0s autopkgtest [14:08:24]: starting date and time: 2026-02-06 14:08:24+0000 0s autopkgtest [14:08:24]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:08:24]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.58frfqhf/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:setuptools --apt-upgrade pyensembl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=setuptools/78.1.1-0.1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-16.secgroup --name adt-resolute-amd64-pyensembl-20260206-140823-juju-7f2275-prod-proposed-migration-environment-20-5afae818-4c5e-4cae-a8c6-5127d71185f9 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-pyensembl-20260206-140823-juju-7f2275-prod-proposed-migration-environment-20-5afae818-4c5e-4cae-a8c6-5127d71185f9 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 74s autopkgtest [14:09:38]: testbed dpkg architecture: amd64 74s autopkgtest [14:09:38]: testbed apt version: 3.1.14 74s autopkgtest [14:09:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s autopkgtest [14:09:38]: testbed release detected to be: None 75s autopkgtest [14:09:39]: updating testbed package index (apt update) 75s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 75s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 75s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 75s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1473 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9256 B] 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [191 kB] 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [30.8 kB] 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [249 kB] 76s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [181 kB] 76s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6436 B] 76s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 76s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [68.4 kB] 76s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 76s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [518 kB] 76s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1348 kB] 76s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [35.8 kB] 76s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 76s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.7 kB] 76s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1060 B] 77s Fetched 4271 kB in 1s (5006 kB/s) 77s Reading package lists... 78s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 78s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 78s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 78s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 79s The following packages will be upgraded: 79s amd64-microcode apt busybox-initramfs busybox-static dmsetup findutils less 79s libapt-pkg7.0 libattr1 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 79s libdrm2 libgpm2 libkeyutils1 libmaxminddb0 libnpth0t64 libsensors-config 79s libsensors5 mawk patch pollinate python3-linkify-it python3-markdown-it 79s python3-pkg-resources python3-referencing python3-setuptools sed tar 79s 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 6787 kB of archives. 79s After this operation, 270 kB disk space will be freed. 79s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 79s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 79s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 79s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 79s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 79s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 79s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 79s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 79s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 79s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 79s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 79s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 79s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 79s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 79s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 79s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 79s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 79s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 79s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 79s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 79s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 79s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 79s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 79s Get:27 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 79s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 79s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 79s dpkg-preconfigure: unable to re-open stdin: No such file or directory 79s Fetched 6787 kB in 0s (20.6 MB/s) 80s (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 ... 83957 files and directories currently installed.) 80s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 80s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 80s Setting up findutils (4.10.0-3build2) ... 80s (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 ... 83957 files and directories currently installed.) 80s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 80s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 80s Setting up sed (4.9-2build3) ... 80s (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 ... 83957 files and directories currently installed.) 80s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 80s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 80s Setting up tar (1.35+dfsg-3.1build2) ... 80s (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 ... 83957 files and directories currently installed.) 80s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 80s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 80s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 80s (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 ... 83957 files and directories currently installed.) 80s Preparing to unpack .../00-mawk_1.3.4.20260129-1_amd64.deb ... 80s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 80s Preparing to unpack .../01-libapt-pkg7.0_3.1.15_amd64.deb ... 80s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ... 80s Preparing to unpack .../02-apt_3.1.15_amd64.deb ... 80s Unpacking apt (3.1.15) over (3.1.14) ... 80s Preparing to unpack .../03-libdevmapper1.02.1_2%3a1.02.205-2ubuntu3_amd64.deb ... 80s Unpacking libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 80s Preparing to unpack .../04-dmsetup_2%3a1.02.205-2ubuntu3_amd64.deb ... 80s Unpacking dmsetup (2:1.02.205-2ubuntu3) over (2:1.02.205-2ubuntu2) ... 80s Preparing to unpack .../05-less_668-1build1_amd64.deb ... 80s Unpacking less (668-1build1) over (668-1) ... 80s Preparing to unpack .../06-libkeyutils1_1.6.3-6ubuntu3_amd64.deb ... 80s Unpacking libkeyutils1:amd64 (1.6.3-6ubuntu3) over (1.6.3-6ubuntu2) ... 80s Preparing to unpack .../07-python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 80s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 80s Preparing to unpack .../08-python3-markdown-it_3.0.0-3build1_all.deb ... 80s Unpacking python3-markdown-it (3.0.0-3build1) over (3.0.0-3) ... 81s Preparing to unpack .../09-busybox-static_1%3a1.37.0-7ubuntu1_amd64.deb ... 81s Unpacking busybox-static (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 81s Preparing to unpack .../10-libdrm-common_2.4.131-1_all.deb ... 81s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 81s Preparing to unpack .../11-libdrm2_2.4.131-1_amd64.deb ... 81s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ... 81s Preparing to unpack .../12-libgpm2_1.20.7-12build1_amd64.deb ... 81s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ... 81s Preparing to unpack .../13-libmaxminddb0_1.12.2-1build2_amd64.deb ... 81s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ... 81s Preparing to unpack .../14-libsensors-config_1%3a3.6.2-2build1_all.deb ... 81s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ... 81s Preparing to unpack .../15-libsensors5_1%3a3.6.2-2build1_amd64.deb ... 81s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ... 81s Preparing to unpack .../16-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ... 81s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 81s Preparing to unpack .../17-libdrm-amdgpu1_2.4.131-1_amd64.deb ... 81s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ... 81s Preparing to unpack .../18-libnpth0t64_1.8-3build1_amd64.deb ... 81s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ... 81s Preparing to unpack .../19-patch_2.8-2build1_amd64.deb ... 81s Unpacking patch (2.8-2build1) over (2.8-2) ... 81s Preparing to unpack .../20-pollinate_4.33-4ubuntu5_all.deb ... 81s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 81s Preparing to unpack .../21-python3-pkg-resources_78.1.1-0.1build1_all.deb ... 81s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 81s Preparing to unpack .../22-python3-setuptools_78.1.1-0.1build1_all.deb ... 81s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 81s Preparing to unpack .../23-python3-referencing_0.36.2-1ubuntu2_all.deb ... 81s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 81s Preparing to unpack .../24-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ... 81s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ... 81s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 81s Setting up libnpth0t64:amd64 (1.8-3build1) ... 81s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 81s Setting up libgpm2:amd64 (1.20.7-12build1) ... 81s Setting up python3-setuptools (78.1.1-0.1build1) ... 82s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 82s Setting up libsensors-config (1:3.6.2-2build1) ... 82s Setting up less (668-1build1) ... 82s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 82s amd64-microcode: microcode will be updated at next boot 82s Setting up pollinate (4.33-4ubuntu5) ... 92s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 92s Setting up patch (2.8-2build1) ... 92s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 92s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 92s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 92s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 92s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 92s Setting up mawk (1.3.4.20260129-1) ... 92s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 92s Setting up libdrm-common (2.4.131-1) ... 92s Setting up python3-referencing (0.36.2-1ubuntu2) ... 93s Setting up apt (3.1.15) ... 93s Setting up python3-markdown-it (3.0.0-3build1) ... 93s Setting up libdrm2:amd64 (2.4.131-1) ... 93s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 93s Processing triggers for libc-bin (2.42-2ubuntu4) ... 93s Processing triggers for man-db (2.13.1-1) ... 94s Processing triggers for install-info (7.2-5) ... 94s Processing triggers for initramfs-tools (0.150ubuntu7) ... 94s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 99s autopkgtest [14:10:03]: upgrading testbed (apt dist-upgrade and autopurge) 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s autopkgtest [14:10:05]: rebooting testbed after setup commands that affected boot 129s autopkgtest [14:10:33]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:49:02 UTC 2026 131s autopkgtest [14:10:35]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 133s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 133s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 133s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 133s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 133s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 133s gpgv: issuer "tchet@debian.org" 133s gpgv: Can't check signature: No public key 133s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 133s autopkgtest [14:10:37]: testing package pyensembl version 2.3.13-2 133s autopkgtest [14:10:37]: build not needed 133s autopkgtest [14:10:37]: test run-unit-test: preparing testbed 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Solving dependencies... 134s The following NEW packages will be installed: 134s libblas3 libgfortran5 liblapack3 libpython3.14-minimal libpython3.14-stdlib 134s pyensembl pylint python3-all python3-astroid python3-datacache python3-dill 134s python3-gtfparse python3-iniconfig python3-isort python3-logilab-common 134s python3-mccabe python3-memoized-property python3-mypy-extensions 134s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 134s python3-platformdirs python3-pluggy python3-pytest python3-pytz 134s python3-serializable python3-tomlkit python3-typechecks python3.14 134s python3.14-minimal 134s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 30.0 MB of archives. 134s After this operation, 152 MB of additional disk space will be used. 134s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 134s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 134s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-12ubuntu1 [939 kB] 134s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 135s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 135s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 135s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 135s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 135s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 135s Get:10 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-isort all 7.0.0-1 [59.7 kB] 135s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 135s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 135s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dill all 0.4.0-1 [84.8 kB] 135s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mccabe all 0.7.0-1build1 [8926 B] 135s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.5.1-1 [17.1 kB] 135s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tomlkit all 0.13.3-2 [39.1 kB] 135s Get:17 http://ftpmaster.internal/ubuntu resolute/universe amd64 pylint all 4.0.4-1 [346 kB] 135s Get:18 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 135s Get:19 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 135s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 136s Get:21 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typechecks all 0.1.0+ds-4 [4562 B] 136s Get:22 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-datacache all 1.4.1-2 [13.1 kB] 136s Get:23 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 136s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-memoized-property all 1.0.3-2build1 [5328 B] 136s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-serializable all 0.4.1+ds-2 [8438 B] 136s Get:26 http://ftpmaster.internal/ubuntu resolute/universe amd64 pyensembl all 2.3.13-2 [37.2 kB] 136s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 136s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.9-3 [890 B] 136s Get:29 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 136s Get:30 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 136s Get:31 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 136s Fetched 30.0 MB in 2s (16.6 MB/s) 136s Selecting previously unselected package python3-numpy-dev:amd64. 136s (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 ... 83962 files and directories currently installed.) 136s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 136s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 136s Selecting previously unselected package libblas3:amd64. 136s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_amd64.deb ... 136s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 136s Selecting previously unselected package libgfortran5:amd64. 136s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_amd64.deb ... 136s Unpacking libgfortran5:amd64 (15.2.0-12ubuntu1) ... 136s Selecting previously unselected package liblapack3:amd64. 136s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 136s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 136s Selecting previously unselected package python3-numpy. 136s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 136s Unpacking python3-numpy (1:2.3.5+ds-3) ... 136s Selecting previously unselected package libpython3.14-minimal:amd64. 136s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_amd64.deb ... 136s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 136s Selecting previously unselected package python3.14-minimal. 136s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_amd64.deb ... 136s Unpacking python3.14-minimal (3.14.2-1) ... 136s Selecting previously unselected package libpython3.14-stdlib:amd64. 136s Preparing to unpack .../07-libpython3.14-stdlib_3.14.2-1_amd64.deb ... 136s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 136s Selecting previously unselected package python3-astroid. 136s Preparing to unpack .../08-python3-astroid_4.0.2-1ubuntu1_all.deb ... 136s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 136s Selecting previously unselected package python3-isort. 136s Preparing to unpack .../09-python3-isort_7.0.0-1_all.deb ... 136s Unpacking python3-isort (7.0.0-1) ... 136s Selecting previously unselected package python3-mypy-extensions. 136s Preparing to unpack .../10-python3-mypy-extensions_1.1.0-1_all.deb ... 136s Unpacking python3-mypy-extensions (1.1.0-1) ... 137s Selecting previously unselected package python3-logilab-common. 137s Preparing to unpack .../11-python3-logilab-common_2.1.0-1build1_all.deb ... 137s Unpacking python3-logilab-common (2.1.0-1build1) ... 137s Selecting previously unselected package python3-dill. 137s Preparing to unpack .../12-python3-dill_0.4.0-1_all.deb ... 137s Unpacking python3-dill (0.4.0-1) ... 137s Selecting previously unselected package python3-mccabe. 137s Preparing to unpack .../13-python3-mccabe_0.7.0-1build1_all.deb ... 137s Unpacking python3-mccabe (0.7.0-1build1) ... 137s Selecting previously unselected package python3-platformdirs. 137s Preparing to unpack .../14-python3-platformdirs_4.5.1-1_all.deb ... 137s Unpacking python3-platformdirs (4.5.1-1) ... 137s Selecting previously unselected package python3-tomlkit. 137s Preparing to unpack .../15-python3-tomlkit_0.13.3-2_all.deb ... 137s Unpacking python3-tomlkit (0.13.3-2) ... 137s Selecting previously unselected package pylint. 137s Preparing to unpack .../16-pylint_4.0.4-1_all.deb ... 137s Unpacking pylint (4.0.4-1) ... 137s Selecting previously unselected package python3-pytz. 137s Preparing to unpack .../17-python3-pytz_2025.2-5_all.deb ... 137s Unpacking python3-pytz (2025.2-5) ... 137s Selecting previously unselected package python3-pandas-lib:amd64. 137s Preparing to unpack .../18-python3-pandas-lib_2.3.3+dfsg-3_amd64.deb ... 137s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 137s Selecting previously unselected package python3-pandas. 137s Preparing to unpack .../19-python3-pandas_2.3.3+dfsg-3_all.deb ... 137s Unpacking python3-pandas (2.3.3+dfsg-3) ... 137s Selecting previously unselected package python3-typechecks. 137s Preparing to unpack .../20-python3-typechecks_0.1.0+ds-4_all.deb ... 137s Unpacking python3-typechecks (0.1.0+ds-4) ... 137s Selecting previously unselected package python3-datacache. 137s Preparing to unpack .../21-python3-datacache_1.4.1-2_all.deb ... 137s Unpacking python3-datacache (1.4.1-2) ... 137s Selecting previously unselected package python3-gtfparse. 137s Preparing to unpack .../22-python3-gtfparse_1.3.0+ds-2_all.deb ... 137s Unpacking python3-gtfparse (1.3.0+ds-2) ... 137s Selecting previously unselected package python3-memoized-property. 137s Preparing to unpack .../23-python3-memoized-property_1.0.3-2build1_all.deb ... 137s Unpacking python3-memoized-property (1.0.3-2build1) ... 137s Selecting previously unselected package python3-serializable. 137s Preparing to unpack .../24-python3-serializable_0.4.1+ds-2_all.deb ... 137s Unpacking python3-serializable (0.4.1+ds-2) ... 137s Selecting previously unselected package pyensembl. 137s Preparing to unpack .../25-pyensembl_2.3.13-2_all.deb ... 137s Unpacking pyensembl (2.3.13-2) ... 137s Selecting previously unselected package python3.14. 137s Preparing to unpack .../26-python3.14_3.14.2-1_amd64.deb ... 137s Unpacking python3.14 (3.14.2-1) ... 137s Selecting previously unselected package python3-all. 137s Preparing to unpack .../27-python3-all_3.13.9-3_amd64.deb ... 137s Unpacking python3-all (3.13.9-3) ... 137s Selecting previously unselected package python3-iniconfig. 137s Preparing to unpack .../28-python3-iniconfig_2.1.0-2_all.deb ... 137s Unpacking python3-iniconfig (2.1.0-2) ... 137s Selecting previously unselected package python3-pluggy. 137s Preparing to unpack .../29-python3-pluggy_1.6.0-2_all.deb ... 137s Unpacking python3-pluggy (1.6.0-2) ... 137s Selecting previously unselected package python3-pytest. 137s Preparing to unpack .../30-python3-pytest_9.0.2-2_all.deb ... 137s Unpacking python3-pytest (9.0.2-2) ... 137s Setting up python3-iniconfig (2.1.0-2) ... 137s Setting up python3-typechecks (0.1.0+ds-4) ... 137s Setting up python3-memoized-property (1.0.3-2build1) ... 137s Setting up python3-mypy-extensions (1.1.0-1) ... 137s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 137s Setting up python3-pytz (2025.2-5) ... 138s Setting up python3-serializable (0.4.1+ds-2) ... 138s Setting up python3-platformdirs (4.5.1-1) ... 138s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 138s 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 138s Setting up python3-dill (0.4.0-1) ... 138s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 138s Setting up libgfortran5:amd64 (15.2.0-12ubuntu1) ... 138s Setting up python3-isort (7.0.0-1) ... 138s Setting up python3-pluggy (1.6.0-2) ... 138s Setting up python3-astroid (4.0.2-1ubuntu1) ... 139s Setting up python3-mccabe (0.7.0-1build1) ... 139s Setting up python3-tomlkit (0.13.3-2) ... 139s Setting up python3.14-minimal (3.14.2-1) ... 139s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 139s 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 139s Setting up python3-logilab-common (2.1.0-1build1) ... 140s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 140s Setting up python3-pytest (9.0.2-2) ... 140s Setting up python3-numpy (1:2.3.5+ds-3) ... 142s Setting up python3.14 (3.14.2-1) ... 143s Setting up pylint (4.0.4-1) ... 143s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 143s Setting up python3-all (3.13.9-3) ... 143s Setting up python3-pandas (2.3.3+dfsg-3) ... 149s Setting up python3-datacache (1.4.1-2) ... 149s Setting up python3-gtfparse (1.3.0+ds-2) ... 149s Setting up pyensembl (2.3.13-2) ... 149s Processing triggers for systemd (259-1ubuntu3) ... 149s Processing triggers for man-db (2.13.1-1) ... 150s Processing triggers for libc-bin (2.42-2ubuntu4) ... 150s autopkgtest [14:10:54]: test run-unit-test: [----------------------- 152s ============================= test session starts ============================== 152s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 152s rootdir: /tmp/autopkgtest.L1JCjv/autopkgtest_tmp 152s plugins: typeguard-4.4.4 152s collected 14 items / 1 error 152s 152s ==================================== ERRORS ==================================== 152s _____________________ ERROR collecting tests/test_shell.py _____________________ 152s tests/test_shell.py:1: in 152s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 152s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 152s release_group = root_group.add_argument_group() 152s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 152s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 152s raise ValueError('argument groups cannot be nested') 152s E ValueError: argument groups cannot be nested 152s =============================== warnings summary =============================== 152s ../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 152s /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 152s import pkg_resources 152s 152s ../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 152s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 152s 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 152s declare_namespace(pkg) 152s 152s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 152s =========================== short test summary info ============================ 152s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 152s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 152s ========================= 2 warnings, 1 error in 0.70s ========================= 152s autopkgtest [14:10:56]: test run-unit-test: -----------------------] 152s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 152s autopkgtest [14:10:56]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 153s autopkgtest [14:10:57]: test pybuild-autopkgtest: preparing testbed 173s Creating nova instance adt-resolute-amd64-pyensembl-20260206-140823-juju-7f2275-prod-proposed-migration-environment-20-5afae818-4c5e-4cae-a8c6-5127d71185f9 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 253s autopkgtest [14:12:37]: testbed dpkg architecture: amd64 253s autopkgtest [14:12:37]: testbed apt version: 3.1.14 253s autopkgtest [14:12:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 253s autopkgtest [14:12:37]: testbed release detected to be: resolute 254s autopkgtest [14:12:38]: updating testbed package index (apt update) 254s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 254s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 254s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 254s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 254s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [191 kB] 254s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1473 kB] 254s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [30.8 kB] 255s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9256 B] 255s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [249 kB] 255s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [181 kB] 255s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [6436 B] 255s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [68.4 kB] 255s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3692 B] 255s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 255s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1348 kB] 255s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [518 kB] 255s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [35.8 kB] 255s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.7 kB] 255s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 255s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [1060 B] 256s Fetched 4271 kB in 1s (3870 kB/s) 256s Reading package lists... 257s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 257s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 257s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 257s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 257s Reading package lists... 257s Reading package lists... 258s Building dependency tree... 258s Reading state information... 258s Calculating upgrade... 258s The following packages will be upgraded: 258s amd64-microcode apt busybox-initramfs busybox-static dmsetup findutils less 258s libapt-pkg7.0 libattr1 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 258s libdrm2 libgpm2 libkeyutils1 libmaxminddb0 libnpth0t64 libsensors-config 258s libsensors5 mawk patch pollinate python3-linkify-it python3-markdown-it 258s python3-pkg-resources python3-referencing python3-setuptools sed tar 258s 29 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 258s Need to get 6787 kB of archives. 258s After this operation, 270 kB disk space will be freed. 258s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 258s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 258s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 258s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 258s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 258s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 258s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 258s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 258s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 258s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 258s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 258s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 258s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 258s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 258s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 258s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 258s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 258s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 258s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 258s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 258s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 258s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 258s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 258s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 258s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 258s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 258s Get:27 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 258s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 258s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 258s dpkg-preconfigure: unable to re-open stdin: No such file or directory 259s Fetched 6787 kB in 0s (21.0 MB/s) 259s (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 ... 83957 files and directories currently installed.) 259s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 259s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 259s Setting up findutils (4.10.0-3build2) ... 259s (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 ... 83957 files and directories currently installed.) 259s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 259s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 259s Setting up sed (4.9-2build3) ... 259s (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 ... 83957 files and directories currently installed.) 259s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 259s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 259s Setting up tar (1.35+dfsg-3.1build2) ... 259s (Reading database ... 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(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 ... 83957 files and directories currently installed.) 259s Preparing to unpack .../00-mawk_1.3.4.20260129-1_amd64.deb ... 259s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 259s Preparing to unpack .../01-libapt-pkg7.0_3.1.15_amd64.deb ... 259s Unpacking libapt-pkg7.0:amd64 (3.1.15) over (3.1.14) ... 259s Preparing to unpack .../02-apt_3.1.15_amd64.deb ... 259s Unpacking apt (3.1.15) over (3.1.14) ... 259s Preparing to unpack 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(1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 260s Preparing to unpack .../10-libdrm-common_2.4.131-1_all.deb ... 260s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 260s Preparing to unpack .../11-libdrm2_2.4.131-1_amd64.deb ... 260s Unpacking libdrm2:amd64 (2.4.131-1) over (2.4.129-1) ... 260s Preparing to unpack .../12-libgpm2_1.20.7-12build1_amd64.deb ... 260s Unpacking libgpm2:amd64 (1.20.7-12build1) over (1.20.7-12) ... 260s Preparing to unpack .../13-libmaxminddb0_1.12.2-1build2_amd64.deb ... 260s Unpacking libmaxminddb0:amd64 (1.12.2-1build2) over (1.12.2-1build1) ... 260s Preparing to unpack .../14-libsensors-config_1%3a3.6.2-2build1_all.deb ... 260s Unpacking libsensors-config (1:3.6.2-2build1) over (1:3.6.2-2) ... 260s Preparing to unpack .../15-libsensors5_1%3a3.6.2-2build1_amd64.deb ... 260s Unpacking libsensors5:amd64 (1:3.6.2-2build1) over (1:3.6.2-2) ... 260s Preparing to unpack .../16-busybox-initramfs_1%3a1.37.0-7ubuntu1_amd64.deb ... 260s Unpacking busybox-initramfs (1:1.37.0-7ubuntu1) over (1:1.37.0-4ubuntu1) ... 260s Preparing to unpack .../17-libdrm-amdgpu1_2.4.131-1_amd64.deb ... 260s Unpacking libdrm-amdgpu1:amd64 (2.4.131-1) over (2.4.129-1) ... 260s Preparing to unpack .../18-libnpth0t64_1.8-3build1_amd64.deb ... 260s Unpacking libnpth0t64:amd64 (1.8-3build1) over (1.8-3) ... 260s Preparing to unpack .../19-patch_2.8-2build1_amd64.deb ... 260s Unpacking patch (2.8-2build1) over (2.8-2) ... 260s Preparing to unpack .../20-pollinate_4.33-4ubuntu5_all.deb ... 260s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 260s Preparing to unpack .../21-python3-pkg-resources_78.1.1-0.1build1_all.deb ... 260s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 260s Preparing to unpack .../22-python3-setuptools_78.1.1-0.1build1_all.deb ... 260s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 260s Preparing to unpack .../23-python3-referencing_0.36.2-1ubuntu2_all.deb ... 261s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 261s Preparing to unpack .../24-amd64-microcode_3.20251202.1ubuntu1_amd64.deb ... 261s Unpacking amd64-microcode (3.20251202.1ubuntu1) over (3.20250708.1ubuntu1) ... 261s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 261s Setting up libnpth0t64:amd64 (1.8-3build1) ... 261s Setting up libkeyutils1:amd64 (1.6.3-6ubuntu3) ... 261s Setting up libgpm2:amd64 (1.20.7-12build1) ... 261s Setting up python3-setuptools (78.1.1-0.1build1) ... 261s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 261s Setting up libsensors-config (1:3.6.2-2build1) ... 261s Setting up less (668-1build1) ... 261s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 261s amd64-microcode: microcode will be updated at next boot 261s Setting up pollinate (4.33-4ubuntu5) ... 272s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 272s Setting up patch (2.8-2build1) ... 272s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 272s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 272s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 272s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 272s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 272s Setting up mawk (1.3.4.20260129-1) ... 272s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 272s Setting up libdrm-common (2.4.131-1) ... 272s Setting up python3-referencing (0.36.2-1ubuntu2) ... 272s Setting up apt (3.1.15) ... 272s Setting up python3-markdown-it (3.0.0-3build1) ... 272s Setting up libdrm2:amd64 (2.4.131-1) ... 272s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 272s Processing triggers for libc-bin (2.42-2ubuntu4) ... 272s Processing triggers for man-db (2.13.1-1) ... 273s Processing triggers for install-info (7.2-5) ... 274s Processing triggers for initramfs-tools (0.150ubuntu7) ... 274s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 278s autopkgtest [14:13:02]: upgrading testbed (apt dist-upgrade and autopurge) 279s Reading package lists... 279s Building dependency tree... 279s Reading state information... 279s Calculating upgrade... 280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Solving dependencies... 280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s autopkgtest [14:13:04]: rebooting testbed after setup commands that affected boot 312s Reading package lists... 312s Building dependency tree... 312s Reading state information... 312s Solving dependencies... 312s The following NEW packages will be installed: 312s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 312s cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper debugedit 312s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-15 312s g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15 312s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 312s libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev libcc1-0 312s libcrypt-dev libdebhelper-perl libfile-stripnondeterminism-perl 312s libgcc-15-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 liblapack3 312s liblsan0 libmpc3 libpython3.14-minimal libpython3.14-stdlib libquadmath0 312s libstdc++-15-dev libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf 312s pybuild-plugin-autopkgtest pyensembl pylint python3-all python3-astroid 312s python3-datacache python3-dill python3-gtfparse python3-iniconfig 312s python3-isort python3-logilab-common python3-mccabe 312s python3-memoized-property python3-mypy-extensions python3-numpy 312s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 312s python3-pluggy python3-pytest python3-pytz python3-serializable 312s python3-tomlkit python3-typechecks python3.14 python3.14-minimal 312s rpcsvc-proto 312s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 312s Need to get 109 MB of archives. 312s After this operation, 425 MB of additional disk space will be used. 312s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.3.5+ds-3 [147 kB] 312s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 312s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-12ubuntu1 [939 kB] 312s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 313s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.3.5+ds-3 [8129 kB] 313s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 313s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14-minimal amd64 3.14.2-1 [2563 kB] 313s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 m4 amd64 1.4.20-2 [217 kB] 313s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 autoconf all 2.72-3.1ubuntu1 [384 kB] 313s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 autotools-dev all 20240727.1build1 [43.4 kB] 313s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 automake all 1:1.18.1-3build1 [582 kB] 313s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 autopoint all 0.23.2-1 [620 kB] 313s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 313s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.18.0-9.9 [1860 kB] 313s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 313s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 313s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 313s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 313s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 313s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 314s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 314s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 314s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 314s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 15.2.0-12ubuntu1 [47.4 kB] 314s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 15.2.0-12ubuntu1 [151 kB] 314s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 15.2.0-12ubuntu1 [29.5 kB] 314s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 15.2.0-12ubuntu1 [3070 kB] 314s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 15.2.0-12ubuntu1 [1360 kB] 314s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 15.2.0-12ubuntu1 [2757 kB] 314s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 15.2.0-12ubuntu1 [1210 kB] 314s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 15.2.0-12ubuntu1 [1685 kB] 314s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 15.2.0-12ubuntu1 [153 kB] 314s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 314s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 314s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 314s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 314s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 314s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 314s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 315s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 315s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 315s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 315s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 315s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 315s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtool all 2.5.4-9 [169 kB] 315s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-autoreconf all 21+nmu1 [11.9 kB] 315s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 315s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 315s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 315s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 debugedit amd64 1:5.2-3build1 [48.8 kB] 315s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 dwz amd64 0.16-2build1 [113 kB] 315s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 gettext amd64 0.23.2-1 [1019 kB] 315s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 315s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 po-debconf all 1.0.22 [215 kB] 315s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 debhelper all 13.28ubuntu1 [916 kB] 315s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 dh-python all 7.20260125 [122 kB] 315s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 315s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 315s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 315s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-isort all 7.0.0-1 [59.7 kB] 315s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mypy-extensions all 1.1.0-1 [6716 B] 315s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 315s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-dill all 0.4.0-1 [84.8 kB] 315s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-mccabe all 0.7.0-1build1 [8926 B] 315s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-platformdirs all 4.5.1-1 [17.1 kB] 315s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-tomlkit all 0.13.3-2 [39.1 kB] 315s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 pylint all 4.0.4-1 [346 kB] 315s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytz all 2025.2-5 [32.4 kB] 315s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-3 [6929 kB] 315s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 315s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-typechecks all 0.1.0+ds-4 [4562 B] 315s Get:72 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-datacache all 1.4.1-2 [13.1 kB] 315s Get:73 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 315s Get:74 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-memoized-property all 1.0.3-2build1 [5328 B] 315s Get:75 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-serializable all 0.4.1+ds-2 [8438 B] 315s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 pyensembl all 2.3.13-2 [37.2 kB] 315s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 python3.14 amd64 3.14.2-1 [816 kB] 315s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.9-3 [890 B] 315s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 2.1.0-2 [6962 B] 315s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-2 [21.1 kB] 315s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 9.0.2-2 [277 kB] 316s Fetched 109 MB in 3s (33.0 MB/s) 316s Selecting previously unselected package python3-numpy-dev:amd64. 316s (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 ... 83962 files and directories currently installed.) 316s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_amd64.deb ... 316s Unpacking python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 316s Selecting previously unselected package libblas3:amd64. 316s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_amd64.deb ... 316s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 316s Selecting previously unselected package libgfortran5:amd64. 316s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_amd64.deb ... 316s Unpacking libgfortran5:amd64 (15.2.0-12ubuntu1) ... 316s Selecting previously unselected package liblapack3:amd64. 316s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_amd64.deb ... 316s Unpacking liblapack3:amd64 (3.12.1-7ubuntu1) ... 316s Selecting previously unselected package python3-numpy. 316s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_amd64.deb ... 316s Unpacking python3-numpy (1:2.3.5+ds-3) ... 316s Selecting previously unselected package libpython3.14-minimal:amd64. 316s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_amd64.deb ... 316s Unpacking libpython3.14-minimal:amd64 (3.14.2-1) ... 316s Selecting previously unselected package python3.14-minimal. 316s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_amd64.deb ... 316s Unpacking python3.14-minimal (3.14.2-1) ... 316s Selecting previously unselected package m4. 316s Preparing to unpack .../07-m4_1.4.20-2_amd64.deb ... 316s Unpacking m4 (1.4.20-2) ... 316s Selecting previously unselected package autoconf. 316s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 316s Unpacking autoconf (2.72-3.1ubuntu1) ... 316s Selecting previously unselected package autotools-dev. 316s Preparing to unpack .../09-autotools-dev_20240727.1build1_all.deb ... 316s Unpacking autotools-dev (20240727.1build1) ... 316s Selecting previously unselected package automake. 316s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 316s Unpacking automake (1:1.18.1-3build1) ... 316s Selecting previously unselected package autopoint. 316s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 316s Unpacking autopoint (0.23.2-1) ... 316s Selecting previously unselected package libc-dev-bin. 316s Preparing to unpack .../12-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 316s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 316s Selecting previously unselected package linux-libc-dev:amd64. 316s Preparing to unpack .../13-linux-libc-dev_6.18.0-9.9_amd64.deb ... 316s Unpacking linux-libc-dev:amd64 (6.18.0-9.9) ... 316s Selecting previously unselected package libcrypt-dev:amd64. 316s Preparing to unpack .../14-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 316s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 316s Selecting previously unselected package rpcsvc-proto. 316s Preparing to unpack .../15-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 316s Unpacking rpcsvc-proto (1.4.3-1build1) ... 316s Selecting previously unselected package libc6-dev:amd64. 316s Preparing to unpack .../16-libc6-dev_2.42-2ubuntu4_amd64.deb ... 316s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 316s Selecting previously unselected package libisl23:amd64. 316s Preparing to unpack .../17-libisl23_0.27-1build1_amd64.deb ... 316s Unpacking libisl23:amd64 (0.27-1build1) ... 316s Selecting previously unselected package libmpc3:amd64. 316s Preparing to unpack .../18-libmpc3_1.3.1-2_amd64.deb ... 316s Unpacking libmpc3:amd64 (1.3.1-2) ... 316s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 316s Preparing to unpack .../19-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 316s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package cpp-15. 317s Preparing to unpack .../20-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package cpp-x86-64-linux-gnu. 317s Preparing to unpack .../21-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 317s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 317s Selecting previously unselected package cpp. 317s Preparing to unpack .../22-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 317s Unpacking cpp (4:15.2.0-4ubuntu1) ... 317s Selecting previously unselected package libcc1-0:amd64. 317s Preparing to unpack .../23-libcc1-0_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libcc1-0:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libgomp1:amd64. 317s Preparing to unpack .../24-libgomp1_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libgomp1:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libitm1:amd64. 317s Preparing to unpack .../25-libitm1_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libitm1:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libasan8:amd64. 317s Preparing to unpack .../26-libasan8_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libasan8:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package liblsan0:amd64. 317s Preparing to unpack .../27-liblsan0_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking liblsan0:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libtsan2:amd64. 317s Preparing to unpack .../28-libtsan2_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libtsan2:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libubsan1:amd64. 317s Preparing to unpack .../29-libubsan1_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libubsan1:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libhwasan0:amd64. 317s Preparing to unpack .../30-libhwasan0_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libhwasan0:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libquadmath0:amd64. 317s Preparing to unpack .../31-libquadmath0_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libquadmath0:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package libgcc-15-dev:amd64. 317s Preparing to unpack .../32-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 317s Preparing to unpack .../33-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 317s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 317s Selecting previously unselected package gcc-15. 317s Preparing to unpack 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unselected package dwz. 317s Preparing to unpack .../50-dwz_0.16-2build1_amd64.deb ... 317s Unpacking dwz (0.16-2build1) ... 317s Selecting previously unselected package gettext. 317s Preparing to unpack .../51-gettext_0.23.2-1_amd64.deb ... 317s Unpacking gettext (0.23.2-1) ... 317s Selecting previously unselected package intltool-debian. 317s Preparing to unpack .../52-intltool-debian_0.35.0+20060710.6build1_all.deb ... 317s Unpacking intltool-debian (0.35.0+20060710.6build1) ... 317s Selecting previously unselected package po-debconf. 317s Preparing to unpack .../53-po-debconf_1.0.22_all.deb ... 317s Unpacking po-debconf (1.0.22) ... 317s Selecting previously unselected package debhelper. 317s Preparing to unpack .../54-debhelper_13.28ubuntu1_all.deb ... 317s Unpacking debhelper (13.28ubuntu1) ... 317s Selecting previously unselected package dh-python. 317s Preparing to unpack .../55-dh-python_7.20260125_all.deb ... 317s Unpacking dh-python (7.20260125) ... 318s Selecting previously unselected package libpython3.14-stdlib:amd64. 318s Preparing to unpack .../56-libpython3.14-stdlib_3.14.2-1_amd64.deb ... 318s Unpacking libpython3.14-stdlib:amd64 (3.14.2-1) ... 318s Selecting previously unselected package pybuild-plugin-autopkgtest. 318s Preparing to unpack .../57-pybuild-plugin-autopkgtest_7.20260125_all.deb ... 318s Unpacking pybuild-plugin-autopkgtest (7.20260125) ... 318s Selecting previously unselected package python3-astroid. 318s Preparing to unpack .../58-python3-astroid_4.0.2-1ubuntu1_all.deb ... 318s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 318s Selecting previously unselected package python3-isort. 318s Preparing to unpack .../59-python3-isort_7.0.0-1_all.deb ... 318s Unpacking python3-isort (7.0.0-1) ... 318s Selecting previously unselected package python3-mypy-extensions. 318s Preparing to unpack .../60-python3-mypy-extensions_1.1.0-1_all.deb ... 318s Unpacking python3-mypy-extensions (1.1.0-1) ... 318s Selecting previously unselected package 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package python3-gtfparse. 318s Preparing to unpack .../72-python3-gtfparse_1.3.0+ds-2_all.deb ... 318s Unpacking python3-gtfparse (1.3.0+ds-2) ... 318s Selecting previously unselected package python3-memoized-property. 318s Preparing to unpack .../73-python3-memoized-property_1.0.3-2build1_all.deb ... 318s Unpacking python3-memoized-property (1.0.3-2build1) ... 318s Selecting previously unselected package python3-serializable. 318s Preparing to unpack .../74-python3-serializable_0.4.1+ds-2_all.deb ... 318s Unpacking python3-serializable (0.4.1+ds-2) ... 318s Selecting previously unselected package pyensembl. 318s Preparing to unpack .../75-pyensembl_2.3.13-2_all.deb ... 318s Unpacking pyensembl (2.3.13-2) ... 318s Selecting previously unselected package python3.14. 318s Preparing to unpack .../76-python3.14_3.14.2-1_amd64.deb ... 318s Unpacking python3.14 (3.14.2-1) ... 318s Selecting previously unselected package python3-all. 318s Preparing to unpack .../77-python3-all_3.13.9-3_amd64.deb ... 318s Unpacking python3-all (3.13.9-3) ... 318s Selecting previously unselected package python3-iniconfig. 318s Preparing to unpack .../78-python3-iniconfig_2.1.0-2_all.deb ... 318s Unpacking python3-iniconfig (2.1.0-2) ... 318s Selecting previously unselected package python3-pluggy. 318s Preparing to unpack .../79-python3-pluggy_1.6.0-2_all.deb ... 318s Unpacking python3-pluggy (1.6.0-2) ... 318s Selecting previously unselected package python3-pytest. 318s Preparing to unpack .../80-python3-pytest_9.0.2-2_all.deb ... 318s Unpacking python3-pytest (9.0.2-2) ... 318s Setting up dh-python (7.20260125) ... 318s Setting up python3-iniconfig (2.1.0-2) ... 318s Setting up python3-typechecks (0.1.0+ds-4) ... 319s Setting up python3-memoized-property (1.0.3-2build1) ... 319s Setting up libarchive-zip-perl (1.68-1) ... 319s Setting up python3-mypy-extensions (1.1.0-1) ... 319s Setting up libdebhelper-perl (13.28ubuntu1) ... 319s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 319s Setting up linux-libc-dev:amd64 (6.18.0-9.9) ... 319s Setting up m4 (1.4.20-2) ... 319s Setting up python3-pytz (2025.2-5) ... 319s Setting up python3-serializable (0.4.1+ds-2) ... 319s Setting up libgomp1:amd64 (15.2.0-12ubuntu1) ... 319s Setting up python3-platformdirs (4.5.1-1) ... 319s Setting up autotools-dev (20240727.1build1) ... 319s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ... 319s 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 319s Setting up rpcsvc-proto (1.4.3-1build1) ... 319s Setting up python3-dill (0.4.0-1) ... 319s Setting up libquadmath0:amd64 (15.2.0-12ubuntu1) ... 319s Setting up libmpc3:amd64 (1.3.1-2) ... 319s Setting up python3-numpy-dev:amd64 (1:2.3.5+ds-3) ... 319s Setting up autopoint (0.23.2-1) ... 319s Setting up libgfortran5:amd64 (15.2.0-12ubuntu1) ... 319s Setting up autoconf (2.72-3.1ubuntu1) ... 319s Setting up python3-isort (7.0.0-1) ... 320s Setting up python3-pluggy (1.6.0-2) ... 320s Setting up libubsan1:amd64 (15.2.0-12ubuntu1) ... 320s Setting up dwz (0.16-2build1) ... 320s Setting up python3-astroid (4.0.2-1ubuntu1) ... 320s Setting up libhwasan0:amd64 (15.2.0-12ubuntu1) ... 320s Setting up libcrypt-dev:amd64 (1:4.5.1-1) ... 320s Setting up libasan8:amd64 (15.2.0-12ubuntu1) ... 320s Setting up debugedit (1:5.2-3build1) ... 320s Setting up python3-mccabe (0.7.0-1build1) ... 320s Setting up libtsan2:amd64 (15.2.0-12ubuntu1) ... 320s Setting up libisl23:amd64 (0.27-1build1) ... 320s Setting up libc-dev-bin (2.42-2ubuntu4) ... 320s Setting up python3-tomlkit (0.13.3-2) ... 320s Setting up python3.14-minimal (3.14.2-1) ... 321s Setting up libcc1-0:amd64 (15.2.0-12ubuntu1) ... 321s Setting up liblsan0:amd64 (15.2.0-12ubuntu1) ... 321s Setting up libitm1:amd64 (15.2.0-12ubuntu1) ... 321s Setting up automake (1:1.18.1-3build1) ... 321s update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode 321s Setting up libfile-stripnondeterminism-perl (1.15.0-1build1) ... 321s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ... 321s 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 321s Setting up gettext (0.23.2-1) ... 321s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 321s Setting up python3-logilab-common (2.1.0-1build1) ... 321s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 321s Setting up python3-pytest (9.0.2-2) ... 322s Setting up cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 322s Setting up intltool-debian (0.35.0+20060710.6build1) ... 322s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 322s Setting up python3-numpy (1:2.3.5+ds-3) ... 324s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 324s Setting up cpp-15 (15.2.0-12ubuntu1) ... 324s Setting up libc6-dev:amd64 (2.42-2ubuntu4) ... 324s Setting up python3.14 (3.14.2-1) ... 325s Setting up pylint (4.0.4-1) ... 325s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 325s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 325s Setting up po-debconf (1.0.22) ... 325s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-3) ... 325s Setting up python3-all (3.13.9-3) ... 325s Setting up gcc-15 (15.2.0-12ubuntu1) ... 325s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 325s Setting up python3-pandas (2.3.3+dfsg-3) ... 331s Setting up cpp (4:15.2.0-4ubuntu1) ... 331s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 331s Setting up python3-datacache (1.4.1-2) ... 331s Setting up libtool (2.5.4-9) ... 331s Setting up python3-gtfparse (1.3.0+ds-2) ... 331s Setting up gcc (4:15.2.0-4ubuntu1) ... 331s Setting up dh-autoreconf (21+nmu1) ... 331s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 331s Setting up pyensembl (2.3.13-2) ... 332s Setting up g++-15 (15.2.0-12ubuntu1) ... 332s Setting up debhelper (13.28ubuntu1) ... 332s Setting up g++ (4:15.2.0-4ubuntu1) ... 332s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 332s Setting up build-essential (12.12ubuntu2) ... 332s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 332s Processing triggers for man-db (2.13.1-1) ... 333s Processing triggers for install-info (7.2-5) ... 333s Processing triggers for libc-bin (2.42-2ubuntu4) ... 333s Processing triggers for systemd (259-1ubuntu3) ... 334s autopkgtest [14:13:58]: test pybuild-autopkgtest: pybuild-autopkgtest 334s autopkgtest [14:13:58]: test pybuild-autopkgtest: [----------------------- 334s pybuild-autopkgtest 335s I: pybuild base:384: cd /tmp/autopkgtest.L1JCjv/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' 335s ============================= test session starts ============================== 335s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 335s cachedir: .pytest_cache 335s rootdir: /tmp/autopkgtest.L1JCjv/autopkgtest_tmp/build 335s plugins: typeguard-4.4.4 336s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 336s 336s ==================================== ERRORS ==================================== 336s _____________________ ERROR collecting tests/test_shell.py _____________________ 336s tests/test_shell.py:1: in 336s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 336s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 336s release_group = root_group.add_argument_group() 336s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 336s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 336s raise ValueError('argument groups cannot be nested') 336s E ValueError: argument groups cannot be nested 336s =============================== warnings summary =============================== 336s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 336s /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 336s import pkg_resources 336s 336s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 336s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 336s 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 336s declare_namespace(pkg) 336s 336s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 336s =========================== short test summary info ============================ 336s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 336s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 336s ================= 98 deselected, 2 warnings, 1 error in 0.88s ================== 336s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.L1JCjv/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' 336s I: pybuild base:384: cd /tmp/autopkgtest.L1JCjv/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' 336s ============================= test session starts ============================== 336s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 336s cachedir: .pytest_cache 336s rootdir: /tmp/autopkgtest.L1JCjv/autopkgtest_tmp/build 336s plugins: typeguard-4.4.4 337s collecting ... collected 126 items / 98 deselected / 28 selected 337s 337s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 337s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 337s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 337s tests/test_locus.py::test_locus_contains PASSED [ 14%] 337s tests/test_locus.py::test_position_offset PASSED [ 17%] 337s tests/test_locus.py::test_range_offset PASSED [ 21%] 337s tests/test_locus.py::test_locus_distance PASSED [ 25%] 337s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 337s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 337s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 337s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 337s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 337s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 337s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 337s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 337s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 337s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 337s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 337s tests/test_release_versions.py::test_int_version PASSED [ 67%] 337s tests/test_release_versions.py::test_str_version PASSED [ 71%] 337s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 337s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 337s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 337s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 337s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 337s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 337s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 337s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 337s 337s =============================== warnings summary =============================== 337s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 337s /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 337s import pkg_resources 337s 337s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 337s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 337s 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 337s declare_namespace(pkg) 337s 337s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 337s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 337s release_group = root_group.add_argument_group() 337s 337s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 337s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 337s path_group = root_group.add_argument_group() 337s 337s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 337s ================ 28 passed, 98 deselected, 4 warnings in 0.62s ================= 337s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 337s make: *** [/tmp/fqOWcfoQR2/run:4: pybuild-autopkgtest] Error 25 337s pybuild-autopkgtest: error: /tmp/fqOWcfoQR2/run pybuild-autopkgtest returned exit code 2 337s autopkgtest [14:14:01]: test pybuild-autopkgtest: -----------------------] 338s autopkgtest [14:14:02]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 338s pybuild-autopkgtest FAIL non-zero exit status 25 338s autopkgtest [14:14:02]: @@@@@@@@@@@@@@@@@@@@ summary 338s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 338s pybuild-autopkgtest FAIL non-zero exit status 25