.13-minimal (3.13.11-1) ... 240s Processing triggers for man-db (2.13.1-1) ... 240s Processing triggers for systemd (259-1ubuntu2) ... 240s (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 ... 124951 files and directories currently installed.) 240s Purging configuration files for python3.13-minimal (3.13.11-1) ... 243s Reading package lists... 243s Building dependency tree... 243s Reading state information... 243s Solving dependencies... 243s The following NEW packages will be installed: 243s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 243s cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 243s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-15 243s g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15 243s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 243s libarchive-zip-perl libasan8 libblas3 libcc1-0 libdebhelper-perl 243s libfile-stripnondeterminism-perl libgcc-15-dev libgfortran5 libgomp1 243s libhwasan0 libisl23 libitm1 liblapack3 liblsan0 libmpc3 libquadmath0 243s libstdc++-15-dev libtool libtsan2 libubsan1 m4 po-debconf 243s pybuild-plugin-autopkgtest pyensembl pylint python3-all python3-astroid 243s python3-datacache python3-dill python3-gtfparse python3-iniconfig 243s python3-isort python3-logilab-common python3-mccabe 243s python3-memoized-property python3-mypy-extensions python3-numpy 243s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 243s python3-pluggy python3-pytest python3-pytz python3-serializable 243s python3-tomlkit python3-typechecks python3.13 python3.13-minimal 243s 0 upgraded, 74 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 101 MB of archives. 243s After this operation, 386 MB of additional disk space will be used. 243s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13-minimal amd64 3.13.11-1 [2408 kB] 243s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 243s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 243s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-11ubuntu1 [939 kB] 243s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 244s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 244s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.13 amd64 3.13.11-1 [758 kB] 244s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 244s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 244s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1 [43.4 kB] 244s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 244s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 244s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 244s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 244s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [12.9 MB] 245s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-11ubuntu1 [1030 B] 245s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 245s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 245s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-11ubuntu1 [47.4 kB] 245s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-11ubuntu1 [151 kB] 245s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-11ubuntu1 [29.5 kB] 245s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-11ubuntu1 [3070 kB] 245s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-11ubuntu1 [1360 kB] 245s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-11ubuntu1 [2757 kB] 245s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-11ubuntu1 [1210 kB] 245s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-11ubuntu1 [1685 kB] 245s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-11ubuntu1 [153 kB] 245s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-11ubuntu1 [2863 kB] 245s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [25.4 MB] 245s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-11ubuntu1 [528 kB] 245s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 245s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 245s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-11ubuntu1 [2574 kB] 245s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-11ubuntu1 [14.4 MB] 246s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-11ubuntu1 [24.6 kB] 246s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 246s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 246s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 246s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 246s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 246s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21 [12.5 kB] 246s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 246s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 246s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 246s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3 [49.9 kB] 246s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2 [115 kB] 246s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 246s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 246s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 246s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 246s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20251231 [122 kB] 246s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 7.20251231 [1748 B] 246s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 246s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-isort all 7.0.0-1 [59.7 kB] 246s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 246s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 246s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dill all 0.4.0-1 [84.8 kB] 246s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mccabe all 0.7.0-1build1 [8926 B] 246s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.5.1-1 [17.1 kB] 246s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tomlkit all 0.13.3-2 [39.1 kB] 246s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 pylint all 4.0.4-1 [346 kB] 246s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 246s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 246s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 246s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typechecks all 0.1.0+ds-4 [4562 B] 246s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-datacache all 1.4.1-2 [13.1 kB] 246s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 246s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-memoized-property all 1.0.3-2build1 [5328 B] 246s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-serializable all 0.4.1+ds-2 [8438 B] 246s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 pyensembl all 2.3.13-2 [37.2 kB] 246s Get:71 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-all amd64 3.14.2-1 [890 B] 246s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 246s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 246s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 246s Fetched 101 MB in 3s (31.7 MB/s) 246s Selecting previously unselected package python3.13-minimal. 246s (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 ... 124953 files and directories currently installed.) 246s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_amd64.deb ... 246s Unpacking python3.13-minimal (3.13.11-1) ... 246s Selecting previously unselected package python3-numpy-dev:amd64. 246s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 246s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 246s Selecting previously unselected package libblas3:amd64. 246s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_amd64.deb ... 246s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 246s Selecting previously unselected package libgfortran5:amd64. 246s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_amd64.deb ... 246s Unpacking libgfortran5:amd64 (15.2.0-11ubuntu1) ... 246s Selecting previously unselected package liblapack3:amd64. 246s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 246s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 246s Selecting previously unselected package python3-numpy. 246s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 246s Unpacking python3-numpy (1:2.3.5+ds-3) ... 247s Selecting previously unselected package python3.13. 247s Preparing to unpack .../06-python3.13_3.13.11-1_amd64.deb ... 247s Unpacking python3.13 (3.13.11-1) ... 247s Selecting previously unselected package m4. 247s Preparing to unpack .../07-m4_1.4.20-2_amd64.deb ... 247s Unpacking m4 (1.4.20-2) ... 247s Selecting previously unselected package autoconf. 247s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 247s Unpacking autoconf (2.72-3.1ubuntu1) ... 247s Selecting previously unselected package autotools-dev. 247s Preparing to unpack .../09-autotools-dev_20240727.1_all.deb ... 247s Unpacking autotools-dev (20240727.1) ... 247s Selecting previously unselected package automake. 247s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 247s Unpacking automake (1:1.18.1-3build1) ... 247s Selecting previously unselected package autopoint. 247s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 247s Unpacking autopoint (0.23.2-1) ... 247s Selecting previously unselected package libisl23:amd64. 247s Preparing to unpack .../12-libisl23_0.27-1build1_amd64.deb ... 247s Unpacking libisl23:amd64 (0.27-1build1) ... 247s Selecting previously unselected package libmpc3:amd64. 247s Preparing to unpack .../13-libmpc3_1.3.1-2_amd64.deb ... 247s Unpacking libmpc3:amd64 (1.3.1-2) ... 247s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 247s Preparing to unpack .../14-cpp-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package cpp-15. 247s Preparing to unpack .../15-cpp-15_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package cpp-x86-64-linux-gnu. 247s Preparing to unpack .../16-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 247s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 247s Selecting previously unselected package cpp. 247s Preparing to unpack .../17-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 247s Unpacking cpp (4:15.2.0-4ubuntu1) ... 247s Selecting previously unselected package libcc1-0:amd64. 247s Preparing to unpack .../18-libcc1-0_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libcc1-0:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libgomp1:amd64. 247s Preparing to unpack .../19-libgomp1_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libgomp1:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libitm1:amd64. 247s Preparing to unpack .../20-libitm1_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libitm1:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libasan8:amd64. 247s Preparing to unpack .../21-libasan8_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libasan8:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package liblsan0:amd64. 247s Preparing to unpack .../22-liblsan0_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking liblsan0:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libtsan2:amd64. 247s Preparing to unpack .../23-libtsan2_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libtsan2:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libubsan1:amd64. 247s Preparing to unpack .../24-libubsan1_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libubsan1:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libhwasan0:amd64. 247s Preparing to unpack .../25-libhwasan0_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libhwasan0:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libquadmath0:amd64. 247s Preparing to unpack .../26-libquadmath0_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libquadmath0:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package libgcc-15-dev:amd64. 247s Preparing to unpack .../27-libgcc-15-dev_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 247s Preparing to unpack .../28-gcc-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package gcc-15. 247s Preparing to unpack .../29-gcc-15_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package gcc-x86-64-linux-gnu. 247s Preparing to unpack .../30-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 247s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 247s Selecting previously unselected package gcc. 247s Preparing to unpack .../31-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 247s Unpacking gcc (4:15.2.0-4ubuntu1) ... 247s Selecting previously unselected package libstdc++-15-dev:amd64. 247s Preparing to unpack .../32-libstdc++-15-dev_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 247s Selecting previously unselected package g++-15-x86-64-linux-gnu. 247s Preparing to unpack .../33-g++-15-x86-64-linux-gnu_15.2.0-11ubuntu1_amd64.deb ... 247s Unpacking g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 248s Selecting previously unselected package g++-15. 248s Preparing to unpack .../34-g++-15_15.2.0-11ubuntu1_amd64.deb ... 248s Unpacking g++-15 (15.2.0-11ubuntu1) ... 248s Selecting previously unselected package g++-x86-64-linux-gnu. 248s Preparing to unpack .../35-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 248s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 248s Selecting previously unselected package g++. 248s Preparing to unpack .../36-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 248s Unpacking g++ (4:15.2.0-4ubuntu1) ... 248s Selecting previously unselected package build-essential. 248s Preparing to unpack .../37-build-essential_12.12ubuntu2_amd64.deb ... 248s Unpacking build-essential (12.12ubuntu2) ... 248s Selecting previously unselected package libdebhelper-perl. 248s Preparing to unpack .../38-libdebhelper-perl_13.28ubuntu1_all.deb ... 248s Unpacking libdebhelper-perl (13.28ubuntu1) ... 248s Selecting previously unselected package libtool. 248s Preparing to unpack .../39-libtool_2.5.4-9_all.deb ... 248s Unpacking libtool (2.5.4-9) ... 248s Selecting previously unselected package dh-autoreconf. 248s Preparing to unpack .../40-dh-autoreconf_21_all.deb ... 248s Unpacking dh-autoreconf (21) ... 248s Selecting previously unselected package libarchive-zip-perl. 248s Preparing to unpack .../41-libarchive-zip-perl_1.68-1_all.deb ... 248s Unpacking libarchive-zip-perl (1.68-1) ... 248s Selecting previously unselected package libfile-stripnondeterminism-perl. 248s Preparing to unpack .../42-libfile-stripnondeterminism-perl_1.15.0-1build1_all.deb ... 248s Unpacking libfile-stripnondeterminism-perl (1.15.0-1build1) ... 248s Selecting previously unselected package dh-strip-nondeterminism. 248s Preparing to unpack .../43-dh-strip-nondeterminism_1.15.0-1build1_all.deb ... 248s Unpacking dh-strip-nondeterminism (1.15.0-1build1) ... 248s Selecting previously unselected package debugedit. 248s Preparing to unpack .../44-debugedit_1%3a5.2-3_amd64.deb ... 248s Unpacking debugedit (1:5.2-3) ... 248s Selecting previously unselected package dwz. 248s Preparing to unpack .../45-dwz_0.16-2_amd64.deb ... 248s Unpacking dwz (0.16-2) ... 248s Selecting previously unselected package gettext. 248s Preparing to unpack .../46-gettext_0.23.2-1_amd64.deb ... 248s Unpacking gettext (0.23.2-1) ... 248s Selecting previously unselected package intltool-debian. 248s Preparing to unpack .../47-intltool-debian_0.35.0+20060710.6build1_all.deb ... 248s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 248s Selecting previously unselected package po-debconf. 248s Preparing to unpack .../48-po-debconf_1.0.22_all.deb ... 248s Unpacking po-debconf (1.0.22) ... 248s Selecting previously unselected package debhelper. 248s Preparing to unpack .../49-debhelper_13.28ubuntu1_all.deb ... 248s Unpacking debhelper (13.28ubuntu1) ... 248s Selecting previously unselected package dh-python. 248s Preparing to unpack .../50-dh-python_7.20251231_all.deb ... 248s Unpacking dh-python (7.20251231) ... 248s Selecting previously unselected package pybuild-plugin-autopkgtest. 248s Preparing to unpack .../51-pybuild-plugin-autopkgtest_7.20251231_all.deb ... 248s Unpacking pybuild-plugin-autopkgtest (7.20251231) ... 248s Selecting previously unselected package python3-astroid. 248s Preparing to unpack .../52-python3-astroid_4.0.2-1ubuntu1_all.deb ... 248s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 248s Selecting previously unselected package python3-isort. 248s Preparing to unpack .../53-python3-isort_7.0.0-1_all.deb ... 248s Unpacking python3-isort (7.0.0-1) ... 248s Selecting previously unselected package python3-mypy-extensions. 248s Preparing to unpack .../54-python3-mypy-extensions_1.1.0-1_all.deb ... 248s Unpacking python3-mypy-extensions (1.1.0-1) ... 248s Selecting previously unselected package python3-logilab-common. 248s Preparing to unpack .../55-python3-logilab-common_2.1.0-1build1_all.deb ... 248s Unpacking python3-logilab-common (2.1.0-1build1) ... 248s Selecting previously unselected package python3-dill. 248s Preparing to unpack .../56-python3-dill_0.4.0-1_all.deb ... 248s Unpacking python3-dill (0.4.0-1) ... 248s Selecting previously unselected package python3-mccabe. 248s Preparing to unpack .../57-python3-mccabe_0.7.0-1build1_all.deb ... 248s Unpacking python3-mccabe (0.7.0-1build1) ... 248s Selecting previously unselected package python3-platformdirs. 248s Preparing to unpack .../58-python3-platformdirs_4.5.1-1_all.deb ... 248s Unpacking python3-platformdirs (4.5.1-1) ... 248s Selecting previously unselected package python3-tomlkit. 248s Preparing to unpack .../59-python3-tomlkit_0.13.3-2_all.deb ... 248s Unpacking python3-tomlkit (0.13.3-2) ... 248s Selecting previously unselected package pylint. 248s Preparing to unpack .../60-pylint_4.0.4-1_all.deb ... 248s Unpacking pylint (4.0.4-1) ... 248s Selecting previously unselected package python3-pytz. 248s Preparing to unpack .../61-python3-pytz_2025.2-5_all.deb ... 248s Unpacking python3-pytz (2025.2-5) ... 248s Selecting previously unselected package python3-pandas-lib:amd64. 248s Preparing to unpack .../62-python3-pandas-lib_2.3.3+dfsg-3_amd64.deb ... 248s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 248s Selecting previously unselected package python3-pandas. 248s Preparing to unpack .../63-python3-pandas_2.3.3+dfsg-3_all.deb ... 248s Unpacking python3-pandas (2.3.3+dfsg-3) ... 248s Selecting previously unselected package python3-typechecks. 248s Preparing to unpack .../64-python3-typechecks_0.1.0+ds-4_all.deb ... 248s Unpacking python3-typechecks (0.1.0+ds-4) ... 248s Selecting previously unselected package python3-datacache. 248s Preparing to unpack .../65-python3-datacache_1.4.1-2_all.deb ... 248s Unpacking python3-datacache (1.4.1-2) ... 248s Selecting previously unselected package python3-gtfparse. 248s Preparing to unpack .../66-python3-gtfparse_1.3.0+ds-2_all.deb ... 248s Unpacking python3-gtfparse (1.3.0+ds-2) ... 248s Selecting previously unselected package python3-memoized-property. 248s Preparing to unpack .../67-python3-memoized-property_1.0.3-2build1_all.deb ... 248s Unpacking python3-memoized-property (1.0.3-2build1) ... 248s Selecting previously unselected package python3-serializable. 248s Preparing to unpack .../68-python3-serializable_0.4.1+ds-2_all.deb ... 248s Unpacking python3-serializable (0.4.1+ds-2) ... 248s Selecting previously unselected package pyensembl. 248s Preparing to unpack .../69-pyensembl_2.3.13-2_all.deb ... 248s Unpacking pyensembl (2.3.13-2) ... 248s Selecting previously unselected package python3-all. 248s Preparing to unpack .../70-python3-all_3.14.2-1_amd64.deb ... 248s Unpacking python3-all (3.14.2-1) ... 248s Selecting previously unselected package python3-iniconfig. 248s Preparing to unpack .../71-python3-iniconfig_2.1.0-2_all.deb ... 248s Unpacking python3-iniconfig (2.1.0-2) ... 248s Selecting previously unselected package python3-pluggy. 248s Preparing to unpack .../72-python3-pluggy_1.6.0-2_all.deb ... 248s Unpacking python3-pluggy (1.6.0-2) ... 248s Selecting previously unselected package python3-pytest. 248s Preparing to unpack .../73-python3-pytest_9.0.2-2_all.deb ... 248s Unpacking python3-pytest (9.0.2-2) ... 248s Setting up dh-python (7.20251231) ... 249s Setting up python3-iniconfig (2.1.0-2) ... 249s Setting up python3-typechecks (0.1.0+ds-4) ... 249s Setting up python3-memoized-property (1.0.3-2build1) ... 249s Setting up libarchive-zip-perl (1.68-1) ... 249s Setting up python3-mypy-extensions (1.1.0-1) ... 249s Setting up libdebhelper-perl (13.28ubuntu1) ... 249s Setting up m4 (1.4.20-2) ... 249s Setting up python3-pytz (2025.2-5) ... 249s Setting up python3-serializable (0.4.1+ds-2) ... 249s Setting up libgomp1:amd64 (15.2.0-11ubuntu1) ... 249s Setting up python3-platformdirs (4.5.1-1) ... 249s Setting up autotools-dev (20240727.1) ... 249s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 249s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 249s Setting up python3-dill (0.4.0-1) ... 250s Setting up libquadmath0:amd64 (15.2.0-11ubuntu1) ... 250s Setting up libmpc3:amd64 (1.3.1-2) ... 250s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 250s Setting up autopoint (0.23.2-1) ... 250s Setting up libgfortran5:amd64 (15.2.0-11ubuntu1) ... 250s Setting up autoconf (2.72-3.1ubuntu1) ... 250s Setting up python3-isort (7.0.0-1) ... 250s Setting up python3-pluggy (1.6.0-2) ... 250s Setting up libubsan1:amd64 (15.2.0-11ubuntu1) ... 250s Setting up dwz (0.16-2) ... 250s Setting up python3-astroid (4.0.2-1ubuntu1) ... 250s Setting up libhwasan0:amd64 (15.2.0-11ubuntu1) ... 250s Setting up libasan8:amd64 (15.2.0-11ubuntu1) ... 250s Setting up debugedit (1:5.2-3) ... 250s Setting up python3.13-minimal (3.13.11-1) ... 251s Setting up python3-mccabe (0.7.0-1build1) ... 251s Setting up libtsan2:amd64 (15.2.0-11ubuntu1) ... 251s Setting up libisl23:amd64 (0.27-1build1) ... 251s Setting up python3-tomlkit (0.13.3-2) ... 251s Setting up libcc1-0:amd64 (15.2.0-11ubuntu1) ... 251s Setting up liblsan0:amd64 (15.2.0-11ubuntu1) ... 251s Setting up libitm1:amd64 (15.2.0-11ubuntu1) ... 251s Setting up automake (1:1.18.1-3build1) ... 251s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 251s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 251s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 251s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 251s Setting up gettext (0.23.2-1) ... 251s Setting up libgcc-15-dev:amd64 (15.2.0-11ubuntu1) ... 251s Setting up python3-logilab-common (2.1.0-1build1) ... 251s Setting up python3.13 (3.13.11-1) ... 252s Setting up python3-pytest (9.0.2-2) ... 252s Setting up python3-all (3.14.2-1) ... 252s Setting up cpp-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 252s Setting up intltool-debian (0.35.0+20060710.6build1) ... 252s Setting up gcc-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 252s Setting up libstdc++-15-dev:amd64 (15.2.0-11ubuntu1) ... 252s Setting up python3-numpy (1:2.3.5+ds-3) ... 254s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 254s Setting up cpp-15 (15.2.0-11ubuntu1) ... 254s Setting up pylint (4.0.4-1) ... 255s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 255s Setting up g++-15-x86-64-linux-gnu (15.2.0-11ubuntu1) ... 255s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 255s Setting up po-debconf (1.0.22) ... 255s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 255s Setting up gcc-15 (15.2.0-11ubuntu1) ... 255s Setting up python3-pandas (2.3.3+dfsg-3) ... 260s Setting up cpp (4:15.2.0-4ubuntu1) ... 260s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 260s Setting up g++-15 (15.2.0-11ubuntu1) ... 260s Setting up python3-datacache (1.4.1-2) ... 260s Setting up libtool (2.5.4-9) ... 260s Setting up python3-gtfparse (1.3.0+ds-2) ... 261s Setting up gcc (4:15.2.0-4ubuntu1) ... 261s Setting up dh-autoreconf (21) ... 261s Setting up g++ (4:15.2.0-4ubuntu1) ... 261s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 261s Setting up build-essential (12.12ubuntu2) ... 261s Setting up pyensembl (2.3.13-2) ... 261s Setting up debhelper (13.28ubuntu1) ... 261s Setting up pybuild-plugin-autopkgtest (7.20251231) ... 261s Processing triggers for man-db (2.13.1-1) ... 261s Processing triggers for install-info (7.2-5) ... 261s Processing triggers for libc-bin (2.42-2ubuntu4) ... 261s Processing triggers for systemd (259-1ubuntu2) ... 263s autopkgtest [12:58:34]: test pybuild-autopkgtest: pybuild-autopkgtest 263s autopkgtest [12:58:34]: test pybuild-autopkgtest: [----------------------- 263s pybuild-autopkgtest 263s I: pybuild base:384: cd /tmp/autopkgtest.gyB75a/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' 263s ============================= test session starts ============================== 263s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 263s cachedir: .pytest_cache 263s rootdir: /tmp/autopkgtest.gyB75a/autopkgtest_tmp/build 263s plugins: typeguard-4.4.4 264s collecting ... collected 126 items / 98 deselected / 28 selected 264s 264s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 264s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 264s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 264s tests/test_locus.py::test_locus_contains PASSED [ 14%] 264s tests/test_locus.py::test_position_offset PASSED [ 17%] 264s tests/test_locus.py::test_range_offset PASSED [ 21%] 264s tests/test_locus.py::test_locus_distance PASSED [ 25%] 264s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 264s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 264s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 264s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 264s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 264s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 264s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 264s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 264s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 264s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 264s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 264s tests/test_release_versions.py::test_int_version PASSED [ 67%] 264s tests/test_release_versions.py::test_str_version PASSED [ 71%] 264s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 264s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 264s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 264s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 264s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 264s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 264s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 264s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 264s 264s =============================== warnings summary =============================== 264s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 264s /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 264s import pkg_resources 264s 264s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 264s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 264s 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 264s declare_namespace(pkg) 264s 264s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 264s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 264s release_group = root_group.add_argument_group() 264s 264s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 264s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 264s path_group = root_group.add_argument_group() 264s 264s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 264s ================ 28 passed, 98 deselected, 4 warnings in 0.76s ================= 264s I: pybuild base:384: cd /tmp/autopkgtest.gyB75a/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' 264s ============================= test session starts ============================== 264s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 264s cachedir: .pytest_cache 264s rootdir: /tmp/autopkgtest.gyB75a/autopkgtest_tmp/build 264s plugins: typeguard-4.4.4 265s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 265s 265s ==================================== ERRORS ==================================== 265s _____________________ ERROR collecting tests/test_shell.py _____________________ 265s tests/test_shell.py:1: in 265s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 265s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 265s release_group = root_group.add_argument_group() 265s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 265s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 265s raise ValueError('argument groups cannot be nested') 265s E ValueError: argument groups cannot be nested 265s =============================== warnings summary =============================== 265s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 265s /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 265s import pkg_resources 265s 265s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 265s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 265s 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 265s declare_namespace(pkg) 265s 265s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 265s =========================== short test summary info ============================ 265s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 265s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 265s ================= 98 deselected, 2 warnings, 1 error in 0.63s ================== 265s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.gyB75a/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' 265s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.14" returned exit code 13 265s make: *** [/tmp/DKoeLs9vxU/run:4: pybuild-autopkgtest] Error 25 265s pybuild-autopkgtest: error: /tmp/DKoeLs9vxU/run pybuild-autopkgtest returned exit code 2 265s autopkgtest [12:58:36]: test pybuild-autopkgtest: -----------------------] 266s autopkgtest [12:58:37]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 266s pybuild-autopkgtest FAIL non-zero exit status 25 266s autopkgtest [12:58:37]: @@@@@@@@@@@@@@@@@@@@ summary 266s run-unit-test FAIL non-zero exit status 2 266s pybuild-autopkgtest FAIL non-zero exit status 25