0s autopkgtest [01:58:13]: starting date and time: 2026-02-06 01:58:13+0000 0s autopkgtest [01:58:13]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:58:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qpav_35a/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-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-arm64-33.secgroup --name adt-resolute-arm64-pyensembl-20260206-015812-juju-7f2275-prod-proposed-migration-environment-2-4d734d88-ac27-4aa3-af8e-33e689c5cfce --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 9s Creating nova instance adt-resolute-arm64-pyensembl-20260206-015812-juju-7f2275-prod-proposed-migration-environment-2-4d734d88-ac27-4aa3-af8e-33e689c5cfce from image adt/ubuntu-resolute-arm64-server-20260205.img (UUID 88169191-3954-4b52-b471-25031b32a3a0)... 93s autopkgtest [01:59:46]: testbed dpkg architecture: arm64 93s autopkgtest [01:59:46]: testbed apt version: 3.1.14 94s autopkgtest [01:59:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s autopkgtest [01:59:47]: testbed release detected to be: None 95s autopkgtest [01:59:48]: updating testbed package index (apt update) 96s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 96s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.4 kB] 96s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1631 kB] 96s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [221 kB] 96s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 97s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [269 kB] 97s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7344 B] 97s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 97s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 97s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1462 kB] 97s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [42.1 kB] 97s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [23.6 kB] 97s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 100s Fetched 3872 kB in 1s (3901 kB/s) 101s Reading package lists... 102s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 103s Reading package lists... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Calculating upgrade... 104s The following packages will be upgraded: 104s libdrm-amdgpu1 libdrm-common libdrm2 mawk python3-pkg-resources 104s python3-setuptools 104s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Need to get 1009 kB of archives. 104s After this operation, 0 B of additional disk space will be used. 104s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 mawk arm64 1.3.4.20260129-1 [128 kB] 104s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-common all 2.4.131-1 [9774 B] 104s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm2 arm64 2.4.131-1 [42.6 kB] 104s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.131-1 [22.6 kB] 104s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 104s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 105s dpkg-preconfigure: unable to re-open stdin: No such file or directory 105s Fetched 1009 kB in 0s (2873 kB/s) 105s (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 ... 89360 files and directories currently installed.) 105s Preparing to unpack .../0-mawk_1.3.4.20260129-1_arm64.deb ... 105s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 105s Preparing to unpack .../1-libdrm-common_2.4.131-1_all.deb ... 105s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 105s Preparing to unpack .../2-libdrm2_2.4.131-1_arm64.deb ... 105s Unpacking libdrm2:arm64 (2.4.131-1) over (2.4.129-1) ... 106s Preparing to unpack .../3-libdrm-amdgpu1_2.4.131-1_arm64.deb ... 106s Unpacking libdrm-amdgpu1:arm64 (2.4.131-1) over (2.4.129-1) ... 106s Preparing to unpack .../4-python3-pkg-resources_78.1.1-0.1build1_all.deb ... 106s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 106s Preparing to unpack .../5-python3-setuptools_78.1.1-0.1build1_all.deb ... 106s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 106s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 106s Setting up python3-setuptools (78.1.1-0.1build1) ... 107s Setting up mawk (1.3.4.20260129-1) ... 107s Setting up libdrm-common (2.4.131-1) ... 107s Setting up libdrm2:arm64 (2.4.131-1) ... 107s Setting up libdrm-amdgpu1:arm64 (2.4.131-1) ... 107s Processing triggers for man-db (2.13.1-1) ... 108s Processing triggers for libc-bin (2.42-2ubuntu4) ... 108s autopkgtest [02:00:01]: upgrading testbed (apt dist-upgrade and autopurge) 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Solving dependencies... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [02:00:07]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 114s autopkgtest [02:00:07]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 115s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (dsc) [2291 B] 115s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (tar) [60.7 kB] 115s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pyensembl 2.3.13-2 (diff) [5448 B] 116s gpgv: Signature made Sun Feb 16 22:16:52 2025 UTC 116s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 116s gpgv: issuer "tchet@debian.org" 116s gpgv: Can't check signature: No public key 116s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-2.dsc: no acceptable signature found 116s autopkgtest [02:00:09]: testing package pyensembl version 2.3.13-2 116s autopkgtest [02:00:09]: build not needed 117s autopkgtest [02:00:10]: test run-unit-test: preparing testbed 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Solving dependencies... 118s The following NEW packages will be installed: 118s libblas3 libgfortran5 liblapack3 libpython3.14-minimal libpython3.14-stdlib 118s pyensembl pylint python3-all python3-astroid python3-datacache python3-dill 118s python3-gtfparse python3-iniconfig python3-isort python3-logilab-common 118s python3-mccabe python3-memoized-property python3-mypy-extensions 118s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 118s python3-platformdirs python3-pluggy python3-pytest python3-pytz 118s python3-serializable python3-tomlkit python3-typechecks python3.14 118s python3.14-minimal 118s 0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded. 118s Need to get 25.0 MB of archives. 118s After this operation, 132 MB of additional disk space will be used. 118s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 118s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 118s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 118s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 119s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 120s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 120s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 120s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 121s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 121s Get:10 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-isort all 7.0.0-1 [59.7 kB] 121s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mypy-extensions all 1.1.0-1 [6716 B] 121s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 121s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dill all 0.4.0-1 [84.8 kB] 121s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mccabe all 0.7.0-1build1 [8926 B] 121s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 121s Get:16 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tomlkit all 0.13.3-2 [39.1 kB] 121s Get:17 http://ftpmaster.internal/ubuntu resolute/universe arm64 pylint all 4.0.4-1 [346 kB] 121s Get:18 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 121s Get:19 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 122s Get:20 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 123s Get:21 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typechecks all 0.1.0+ds-4 [4562 B] 123s Get:22 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datacache all 1.4.1-2 [13.1 kB] 123s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 123s Get:24 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-memoized-property all 1.0.3-2build1 [5328 B] 123s Get:25 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-serializable all 0.4.1+ds-2 [8438 B] 123s Get:26 http://ftpmaster.internal/ubuntu resolute/universe arm64 pyensembl all 2.3.13-2 [37.2 kB] 123s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 123s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 123s Get:29 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 123s Get:30 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 123s Get:31 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 124s Fetched 25.0 MB in 5s (4687 kB/s) 124s Selecting previously unselected package python3-numpy-dev:arm64. 124s (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 ... 89360 files and directories currently installed.) 124s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 124s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 124s Selecting previously unselected package libblas3:arm64. 124s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 124s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 124s Selecting previously unselected package libgfortran5:arm64. 124s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 124s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 124s Selecting previously unselected package liblapack3:arm64. 124s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 124s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 124s Selecting previously unselected package python3-numpy. 124s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 124s Unpacking python3-numpy (1:2.3.5+ds-3) ... 124s Selecting previously unselected package libpython3.14-minimal:arm64. 124s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_arm64.deb ... 124s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 124s Selecting previously unselected package python3.14-minimal. 124s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_arm64.deb ... 124s Unpacking python3.14-minimal (3.14.2-1) ... 124s Selecting previously unselected package libpython3.14-stdlib:arm64. 124s Preparing to unpack .../07-libpython3.14-stdlib_3.14.2-1_arm64.deb ... 124s Unpacking libpython3.14-stdlib:arm64 (3.14.2-1) ... 124s Selecting previously unselected package python3-astroid. 125s Preparing to unpack .../08-python3-astroid_4.0.2-1ubuntu1_all.deb ... 125s Unpacking python3-astroid (4.0.2-1ubuntu1) ... 125s Selecting previously unselected package python3-isort. 125s Preparing to unpack .../09-python3-isort_7.0.0-1_all.deb ... 125s Unpacking python3-isort (7.0.0-1) ... 125s Selecting previously unselected package python3-mypy-extensions. 125s Preparing to unpack .../10-python3-mypy-extensions_1.1.0-1_all.deb ... 125s Unpacking python3-mypy-extensions (1.1.0-1) ... 125s Selecting previously unselected package python3-logilab-common. 125s Preparing to unpack .../11-python3-logilab-common_2.1.0-1build1_all.deb ... 125s Unpacking python3-logilab-common (2.1.0-1build1) ... 125s Selecting previously unselected package python3-dill. 125s Preparing to unpack .../12-python3-dill_0.4.0-1_all.deb ... 125s Unpacking python3-dill (0.4.0-1) ... 125s Selecting previously unselected package python3-mccabe. 125s Preparing to unpack .../13-python3-mccabe_0.7.0-1build1_all.deb ... 125s Unpacking python3-mccabe (0.7.0-1build1) ... 125s Selecting previously unselected package python3-platformdirs. 125s Preparing to unpack .../14-python3-platformdirs_4.5.1-1_all.deb ... 125s Unpacking python3-platformdirs (4.5.1-1) ... 125s Selecting previously unselected package python3-tomlkit. 125s Preparing to unpack .../15-python3-tomlkit_0.13.3-2_all.deb ... 125s Unpacking python3-tomlkit (0.13.3-2) ... 125s Selecting previously unselected package pylint. 125s Preparing to unpack .../16-pylint_4.0.4-1_all.deb ... 125s Unpacking pylint (4.0.4-1) ... 125s Selecting previously unselected package python3-pytz. 125s Preparing to unpack .../17-python3-pytz_2025.2-5_all.deb ... 125s Unpacking python3-pytz (2025.2-5) ... 125s Selecting previously unselected package python3-pandas-lib:arm64. 125s Preparing to unpack .../18-python3-pandas-lib_2.3.3+dfsg-3_arm64.deb ... 125s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 125s Selecting previously unselected package python3-pandas. 125s Preparing to unpack .../19-python3-pandas_2.3.3+dfsg-3_all.deb ... 125s Unpacking python3-pandas (2.3.3+dfsg-3) ... 125s Selecting previously unselected package python3-typechecks. 125s Preparing to unpack .../20-python3-typechecks_0.1.0+ds-4_all.deb ... 125s Unpacking python3-typechecks (0.1.0+ds-4) ... 125s Selecting previously unselected package python3-datacache. 125s Preparing to unpack .../21-python3-datacache_1.4.1-2_all.deb ... 125s Unpacking python3-datacache (1.4.1-2) ... 125s Selecting previously unselected package python3-gtfparse. 125s Preparing to unpack .../22-python3-gtfparse_1.3.0+ds-2_all.deb ... 125s Unpacking python3-gtfparse (1.3.0+ds-2) ... 125s Selecting previously unselected package python3-memoized-property. 125s Preparing to unpack .../23-python3-memoized-property_1.0.3-2build1_all.deb ... 125s Unpacking python3-memoized-property (1.0.3-2build1) ... 125s Selecting previously unselected package python3-serializable. 125s Preparing to unpack .../24-python3-serializable_0.4.1+ds-2_all.deb ... 125s Unpacking python3-serializable (0.4.1+ds-2) ... 125s Selecting previously unselected package pyensembl. 126s Preparing to unpack .../25-pyensembl_2.3.13-2_all.deb ... 126s Unpacking pyensembl (2.3.13-2) ... 126s Selecting previously unselected package python3.14. 126s Preparing to unpack .../26-python3.14_3.14.2-1_arm64.deb ... 126s Unpacking python3.14 (3.14.2-1) ... 126s Selecting previously unselected package python3-all. 126s Preparing to unpack .../27-python3-all_3.13.9-3_arm64.deb ... 126s Unpacking python3-all (3.13.9-3) ... 126s Selecting previously unselected package python3-iniconfig. 126s Preparing to unpack .../28-python3-iniconfig_2.1.0-2_all.deb ... 126s Unpacking python3-iniconfig (2.1.0-2) ... 126s Selecting previously unselected package python3-pluggy. 126s Preparing to unpack .../29-python3-pluggy_1.6.0-2_all.deb ... 126s Unpacking python3-pluggy (1.6.0-2) ... 126s Selecting previously unselected package python3-pytest. 126s Preparing to unpack .../30-python3-pytest_9.0.2-2_all.deb ... 126s Unpacking python3-pytest (9.0.2-2) ... 126s Setting up python3-iniconfig (2.1.0-2) ... 126s Setting up python3-typechecks (0.1.0+ds-4) ... 126s Setting up python3-memoized-property (1.0.3-2build1) ... 127s Setting up python3-mypy-extensions (1.1.0-1) ... 127s Setting up libpython3.14-minimal:arm64 (3.14.2-1) ... 127s Setting up python3-pytz (2025.2-5) ... 127s Setting up python3-serializable (0.4.1+ds-2) ... 127s Setting up python3-platformdirs (4.5.1-1) ... 127s Setting up libblas3:arm64 (3.12.1-7ubuntu1) ... 127s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 127s Setting up python3-dill (0.4.0-1) ... 128s Setting up python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 128s Setting up libgfortran5:arm64 (15.2.0-12ubuntu1) ... 128s Setting up python3-isort (7.0.0-1) ... 128s Setting up python3-pluggy (1.6.0-2) ... 128s Setting up python3-astroid (4.0.2-1ubuntu1) ... 129s Setting up python3-mccabe (0.7.0-1build1) ... 129s Setting up python3-tomlkit (0.13.3-2) ... 130s Setting up python3.14-minimal (3.14.2-1) ... 130s Setting up liblapack3:arm64 (3.12.1-7ubuntu1) ... 130s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 130s Setting up python3-logilab-common (2.1.0-1build1) ... 131s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 131s Setting up python3-pytest (9.0.2-2) ... 131s Setting up python3-numpy (1:2.3.5+ds-3) ... 135s Setting up python3.14 (3.14.2-1) ... 136s Setting up pylint (4.0.4-1) ... 137s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 137s Setting up python3-all (3.13.9-3) ... 137s Setting up python3-pandas (2.3.3+dfsg-3) ... 147s Setting up python3-datacache (1.4.1-2) ... 147s Setting up python3-gtfparse (1.3.0+ds-2) ... 148s Setting up pyensembl (2.3.13-2) ... 148s Processing triggers for systemd (259-1ubuntu3) ... 148s Processing triggers for man-db (2.13.1-1) ... 148s Processing triggers for libc-bin (2.42-2ubuntu4) ... 150s autopkgtest [02:00:42]: 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.MlnjsD/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 1.44s ========================= 153s autopkgtest [02:00:46]: test run-unit-test: -----------------------] 153s autopkgtest [02:00:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 153s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 185s autopkgtest [02:01:18]: test pybuild-autopkgtest: preparing testbed 224s Creating nova instance adt-resolute-arm64-pyensembl-20260206-015812-juju-7f2275-prod-proposed-migration-environment-2-4d734d88-ac27-4aa3-af8e-33e689c5cfce from image adt/ubuntu-resolute-arm64-server-20260205.img (UUID 88169191-3954-4b52-b471-25031b32a3a0)... 369s autopkgtest [02:04:22]: testbed dpkg architecture: arm64 369s autopkgtest [02:04:22]: testbed apt version: 3.1.14 370s autopkgtest [02:04:23]: @@@@@@@@@@@@@@@@@@@@ test bed setup 370s autopkgtest [02:04:23]: testbed release detected to be: resolute 372s autopkgtest [02:04:25]: updating testbed package index (apt update) 372s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 372s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 372s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 372s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 372s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 372s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1631 kB] 372s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [221 kB] 372s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.4 kB] 372s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [269 kB] 373s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7344 B] 373s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 373s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 373s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1462 kB] 373s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [42.1 kB] 373s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [23.6 kB] 373s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 376s Fetched 3872 kB in 1s (4776 kB/s) 377s Reading package lists... 378s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 378s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 378s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 378s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 379s Reading package lists... 379s Reading package lists... 379s Building dependency tree... 379s Reading state information... 380s Calculating upgrade... 380s The following packages will be upgraded: 380s libdrm-amdgpu1 libdrm-common libdrm2 mawk python3-pkg-resources 380s python3-setuptools 380s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 380s Need to get 1009 kB of archives. 380s After this operation, 0 B of additional disk space will be used. 380s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 mawk arm64 1.3.4.20260129-1 [128 kB] 380s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-common all 2.4.131-1 [9774 B] 380s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm2 arm64 2.4.131-1 [42.6 kB] 380s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libdrm-amdgpu1 arm64 2.4.131-1 [22.6 kB] 380s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-pkg-resources all 78.1.1-0.1build1 [144 kB] 380s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 python3-setuptools all 78.1.1-0.1build1 [661 kB] 381s dpkg-preconfigure: unable to re-open stdin: No such file or directory 381s Fetched 1009 kB in 0s (3326 kB/s) 381s (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 ... 89360 files and directories currently installed.) 381s Preparing to unpack .../0-mawk_1.3.4.20260129-1_arm64.deb ... 381s Unpacking mawk (1.3.4.20260129-1) over (1.3.4.20250131-2) ... 381s Preparing to unpack .../1-libdrm-common_2.4.131-1_all.deb ... 381s Unpacking libdrm-common (2.4.131-1) over (2.4.129-1) ... 381s Preparing to unpack .../2-libdrm2_2.4.131-1_arm64.deb ... 381s Unpacking libdrm2:arm64 (2.4.131-1) over (2.4.129-1) ... 381s Preparing to unpack .../3-libdrm-amdgpu1_2.4.131-1_arm64.deb ... 381s Unpacking libdrm-amdgpu1:arm64 (2.4.131-1) over (2.4.129-1) ... 381s Preparing to unpack .../4-python3-pkg-resources_78.1.1-0.1build1_all.deb ... 381s Unpacking python3-pkg-resources (78.1.1-0.1build1) over (78.1.1-0.1) ... 381s Preparing to unpack .../5-python3-setuptools_78.1.1-0.1build1_all.deb ... 382s Unpacking python3-setuptools (78.1.1-0.1build1) over (78.1.1-0.1) ... 382s Setting up python3-pkg-resources (78.1.1-0.1build1) ... 382s Setting up python3-setuptools (78.1.1-0.1build1) ... 383s Setting up mawk (1.3.4.20260129-1) ... 383s Setting up libdrm-common (2.4.131-1) ... 383s Setting up libdrm2:arm64 (2.4.131-1) ... 383s Setting up libdrm-amdgpu1:arm64 (2.4.131-1) ... 383s Processing triggers for man-db (2.13.1-1) ... 383s Processing triggers for libc-bin (2.42-2ubuntu4) ... 384s autopkgtest [02:04:37]: upgrading testbed (apt dist-upgrade and autopurge) 384s Reading package lists... 384s Building dependency tree... 384s Reading state information... 384s Calculating upgrade... 385s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 385s Reading package lists... 385s Building dependency tree... 385s Reading state information... 385s Solving dependencies... 386s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 390s Reading package lists... 390s Building dependency tree... 390s Reading state information... 390s Solving dependencies... 391s The following NEW packages will be installed: 391s autoconf automake autopoint autotools-dev build-essential cpp cpp-15 391s cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 391s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-15 391s g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 391s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 391s libarchive-zip-perl libasan8 libblas3 libc-dev-bin libc6-dev libcc1-0 391s libcrypt-dev libdebhelper-perl libfile-stripnondeterminism-perl 391s libgcc-15-dev libgfortran5 libgomp1 libhwasan0 libisl23 libitm1 liblapack3 391s liblsan0 libmpc3 libpython3.14-minimal libpython3.14-stdlib libstdc++-15-dev 391s libtool libtsan2 libubsan1 linux-libc-dev m4 po-debconf 391s pybuild-plugin-autopkgtest pyensembl pylint python3-all python3-astroid 391s python3-datacache python3-dill python3-gtfparse python3-iniconfig 391s python3-isort python3-logilab-common python3-mccabe 391s python3-memoized-property python3-mypy-extensions python3-numpy 391s python3-numpy-dev python3-pandas python3-pandas-lib python3-platformdirs 391s python3-pluggy python3-pytest python3-pytz python3-serializable 391s python3-tomlkit python3-typechecks python3.14 python3.14-minimal 391s rpcsvc-proto 391s 0 upgraded, 80 newly installed, 0 to remove and 0 not upgraded. 391s Need to get 98.0 MB of archives. 391s After this operation, 390 MB of additional disk space will be used. 391s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.3.5+ds-3 [366 kB] 391s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-7ubuntu1 [181 kB] 391s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-12ubuntu1 [451 kB] 391s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-7ubuntu1 [2299 kB] 391s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.3.5+ds-3 [4569 kB] 392s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-minimal arm64 3.14.2-1 [917 kB] 392s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14-minimal arm64 3.14.2-1 [2548 kB] 393s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 m4 arm64 1.4.20-2 [213 kB] 393s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 autoconf all 2.72-3.1ubuntu1 [384 kB] 393s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 autotools-dev all 20240727.1 [43.4 kB] 393s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 automake all 1:1.18.1-3build1 [582 kB] 394s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 autopoint all 0.23.2-1 [620 kB] 394s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libc-dev-bin arm64 2.42-2ubuntu4 [22.5 kB] 394s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.18.0-9.9 [1834 kB] 396s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 396s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 396s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libc6-dev arm64 2.42-2ubuntu4 [1765 kB] 398s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 398s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 398s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 404s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 404s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 404s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 404s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 404s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 404s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 404s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 406s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 406s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 408s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 408s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 409s Get:32 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 410s Get:33 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 417s Get:34 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 417s Get:35 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 417s Get:36 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 417s Get:37 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 418s Get:38 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 420s Get:39 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 420s Get:40 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 420s Get:41 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 421s Get:42 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 421s Get:43 http://ftpmaster.internal/ubuntu resolute/main arm64 libdebhelper-perl all 13.28ubuntu1 [97.4 kB] 421s Get:44 http://ftpmaster.internal/ubuntu resolute/main arm64 libtool all 2.5.4-9 [169 kB] 421s Get:45 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-autoreconf all 21 [12.5 kB] 421s Get:46 http://ftpmaster.internal/ubuntu resolute/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 421s Get:47 http://ftpmaster.internal/ubuntu resolute/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1build1 [20.6 kB] 421s Get:48 http://ftpmaster.internal/ubuntu resolute/main arm64 dh-strip-nondeterminism all 1.15.0-1build1 [5110 B] 421s Get:49 http://ftpmaster.internal/ubuntu resolute/main arm64 debugedit arm64 1:5.2-3build1 [47.9 kB] 421s Get:50 http://ftpmaster.internal/ubuntu resolute/main arm64 dwz arm64 0.16-2 [113 kB] 421s Get:51 http://ftpmaster.internal/ubuntu resolute/main arm64 gettext arm64 0.23.2-1 [998 kB] 421s Get:52 http://ftpmaster.internal/ubuntu resolute/main arm64 intltool-debian all 0.35.0+20060710.6build1 [24.1 kB] 421s Get:53 http://ftpmaster.internal/ubuntu resolute/main arm64 po-debconf all 1.0.22 [215 kB] 421s Get:54 http://ftpmaster.internal/ubuntu resolute/main arm64 debhelper all 13.28ubuntu1 [916 kB] 421s Get:55 http://ftpmaster.internal/ubuntu resolute/universe arm64 dh-python all 7.20260125 [122 kB] 421s Get:56 http://ftpmaster.internal/ubuntu resolute/main arm64 libpython3.14-stdlib arm64 3.14.2-1 [2351 kB] 422s Get:57 http://ftpmaster.internal/ubuntu resolute/universe arm64 pybuild-plugin-autopkgtest all 7.20260125 [1744 B] 422s Get:58 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-astroid all 4.0.2-1ubuntu1 [172 kB] 422s Get:59 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-isort all 7.0.0-1 [59.7 kB] 422s Get:60 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mypy-extensions all 1.1.0-1 [6716 B] 422s Get:61 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-logilab-common all 2.1.0-1build1 [95.9 kB] 422s Get:62 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-dill all 0.4.0-1 [84.8 kB] 422s Get:63 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-mccabe all 0.7.0-1build1 [8926 B] 422s Get:64 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-platformdirs all 4.5.1-1 [17.1 kB] 422s Get:65 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-tomlkit all 0.13.3-2 [39.1 kB] 422s Get:66 http://ftpmaster.internal/ubuntu resolute/universe arm64 pylint all 4.0.4-1 [346 kB] 422s Get:67 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytz all 2025.2-5 [32.4 kB] 422s Get:68 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-3 [6290 kB] 423s Get:69 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-3 [2948 kB] 424s Get:70 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-typechecks all 0.1.0+ds-4 [4562 B] 424s Get:71 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-datacache all 1.4.1-2 [13.1 kB] 424s Get:72 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-gtfparse all 1.3.0+ds-2 [10.3 kB] 424s Get:73 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-memoized-property all 1.0.3-2build1 [5328 B] 424s Get:74 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-serializable all 0.4.1+ds-2 [8438 B] 424s Get:75 http://ftpmaster.internal/ubuntu resolute/universe arm64 pyensembl all 2.3.13-2 [37.2 kB] 424s Get:76 http://ftpmaster.internal/ubuntu resolute/main arm64 python3.14 arm64 3.14.2-1 [816 kB] 424s Get:77 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.9-3 [890 B] 424s Get:78 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 2.1.0-2 [6962 B] 424s Get:79 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-2 [21.1 kB] 424s Get:80 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 9.0.2-2 [277 kB] 425s Fetched 98.0 MB in 34s (2921 kB/s) 425s Selecting previously unselected package python3-numpy-dev:arm64. 425s (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 ... 89360 files and directories currently installed.) 425s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_arm64.deb ... 425s Unpacking python3-numpy-dev:arm64 (1:2.3.5+ds-3) ... 425s Selecting previously unselected package libblas3:arm64. 425s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_arm64.deb ... 425s Unpacking libblas3:arm64 (3.12.1-7ubuntu1) ... 425s Selecting previously unselected package libgfortran5:arm64. 425s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_arm64.deb ... 425s Unpacking libgfortran5:arm64 (15.2.0-12ubuntu1) ... 425s Selecting previously unselected package liblapack3:arm64. 425s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_arm64.deb ... 425s Unpacking liblapack3:arm64 (3.12.1-7ubuntu1) ... 425s Selecting previously unselected package python3-numpy. 425s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_arm64.deb ... 425s Unpacking python3-numpy (1:2.3.5+ds-3) ... 425s Selecting previously unselected package libpython3.14-minimal:arm64. 425s Preparing to unpack .../05-libpython3.14-minimal_3.14.2-1_arm64.deb ... 425s Unpacking libpython3.14-minimal:arm64 (3.14.2-1) ... 425s Selecting previously unselected package python3.14-minimal. 425s Preparing to unpack .../06-python3.14-minimal_3.14.2-1_arm64.deb ... 425s Unpacking python3.14-minimal (3.14.2-1) ... 425s Selecting previously unselected package m4. 425s Preparing to unpack .../07-m4_1.4.20-2_arm64.deb ... 425s Unpacking m4 (1.4.20-2) ... 425s Selecting previously unselected package autoconf. 425s Preparing to unpack .../08-autoconf_2.72-3.1ubuntu1_all.deb ... 425s Unpacking autoconf (2.72-3.1ubuntu1) ... 425s Selecting previously unselected package autotools-dev. 425s Preparing to unpack .../09-autotools-dev_20240727.1_all.deb ... 425s Unpacking autotools-dev (20240727.1) ... 425s Selecting previously unselected package automake. 425s Preparing to unpack .../10-automake_1%3a1.18.1-3build1_all.deb ... 425s Unpacking automake (1:1.18.1-3build1) ... 425s Selecting previously unselected package autopoint. 425s Preparing to unpack .../11-autopoint_0.23.2-1_all.deb ... 425s Unpacking autopoint (0.23.2-1) ... 426s Selecting previously unselected package libc-dev-bin. 426s Preparing to unpack .../12-libc-dev-bin_2.42-2ubuntu4_arm64.deb ... 426s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 426s Selecting previously unselected package linux-libc-dev:arm64. 426s Preparing to unpack .../13-linux-libc-dev_6.18.0-9.9_arm64.deb ... 426s Unpacking linux-libc-dev:arm64 (6.18.0-9.9) ... 426s Selecting previously unselected package libcrypt-dev:arm64. 426s Preparing to unpack .../14-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 426s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 426s Selecting previously unselected package rpcsvc-proto. 426s Preparing to unpack .../15-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 426s Unpacking rpcsvc-proto (1.4.3-1build1) ... 426s Selecting previously unselected package libc6-dev:arm64. 426s Preparing to unpack .../16-libc6-dev_2.42-2ubuntu4_arm64.deb ... 426s Unpacking libc6-dev:arm64 (2.42-2ubuntu4) ... 426s Selecting previously unselected package libisl23:arm64. 426s Preparing to unpack .../17-libisl23_0.27-1build1_arm64.deb ... 426s Unpacking libisl23:arm64 (0.27-1build1) ... 426s Selecting previously unselected package libmpc3:arm64. 426s Preparing to unpack .../18-libmpc3_1.3.1-2_arm64.deb ... 426s Unpacking libmpc3:arm64 (1.3.1-2) ... 426s 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/usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 435s Setting up gettext (0.23.2-1) ... 435s Setting up libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 435s Setting up python3-logilab-common (2.1.0-1build1) ... 435s Setting up libpython3.14-stdlib:arm64 (3.14.2-1) ... 435s Setting up python3-pytest (9.0.2-2) ... 436s Setting up intltool-debian (0.35.0+20060710.6build1) ... 436s Setting up cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 436s Setting up python3-numpy (1:2.3.5+ds-3) ... 439s Setting up dh-strip-nondeterminism (1.15.0-1build1) ... 439s Setting up cpp-15 (15.2.0-12ubuntu1) ... 439s Setting up cpp (4:15.2.0-4ubuntu1) ... 439s Setting up libc6-dev:arm64 (2.42-2ubuntu4) ... 439s Setting up python3.14 (3.14.2-1) ... 441s Setting up pylint (4.0.4-1) ... 441s Setting up gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 441s Setting up po-debconf (1.0.22) ... 441s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-3) ... 441s Setting up python3-all (3.13.9-3) ... 441s Setting up gcc-15 (15.2.0-12ubuntu1) ... 441s Setting up libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 441s Setting up python3-pandas (2.3.3+dfsg-3) ... 451s Setting up g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 451s Setting up g++-15 (15.2.0-12ubuntu1) ... 451s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 451s Setting up python3-datacache (1.4.1-2) ... 451s Setting up libtool (2.5.4-9) ... 451s Setting up python3-gtfparse (1.3.0+ds-2) ... 452s Setting up gcc (4:15.2.0-4ubuntu1) ... 452s Setting up dh-autoreconf (21) ... 452s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 452s Setting up pyensembl (2.3.13-2) ... 452s Setting up debhelper (13.28ubuntu1) ... 452s Setting up g++ (4:15.2.0-4ubuntu1) ... 452s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 452s Setting up build-essential (12.12ubuntu2) ... 452s Setting up pybuild-plugin-autopkgtest (7.20260125) ... 452s Processing triggers for man-db (2.13.1-1) ... 453s Processing triggers for install-info (7.2-5) ... 453s Processing triggers for libc-bin (2.42-2ubuntu4) ... 453s Processing triggers for systemd (259-1ubuntu3) ... 455s autopkgtest [02:05:48]: test pybuild-autopkgtest: pybuild-autopkgtest 455s autopkgtest [02:05:48]: test pybuild-autopkgtest: [----------------------- 455s pybuild-autopkgtest 455s I: pybuild base:384: cd /tmp/autopkgtest.MlnjsD/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' 456s ============================= test session starts ============================== 456s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 456s cachedir: .pytest_cache 456s rootdir: /tmp/autopkgtest.MlnjsD/autopkgtest_tmp/build 456s plugins: typeguard-4.4.4 458s collecting ... collected 125 items / 1 error / 98 deselected / 27 selected 458s 458s ==================================== ERRORS ==================================== 458s _____________________ ERROR collecting tests/test_shell.py _____________________ 458s tests/test_shell.py:1: in 458s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 458s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: in 458s release_group = root_group.add_argument_group() 458s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 458s /usr/lib/python3.14/argparse.py:1805: in add_argument_group 458s raise ValueError('argument groups cannot be nested') 458s E ValueError: argument groups cannot be nested 458s =============================== warnings summary =============================== 458s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 458s /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 458s import pkg_resources 458s 458s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 458s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 458s 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 458s declare_namespace(pkg) 458s 458s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 458s =========================== short test summary info ============================ 458s ERROR tests/test_shell.py - ValueError: argument groups cannot be nested 458s !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!! 458s ================= 98 deselected, 2 warnings, 1 error in 1.42s ================== 458s E: pybuild pybuild:483: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.MlnjsD/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' 458s I: pybuild base:384: cd /tmp/autopkgtest.MlnjsD/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' 458s ============================= test session starts ============================== 458s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 458s cachedir: .pytest_cache 458s rootdir: /tmp/autopkgtest.MlnjsD/autopkgtest_tmp/build 458s plugins: typeguard-4.4.4 459s collecting ... collected 126 items / 98 deselected / 28 selected 459s 459s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 459s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 459s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 459s tests/test_locus.py::test_locus_contains PASSED [ 14%] 459s tests/test_locus.py::test_position_offset PASSED [ 17%] 459s tests/test_locus.py::test_range_offset PASSED [ 21%] 459s tests/test_locus.py::test_locus_distance PASSED [ 25%] 459s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 459s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 459s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 459s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 459s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 459s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 459s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 459s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 459s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 459s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 459s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 459s tests/test_release_versions.py::test_int_version PASSED [ 67%] 459s tests/test_release_versions.py::test_str_version PASSED [ 71%] 459s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 459s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 459s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 459s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 459s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 459s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 459s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 459s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 459s 459s =============================== warnings summary =============================== 459s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 459s /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 459s import pkg_resources 459s 459s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147 459s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3147: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 459s 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 459s declare_namespace(pkg) 459s 459s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 459s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 459s release_group = root_group.add_argument_group() 459s 459s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 459s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 459s path_group = root_group.add_argument_group() 459s 459s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 459s ================ 28 passed, 98 deselected, 4 warnings in 0.94s ================= 459s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 459s make: *** [/tmp/_VIJDvF17y/run:4: pybuild-autopkgtest] Error 25 459s pybuild-autopkgtest: error: /tmp/_VIJDvF17y/run pybuild-autopkgtest returned exit code 2 460s autopkgtest [02:05:53]: test pybuild-autopkgtest: -----------------------] 460s autopkgtest [02:05:53]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 460s pybuild-autopkgtest FAIL non-zero exit status 25 461s autopkgtest [02:05:54]: @@@@@@@@@@@@@@@@@@@@ summary 461s run-unit-test SKIP Failed, but test has needs-internet and that's not guaranteed 461s pybuild-autopkgtest FAIL non-zero exit status 25