0s autopkgtest [09:57:36]: starting date and time: 2024-11-13 09:57:36+0000 0s autopkgtest [09:57:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:57:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.csfn4vk6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade pyensembl --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-48.secgroup --name adt-plucky-arm64-pyensembl-20241113-095736-juju-7f2275-prod-proposed-migration-environment-15-a5c79e5d-d9d8-485e-8553-4be16e356ed5 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 113s autopkgtest [09:59:29]: testbed dpkg architecture: arm64 113s autopkgtest [09:59:29]: testbed apt version: 2.9.8 113s autopkgtest [09:59:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 114s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 114s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 114s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 114s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 115s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 115s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 115s Fetched 1794 kB in 1s (1825 kB/s) 115s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s Calculating upgrade... 120s The following NEW packages will be installed: 120s python3.13-gdbm 120s The following packages will be upgraded: 120s libpython3-stdlib python3 python3-gdbm python3-minimal 120s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 120s Need to get 101 kB of archives. 120s After this operation, 141 kB of additional disk space will be used. 120s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 121s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 121s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 121s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 121s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 121s Fetched 101 kB in 0s (272 kB/s) 121s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 121s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 121s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Setting up python3-minimal (3.12.7-1) ... 122s (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 ... 79924 files and directories currently installed.) 122s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 122s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 122s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 122s Selecting previously unselected package python3.13-gdbm. 122s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 122s Unpacking python3.13-gdbm (3.13.0-2) ... 122s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 122s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 122s Setting up python3.13-gdbm (3.13.0-2) ... 122s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 122s Setting up python3 (3.12.7-1) ... 123s Setting up python3-gdbm:arm64 (3.12.7-1) ... 123s Processing triggers for man-db (2.12.1-3) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 126s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 127s Reading package lists... 127s Reading package lists... 128s Building dependency tree... 128s Reading state information... 129s Calculating upgrade... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 132s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s autopkgtest [09:59:51]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 135s autopkgtest [09:59:51]: @@@@@@@@@@@@@@@@@@@@ apt-source pyensembl 137s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pyensembl 2.3.13-1 (dsc) [2291 B] 137s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pyensembl 2.3.13-1 (tar) [60.7 kB] 137s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pyensembl 2.3.13-1 (diff) [5404 B] 137s gpgv: Signature made Sat May 11 16:47:07 2024 UTC 137s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 137s gpgv: issuer "tchet@debian.org" 137s gpgv: Can't check signature: No public key 137s dpkg-source: warning: cannot verify inline signature for ./pyensembl_2.3.13-1.dsc: no acceptable signature found 137s autopkgtest [09:59:53]: testing package pyensembl version 2.3.13-1 138s autopkgtest [09:59:54]: build not needed 138s autopkgtest [09:59:54]: test run-unit-test: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 143s The following additional packages will be installed: 143s libblas3 libgfortran5 libjs-jquery libjs-sphinxdoc libjs-underscore 143s liblapack3 libpython3.13-minimal libpython3.13-stdlib pyensembl pylint 143s python3-all python3-astroid python3-datacache python3-dateutil python3-dill 143s python3-gtfparse python3-iniconfig python3-isort python3-logilab-common 143s python3-mccabe python3-memoized-property python3-mypy-extensions 143s python3-numpy python3-packaging python3-pandas python3-pandas-lib 143s python3-platformdirs python3-pluggy python3-pytest python3-serializable 143s python3-simplejson python3-six python3-tomlkit python3-typechecks python3-tz 143s python3.13 python3.13-minimal 143s Suggested packages: 143s python3-objgraph gcc gfortran python-numpy-doc python3-dev python-pandas-doc 143s python3-statsmodels python3.13-venv python3.13-doc binfmt-support 143s Recommended packages: 143s javascript-common python3-tk python3-scipy python3-matplotlib 143s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 143s python3-html5lib python3-lxml python3-tables 143s The following NEW packages will be installed: 143s autopkgtest-satdep libblas3 libgfortran5 libjs-jquery libjs-sphinxdoc 143s libjs-underscore liblapack3 libpython3.13-minimal libpython3.13-stdlib 143s pyensembl pylint python3-all python3-astroid python3-datacache 143s python3-dateutil python3-dill python3-gtfparse python3-iniconfig 143s python3-isort python3-logilab-common python3-mccabe 143s python3-memoized-property python3-mypy-extensions python3-numpy 143s python3-packaging python3-pandas python3-pandas-lib python3-platformdirs 143s python3-pluggy python3-pytest python3-serializable python3-simplejson 143s python3-six python3-tomlkit python3-typechecks python3-tz python3.13 143s python3.13-minimal 143s 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. 143s Need to get 22.0 MB/22.0 MB of archives. 143s After this operation, 107 MB of additional disk space will be used. 143s Get:1 /tmp/autopkgtest.POlK2Q/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 143s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 144s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 144s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 144s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 144s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 144s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 144s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-astroid all 3.2.2-1 [174 kB] 144s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-isort all 5.13.2-2 [59.3 kB] 144s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mypy-extensions all 1.0.0-1 [6148 B] 144s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-logilab-common all 2.0.0-1 [281 kB] 144s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-dill all 0.3.9-1 [84.5 kB] 144s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mccabe all 0.7.0-1 [8678 B] 144s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-platformdirs all 4.3.6-1 [16.8 kB] 144s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tomlkit all 0.13.2-1 [37.6 kB] 144s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 pylint all 3.2.7-1 [343 kB] 144s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 144s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 144s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 144s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 144s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 145s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 145s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-typechecks all 0.1.0+ds-4 [4562 B] 145s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-datacache all 1.4.1-2 [13.1 kB] 145s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-gtfparse all 1.3.0+ds-1 [10.1 kB] 145s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-memoized-property all 1.0.3-2 [5286 B] 145s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-simplejson arm64 3.19.3-1 [53.9 kB] 145s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-serializable all 0.4.1+ds-1 [8392 B] 145s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 pyensembl all 2.3.13-1 [37.1 kB] 145s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 145s Get:34 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 145s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 145s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 145s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 145s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 145s Fetched 22.0 MB in 2s (13.3 MB/s) 145s Selecting previously unselected package libpython3.13-minimal:arm64. 145s (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 ... 79931 files and directories currently installed.) 145s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 145s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 146s Selecting previously unselected package python3.13-minimal. 146s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 146s Unpacking python3.13-minimal (3.13.0-2) ... 146s Selecting previously unselected package libblas3:arm64. 146s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ... 146s Unpacking libblas3:arm64 (3.12.0-3build2) ... 146s Selecting previously unselected package libgfortran5:arm64. 146s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 146s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 146s Selecting previously unselected package libjs-jquery. 146s Preparing to unpack .../04-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 146s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 146s Selecting previously unselected package libjs-underscore. 146s Preparing to unpack .../05-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 146s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 146s Selecting previously unselected package libjs-sphinxdoc. 146s Preparing to unpack .../06-libjs-sphinxdoc_7.4.7-4_all.deb ... 146s Unpacking libjs-sphinxdoc (7.4.7-4) ... 146s Selecting previously unselected package liblapack3:arm64. 146s Preparing to unpack .../07-liblapack3_3.12.0-3build2_arm64.deb ... 146s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 146s Selecting previously unselected package libpython3.13-stdlib:arm64. 146s Preparing to unpack .../08-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 146s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 146s Selecting previously unselected package python3-astroid. 146s Preparing to unpack .../09-python3-astroid_3.2.2-1_all.deb ... 146s Unpacking python3-astroid (3.2.2-1) ... 146s Selecting previously unselected package python3-isort. 146s Preparing to unpack .../10-python3-isort_5.13.2-2_all.deb ... 146s Unpacking python3-isort (5.13.2-2) ... 147s Selecting previously unselected package python3-mypy-extensions. 147s Preparing to unpack .../11-python3-mypy-extensions_1.0.0-1_all.deb ... 147s Unpacking python3-mypy-extensions (1.0.0-1) ... 147s Selecting previously unselected package python3-logilab-common. 147s Preparing to unpack .../12-python3-logilab-common_2.0.0-1_all.deb ... 147s Unpacking python3-logilab-common (2.0.0-1) ... 147s Selecting previously unselected package python3-dill. 147s Preparing to unpack .../13-python3-dill_0.3.9-1_all.deb ... 147s Unpacking python3-dill (0.3.9-1) ... 147s Selecting previously unselected package python3-mccabe. 147s Preparing to unpack .../14-python3-mccabe_0.7.0-1_all.deb ... 147s Unpacking python3-mccabe (0.7.0-1) ... 147s Selecting previously unselected package python3-platformdirs. 147s Preparing to unpack .../15-python3-platformdirs_4.3.6-1_all.deb ... 147s Unpacking python3-platformdirs (4.3.6-1) ... 147s Selecting previously unselected package python3-tomlkit. 147s Preparing to unpack .../16-python3-tomlkit_0.13.2-1_all.deb ... 147s Unpacking python3-tomlkit (0.13.2-1) ... 147s Selecting previously unselected package pylint. 147s Preparing to unpack .../17-pylint_3.2.7-1_all.deb ... 147s Unpacking pylint (3.2.7-1) ... 147s Selecting previously unselected package python3-six. 147s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ... 147s Unpacking python3-six (1.16.0-7) ... 147s Selecting previously unselected package python3-dateutil. 147s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ... 147s Unpacking python3-dateutil (2.9.0-2) ... 147s Selecting previously unselected package python3-numpy. 147s Preparing to unpack .../20-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 147s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 147s Selecting previously unselected package python3-tz. 147s Preparing to unpack .../21-python3-tz_2024.1-2_all.deb ... 147s Unpacking python3-tz (2024.1-2) ... 147s Selecting previously unselected package python3-pandas-lib:arm64. 148s Preparing to unpack .../22-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 148s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 148s Selecting previously unselected package python3-pandas. 148s Preparing to unpack .../23-python3-pandas_2.2.3+dfsg-5_all.deb ... 148s Unpacking python3-pandas (2.2.3+dfsg-5) ... 148s Selecting previously unselected package python3-typechecks. 148s Preparing to unpack .../24-python3-typechecks_0.1.0+ds-4_all.deb ... 148s Unpacking python3-typechecks (0.1.0+ds-4) ... 148s Selecting previously unselected package python3-datacache. 148s Preparing to unpack .../25-python3-datacache_1.4.1-2_all.deb ... 148s Unpacking python3-datacache (1.4.1-2) ... 148s Selecting previously unselected package python3-gtfparse. 148s Preparing to unpack .../26-python3-gtfparse_1.3.0+ds-1_all.deb ... 148s Unpacking python3-gtfparse (1.3.0+ds-1) ... 148s Selecting previously unselected package python3-memoized-property. 148s Preparing to unpack .../27-python3-memoized-property_1.0.3-2_all.deb ... 148s Unpacking python3-memoized-property (1.0.3-2) ... 148s Selecting previously unselected package python3-simplejson. 148s Preparing to unpack .../28-python3-simplejson_3.19.3-1_arm64.deb ... 148s Unpacking python3-simplejson (3.19.3-1) ... 148s Selecting previously unselected package python3-serializable. 148s Preparing to unpack .../29-python3-serializable_0.4.1+ds-1_all.deb ... 148s Unpacking python3-serializable (0.4.1+ds-1) ... 148s Selecting previously unselected package pyensembl. 148s Preparing to unpack .../30-pyensembl_2.3.13-1_all.deb ... 148s Unpacking pyensembl (2.3.13-1) ... 148s Selecting previously unselected package python3.13. 148s Preparing to unpack .../31-python3.13_3.13.0-2_arm64.deb ... 148s Unpacking python3.13 (3.13.0-2) ... 149s Selecting previously unselected package python3-all. 149s Preparing to unpack .../32-python3-all_3.12.7-1_arm64.deb ... 149s Unpacking python3-all (3.12.7-1) ... 149s Selecting previously unselected package python3-iniconfig. 149s Preparing to unpack .../33-python3-iniconfig_1.1.1-2_all.deb ... 149s Unpacking python3-iniconfig (1.1.1-2) ... 149s Selecting previously unselected package python3-packaging. 149s Preparing to unpack .../34-python3-packaging_24.1-1_all.deb ... 150s Unpacking python3-packaging (24.1-1) ... 150s Selecting previously unselected package python3-pluggy. 150s Preparing to unpack .../35-python3-pluggy_1.5.0-1_all.deb ... 150s Unpacking python3-pluggy (1.5.0-1) ... 150s Selecting previously unselected package python3-pytest. 150s Preparing to unpack .../36-python3-pytest_8.3.3-1_all.deb ... 150s Unpacking python3-pytest (8.3.3-1) ... 150s Selecting previously unselected package autopkgtest-satdep. 150s Preparing to unpack .../37-1-autopkgtest-satdep.deb ... 150s Unpacking autopkgtest-satdep (0) ... 150s Setting up python3-iniconfig (1.1.1-2) ... 150s Setting up python3-typechecks (0.1.0+ds-4) ... 150s Setting up python3-memoized-property (1.0.3-2) ... 150s Setting up python3-mypy-extensions (1.0.0-1) ... 150s Setting up python3-platformdirs (4.3.6-1) ... 151s Setting up python3-tz (2024.1-2) ... 151s Setting up python3-six (1.16.0-7) ... 152s Setting up python3-simplejson (3.19.3-1) ... 152s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 152s Setting up libblas3:arm64 (3.12.0-3build2) ... 152s 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 152s Setting up python3-packaging (24.1-1) ... 153s Setting up python3-dill (0.3.9-1) ... 153s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 153s Setting up python3-isort (5.13.2-2) ... 155s Setting up python3-pluggy (1.5.0-1) ... 155s Setting up python3-astroid (3.2.2-1) ... 155s Setting up python3.13-minimal (3.13.0-2) ... 157s Setting up python3-dateutil (2.9.0-2) ... 157s Setting up python3-mccabe (0.7.0-1) ... 157s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 157s Setting up python3-tomlkit (0.13.2-1) ... 158s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 158s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 158s Setting up liblapack3:arm64 (3.12.0-3build2) ... 158s 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 158s Setting up python3.13 (3.13.0-2) ... 160s Setting up python3-pytest (8.3.3-1) ... 161s Setting up python3-all (3.12.7-1) ... 161s Setting up python3-serializable (0.4.1+ds-1) ... 161s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 167s Setting up libjs-sphinxdoc (7.4.7-4) ... 167s Setting up python3-logilab-common (2.0.0-1) ... 167s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 167s Setting up python3-pandas (2.2.3+dfsg-5) ... 184s Setting up pylint (3.2.7-1) ... 185s Setting up python3-datacache (1.4.1-2) ... 186s Setting up python3-gtfparse (1.3.0+ds-1) ... 186s Setting up pyensembl (2.3.13-1) ... 186s Setting up autopkgtest-satdep (0) ... 186s Processing triggers for systemd (256.5-2ubuntu4) ... 186s Processing triggers for man-db (2.12.1-3) ... 187s Processing triggers for libc-bin (2.40-1ubuntu3) ... 194s (Reading database ... 84369 files and directories currently installed.) 194s Removing autopkgtest-satdep (0) ... 195s autopkgtest [10:00:51]: test run-unit-test: [----------------------- 197s ============================= test session starts ============================== 197s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 197s rootdir: /tmp/autopkgtest.POlK2Q/autopkgtest_tmp 197s plugins: typeguard-4.4.1 197s collected 0 items / 4 errors 197s 197s ==================================== ERRORS ==================================== 197s ___________ ERROR collecting tests/test_ensembl_object_properties.py ___________ 197s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/tests/test_ensembl_object_properties.py'. 197s Hint: make sure your test modules/packages have valid Python names. 197s Traceback: 197s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 197s return _bootstrap._gcd_import(name[level:], package, level) 197s tests/test_ensembl_object_properties.py:8: in 197s from .common import eq_ 197s tests/common.py:3: in 197s from pyensembl import genome_for_reference_name, cached_release 197s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 197s from .database import Database 197s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 197s import datacache 197s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 197s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 197s /usr/lib/python3/dist-packages/datacache/download.py:24: in 197s import pandas as pd 197s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 197s raise ImportError( 197s E ImportError: Unable to import required dependencies: 197s E numpy: Error importing numpy: you should not try to import numpy from 197s E its source directory; please exit the numpy source tree, and relaunch 197s E your python interpreter from there. 197s _____________________ ERROR collecting tests/test_locus.py _____________________ 197s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/tests/test_locus.py'. 197s Hint: make sure your test modules/packages have valid Python names. 197s Traceback: 197s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 197s return _bootstrap._gcd_import(name[level:], package, level) 197s tests/test_locus.py:1: in 197s from pyensembl.locus import Locus 197s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 197s from .database import Database 197s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 197s import datacache 197s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 197s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 197s /usr/lib/python3/dist-packages/datacache/download.py:24: in 197s import pandas as pd 197s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 197s raise ImportError( 197s E ImportError: Unable to import required dependencies: 197s E numpy: Error importing numpy: you should not try to import numpy from 197s E its source directory; please exit the numpy source tree, and relaunch 197s E your python interpreter from there. 197s _______________ ERROR collecting tests/test_release_versions.py ________________ 197s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/tests/test_release_versions.py'. 197s Hint: make sure your test modules/packages have valid Python names. 197s Traceback: 197s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 197s return _bootstrap._gcd_import(name[level:], package, level) 197s tests/test_release_versions.py:1: in 197s from pyensembl import EnsemblRelease, MAX_ENSEMBL_RELEASE 197s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 197s from .database import Database 197s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 197s import datacache 197s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 197s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 197s /usr/lib/python3/dist-packages/datacache/download.py:24: in 197s import pandas as pd 197s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 197s raise ImportError( 197s E ImportError: Unable to import required dependencies: 197s E numpy: Error importing numpy: you should not try to import numpy from 197s E its source directory; please exit the numpy source tree, and relaunch 197s E your python interpreter from there. 197s _____________________ ERROR collecting tests/test_shell.py _____________________ 197s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/tests/test_shell.py'. 197s Hint: make sure your test modules/packages have valid Python names. 197s Traceback: 197s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 197s return _bootstrap._gcd_import(name[level:], package, level) 197s tests/test_shell.py:1: in 197s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 197s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 197s from .database import Database 197s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 197s import datacache 197s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 197s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 197s /usr/lib/python3/dist-packages/datacache/download.py:24: in 197s import pandas as pd 197s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 197s raise ImportError( 197s E ImportError: Unable to import required dependencies: 197s E numpy: Error importing numpy: you should not try to import numpy from 197s E its source directory; please exit the numpy source tree, and relaunch 197s E your python interpreter from there. 197s =========================== short test summary info ============================ 197s ERROR tests/test_ensembl_object_properties.py 197s ERROR tests/test_locus.py 197s ERROR tests/test_release_versions.py 197s ERROR tests/test_shell.py 197s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 197s ============================== 4 errors in 1.27s =============================== 198s autopkgtest [10:00:54]: test run-unit-test: -----------------------] 199s autopkgtest [10:00:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 199s run-unit-test FAIL non-zero exit status 2 199s autopkgtest [10:00:55]: test pybuild-autopkgtest: preparing testbed 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Starting pkgProblemResolver with broken count: 0 204s Starting 2 pkgProblemResolver with broken count: 0 204s Done 206s The following additional packages will be installed: 206s autoconf automake autopoint autotools-dev build-essential cpp cpp-14 206s cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper debugedit 206s dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 206s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 206s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 206s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 206s libfile-stripnondeterminism-perl libgcc-14-dev libgomp1 libhwasan0 libisl23 206s libitm1 liblsan0 libmpc3 libstdc++-14-dev libtool libtsan2 libubsan1 m4 206s po-debconf pybuild-plugin-autopkgtest 206s Suggested packages: 206s autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales 206s cpp-14-doc dh-make flit python3-build python3-installer python3-wheel 206s gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc 206s gdb-aarch64-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev 206s libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 206s libmail-box-perl 206s Recommended packages: 206s libarchive-cpio-perl libltdl-dev libmail-sendmail-perl 206s The following NEW packages will be installed: 206s autoconf automake autopkgtest-satdep autopoint autotools-dev build-essential 206s cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu debhelper 206s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz g++ g++-14 206s g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14 206s gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gettext intltool-debian 206s libarchive-zip-perl libasan8 libcc1-0 libdebhelper-perl 206s libfile-stripnondeterminism-perl libgcc-14-dev libgomp1 libhwasan0 libisl23 206s libitm1 liblsan0 libmpc3 libstdc++-14-dev libtool libtsan2 libubsan1 m4 206s po-debconf pybuild-plugin-autopkgtest 206s 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. 206s Need to get 64.4 MB/64.4 MB of archives. 206s After this operation, 220 MB of additional disk space will be used. 206s Get:1 /tmp/autopkgtest.POlK2Q/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [836 B] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 m4 arm64 1.4.19-4build1 [240 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 autoconf all 2.72-3 [382 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 autotools-dev all 20220109.1 [44.9 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] 207s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 autopoint all 0.22.5-2 [616 kB] 207s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 207s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 207s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 207s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 207s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 207s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 207s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 207s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 207s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 207s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 207s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 208s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 208s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 208s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 208s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 208s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 208s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 208s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 208s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 208s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 208s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 209s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 209s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 209s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 209s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 209s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libdebhelper-perl all 13.20ubuntu1 [94.2 kB] 209s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libtool all 2.4.7-7build1 [166 kB] 209s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-autoreconf all 20 [16.1 kB] 209s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] 209s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] 209s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 dh-strip-nondeterminism all 1.14.0-1 [5058 B] 209s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 debugedit arm64 1:5.1-1 [45.9 kB] 209s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 dwz arm64 0.15-1build6 [113 kB] 209s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 gettext arm64 0.22.5-2 [930 kB] 209s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 209s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] 209s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 debhelper all 13.20ubuntu1 [893 kB] 209s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 dh-python all 6.20241024 [112 kB] 209s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 pybuild-plugin-autopkgtest all 6.20241024 [1746 B] 210s Fetched 64.4 MB in 3s (23.6 MB/s) 210s Selecting previously unselected package m4. 210s (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 ... 84369 files and directories currently installed.) 210s Preparing to unpack .../00-m4_1.4.19-4build1_arm64.deb ... 210s Unpacking m4 (1.4.19-4build1) ... 210s Selecting previously unselected package autoconf. 210s Preparing to unpack .../01-autoconf_2.72-3_all.deb ... 210s Unpacking autoconf (2.72-3) ... 210s Selecting previously unselected package autotools-dev. 210s Preparing to unpack .../02-autotools-dev_20220109.1_all.deb ... 210s Unpacking autotools-dev (20220109.1) ... 210s Selecting previously unselected package automake. 210s Preparing to unpack .../03-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... 210s Unpacking automake (1:1.16.5-1.3ubuntu1) ... 210s Selecting previously unselected package autopoint. 210s Preparing to unpack .../04-autopoint_0.22.5-2_all.deb ... 210s Unpacking autopoint (0.22.5-2) ... 210s Selecting previously unselected package libisl23:arm64. 210s Preparing to unpack .../05-libisl23_0.27-1_arm64.deb ... 210s Unpacking libisl23:arm64 (0.27-1) ... 210s Selecting previously unselected package libmpc3:arm64. 210s Preparing to unpack .../06-libmpc3_1.3.1-1build2_arm64.deb ... 210s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 210s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 210s Preparing to unpack .../07-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 210s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package cpp-14. 211s Preparing to unpack .../08-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package cpp-aarch64-linux-gnu. 211s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 211s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 211s Selecting previously unselected package cpp. 211s Preparing to unpack .../10-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 211s Unpacking cpp (4:14.1.0-2ubuntu1) ... 211s Selecting previously unselected package libcc1-0:arm64. 211s Preparing to unpack .../11-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libgomp1:arm64. 211s Preparing to unpack .../12-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libitm1:arm64. 211s Preparing to unpack .../13-libitm1_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libasan8:arm64. 211s Preparing to unpack .../14-libasan8_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package liblsan0:arm64. 211s Preparing to unpack .../15-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libtsan2:arm64. 211s Preparing to unpack .../16-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libubsan1:arm64. 211s Preparing to unpack .../17-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libhwasan0:arm64. 211s Preparing to unpack .../18-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 211s Selecting previously unselected package libgcc-14-dev:arm64. 211s Preparing to unpack .../19-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 211s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 212s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 212s Preparing to unpack .../20-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 212s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 212s Selecting previously unselected package gcc-14. 212s Preparing to unpack .../21-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 212s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 212s Selecting previously unselected package gcc-aarch64-linux-gnu. 212s Preparing to unpack .../22-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 212s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 212s Selecting previously unselected package gcc. 212s Preparing to unpack .../23-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 212s Unpacking gcc (4:14.1.0-2ubuntu1) ... 212s Selecting previously unselected package libstdc++-14-dev:arm64. 212s Preparing to unpack .../24-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 212s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package g++-14-aarch64-linux-gnu. 213s Preparing to unpack .../25-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package g++-14. 213s Preparing to unpack .../26-g++-14_14.2.0-8ubuntu1_arm64.deb ... 213s Unpacking g++-14 (14.2.0-8ubuntu1) ... 213s Selecting previously unselected package g++-aarch64-linux-gnu. 213s Preparing to unpack .../27-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 213s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 213s Selecting previously unselected package g++. 213s Preparing to unpack .../28-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 213s Unpacking g++ (4:14.1.0-2ubuntu1) ... 213s Selecting previously unselected package build-essential. 213s 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libgomp1:arm64 (14.2.0-8ubuntu1) ... 215s Setting up autotools-dev (20220109.1) ... 215s Setting up libmpc3:arm64 (1.3.1-1build2) ... 215s Setting up autopoint (0.22.5-2) ... 215s Setting up autoconf (2.72-3) ... 215s Setting up libubsan1:arm64 (14.2.0-8ubuntu1) ... 215s Setting up dwz (0.15-1build6) ... 215s Setting up libhwasan0:arm64 (14.2.0-8ubuntu1) ... 215s Setting up libasan8:arm64 (14.2.0-8ubuntu1) ... 215s Setting up debugedit (1:5.1-1) ... 215s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ... 215s Setting up libisl23:arm64 (0.27-1) ... 215s Setting up libcc1-0:arm64 (14.2.0-8ubuntu1) ... 215s Setting up liblsan0:arm64 (14.2.0-8ubuntu1) ... 215s Setting up libitm1:arm64 (14.2.0-8ubuntu1) ... 215s Setting up automake (1:1.16.5-1.3ubuntu1) ... 215s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode 215s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 215s Setting up gettext (0.22.5-2) ... 215s Setting up intltool-debian (0.35.0+20060710.6) ... 215s Setting up dh-strip-nondeterminism (1.14.0-1) ... 215s Setting up cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 215s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 215s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 215s Setting up po-debconf (1.0.21+nmu1) ... 215s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 215s Setting up cpp-14 (14.2.0-8ubuntu1) ... 215s Setting up cpp (4:14.1.0-2ubuntu1) ... 215s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 215s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 215s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 215s Setting up gcc-14 (14.2.0-8ubuntu1) ... 215s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 215s Setting up g++-14 (14.2.0-8ubuntu1) ... 215s Setting up libtool (2.4.7-7build1) ... 215s Setting up gcc (4:14.1.0-2ubuntu1) ... 215s Setting up dh-autoreconf (20) ... 215s Setting up g++ (4:14.1.0-2ubuntu1) ... 215s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 215s Setting up build-essential (12.10ubuntu1) ... 215s Setting up debhelper (13.20ubuntu1) ... 215s Setting up pybuild-plugin-autopkgtest (6.20241024) ... 215s Setting up autopkgtest-satdep (0) ... 215s Processing triggers for man-db (2.12.1-3) ... 216s Processing triggers for install-info (7.1.1-1) ... 216s Processing triggers for libc-bin (2.40-1ubuntu3) ... 222s (Reading database ... 86659 files and directories currently installed.) 222s Removing autopkgtest-satdep (0) ... 222s autopkgtest [10:01:18]: test pybuild-autopkgtest: pybuild-autopkgtest 222s autopkgtest [10:01:18]: test pybuild-autopkgtest: [----------------------- 223s pybuild-autopkgtest 223s I: pybuild base:311: cd /tmp/autopkgtest.POlK2Q/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' 224s ============================= test session starts ============================== 224s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 224s cachedir: .pytest_cache 224s rootdir: /tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build 224s plugins: typeguard-4.4.1 225s collecting ... collected 0 items / 25 errors 225s 225s ==================================== ERRORS ==================================== 225s ____________________ ERROR collecting tests/test_contigs.py ____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_contigs.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_contigs.py:1: in 225s from pyensembl import genome_for_reference_name 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ________________ ERROR collecting tests/test_download_cache.py _________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_download_cache.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_download_cache.py:5: in 225s from pyensembl.download_cache import DownloadCache, MissingLocalFile, MissingRemoteFile 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s __________________ ERROR collecting tests/test_ensembl_gtf.py __________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_ensembl_gtf.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_ensembl_gtf.py:5: in 225s from .common import run_multiple_genomes 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ___________ ERROR collecting tests/test_ensembl_object_properties.py ___________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_ensembl_object_properties.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_ensembl_object_properties.py:8: in 225s from .common import eq_ 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ____________________ ERROR collecting tests/test_exon_id.py ____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_exon_id.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_exon_id.py:7: in 225s from pyensembl import cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s __________________ ERROR collecting tests/test_exon_object.py __________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_exon_object.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_exon_object.py:8: in 225s from pyensembl import cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ___________________ ERROR collecting tests/test_gene_ids.py ____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_gene_ids.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_gene_ids.py:10: in 225s from pyensembl import ensembl_grch38, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s __________________ ERROR collecting tests/test_gene_names.py ___________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_gene_names.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_gene_names.py:6: in 225s from pyensembl import genome_for_reference_name 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _________________ ERROR collecting tests/test_gene_objects.py __________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_gene_objects.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_gene_objects.py:1: in 225s from .common import eq_ 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ___________________ ERROR collecting tests/test_id_length.py ___________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_id_length.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_id_length.py:1: in 225s from .common import major_releases 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _____________________ ERROR collecting tests/test_locus.py _____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_locus.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_locus.py:1: in 225s from pyensembl.locus import Locus 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ____________ ERROR collecting tests/test_missing_genome_sources.py _____________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_missing_genome_sources.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_missing_genome_sources.py:1: in 225s from pyensembl import Genome 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _____________________ ERROR collecting tests/test_mouse.py _____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_mouse.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_mouse.py:1: in 225s from .common import eq_ 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _______________ ERROR collecting tests/test_release_versions.py ________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_release_versions.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_release_versions.py:1: in 225s from pyensembl import EnsemblRelease, MAX_ENSEMBL_RELEASE 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ____________________ ERROR collecting tests/test_search.py _____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_search.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_search.py:1: in 225s from pyensembl import find_nearest_locus 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _________________ ERROR collecting tests/test_sequence_data.py _________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_sequence_data.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_sequence_data.py:8: in 225s from pyensembl import SequenceData 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _________________ ERROR collecting tests/test_serialization.py _________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_serialization.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_serialization.py:15: in 225s from pyensembl import Genome, Transcript, Gene, Exon 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _____________________ ERROR collecting tests/test_shell.py _____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_shell.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_shell.py:1: in 225s from pyensembl.shell import parser, all_combinations_of_ensembl_genomes 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _____________ ERROR collecting tests/test_string_representation.py _____________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_string_representation.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_string_representation.py:1: in 225s from pyensembl import Locus, Gene, ensembl_grch37, Transcript, Exon 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ____________________ ERROR collecting tests/test_timings.py ____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_timings.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_timings.py:1: in 225s from pyensembl import genome_for_reference_name 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ________________ ERROR collecting tests/test_transcript_ids.py _________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_transcript_ids.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_transcript_ids.py:7: in 225s from pyensembl import genome_for_reference_name 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ______________ ERROR collecting tests/test_transcript_objects.py _______________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_transcript_objects.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_transcript_objects.py:1: in 225s from pyensembl import Locus, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s _____________ ERROR collecting tests/test_transcript_sequences.py ______________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_transcript_sequences.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_transcript_sequences.py:7: in 225s from .common import eq_ 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ___________ ERROR collecting tests/test_transcript_support_level.py ____________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_transcript_support_level.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_transcript_support_level.py:7: in 225s from .common import eq_ 225s tests/common.py:3: in 225s from pyensembl import genome_for_reference_name, cached_release 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s ___________________ ERROR collecting tests/test_ucsc_gtf.py ____________________ 225s ImportError while importing test module '/tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build/tests/test_ucsc_gtf.py'. 225s Hint: make sure your test modules/packages have valid Python names. 225s Traceback: 225s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 225s return _bootstrap._gcd_import(name[level:], package, level) 225s tests/test_ucsc_gtf.py:1: in 225s from pyensembl import Genome, Database 225s /usr/lib/python3/dist-packages/pyensembl/__init__.py:13: in 225s from .database import Database 225s /usr/lib/python3/dist-packages/pyensembl/database.py:17: in 225s import datacache 225s /usr/lib/python3/dist-packages/datacache/__init__.py:13: in 225s from .download import fetch_file, fetch_and_transform, fetch_csv_dataframe 225s /usr/lib/python3/dist-packages/datacache/download.py:24: in 225s import pandas as pd 225s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 225s raise ImportError( 225s E ImportError: Unable to import required dependencies: 225s E numpy: Error importing numpy: you should not try to import numpy from 225s E its source directory; please exit the numpy source tree, and relaunch 225s E your python interpreter from there. 225s =========================== short test summary info ============================ 225s ERROR tests/test_contigs.py 225s ERROR tests/test_download_cache.py 225s ERROR tests/test_ensembl_gtf.py 225s ERROR tests/test_ensembl_object_properties.py 225s ERROR tests/test_exon_id.py 225s ERROR tests/test_exon_object.py 225s ERROR tests/test_gene_ids.py 225s ERROR tests/test_gene_names.py 225s ERROR tests/test_gene_objects.py 225s ERROR tests/test_id_length.py 225s ERROR tests/test_locus.py 225s ERROR tests/test_missing_genome_sources.py 225s ERROR tests/test_mouse.py 225s ERROR tests/test_release_versions.py 225s ERROR tests/test_search.py 225s ERROR tests/test_sequence_data.py 225s ERROR tests/test_serialization.py 225s ERROR tests/test_shell.py 225s ERROR tests/test_string_representation.py 225s ERROR tests/test_timings.py 225s ERROR tests/test_transcript_ids.py 225s ERROR tests/test_transcript_objects.py 225s ERROR tests/test_transcript_sequences.py 225s ERROR tests/test_transcript_support_level.py 225s ERROR tests/test_ucsc_gtf.py 225s !!!!!!!!!!!!!!!!!!! Interrupted: 25 errors during collection !!!!!!!!!!!!!!!!!!! 225s ============================== 25 errors in 1.62s ============================== 225s E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /tmp/autopkgtest.POlK2Q/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' 225s I: pybuild base:311: cd /tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build; python3.12 -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' 226s ============================= test session starts ============================== 226s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 226s cachedir: .pytest_cache 226s rootdir: /tmp/autopkgtest.POlK2Q/autopkgtest_tmp/build 226s plugins: typeguard-4.4.1 227s collecting ... collected 126 items / 98 deselected / 28 selected 227s 227s tests/test_ensembl_object_properties.py::test_human_reference_name PASSED [ 3%] 227s tests/test_locus.py::test_normalize_chromosome PASSED [ 7%] 227s tests/test_locus.py::test_locus_overlaps PASSED [ 10%] 227s tests/test_locus.py::test_locus_contains PASSED [ 14%] 227s tests/test_locus.py::test_position_offset PASSED [ 17%] 227s tests/test_locus.py::test_range_offset PASSED [ 21%] 227s tests/test_locus.py::test_locus_distance PASSED [ 25%] 227s tests/test_missing_genome_sources.py::test_transcript_fasta_only PASSED [ 28%] 227s tests/test_missing_genome_sources.py::test_protein_fasta_only PASSED [ 32%] 227s tests/test_missing_genome_sources.py::test_gtf_only PASSED [ 35%] 227s tests/test_missing_genome_sources.py::test_gtf_transcript_only PASSED [ 39%] 227s tests/test_missing_genome_sources.py::test_gtf_protein_only PASSED [ 42%] 227s tests/test_mouse.py::test_mouse_ENSMUSG00000017167 PASSED [ 46%] 227s tests/test_release_versions.py::test_version_too_old_1 PASSED [ 50%] 227s tests/test_release_versions.py::test_version_too_old_47 PASSED [ 53%] 227s tests/test_release_versions.py::test_version_is_not_numeric PASSED [ 57%] 227s tests/test_release_versions.py::test_version_is_none PASSED [ 60%] 227s tests/test_release_versions.py::test_max_ensembl_release PASSED [ 64%] 227s tests/test_release_versions.py::test_int_version PASSED [ 67%] 228s tests/test_release_versions.py::test_str_version PASSED [ 71%] 228s tests/test_sequence_data.py::test_sequence_type PASSED [ 75%] 228s tests/test_sequence_data.py::test_missing_sequence PASSED [ 78%] 228s tests/test_sequence_data.py::test_clear_cache PASSED [ 82%] 228s tests/test_shell.py::test_genome_selection_grch38 PASSED [ 85%] 228s tests/test_ucsc_gtf.py::test_ucsc_gencode_gtf PASSED [ 89%] 228s tests/test_ucsc_gtf.py::test_ucsc_gencode_genome PASSED [ 92%] 228s tests/test_ucsc_gtf.py::test_ucsc_refseq_gtf PASSED [ 96%] 228s tests/test_ucsc_gtf.py::test_ucsc_refseq_genome PASSED [100%] 228s 228s =============================== warnings summary =============================== 228s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:43 228s /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 228s import pkg_resources 228s 228s ../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154 228s /usr/lib/python3/dist-packages/pkg_resources/__init__.py:3154: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('logilab')`. 228s 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 228s declare_namespace(pkg) 228s 228s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:74 228s /usr/lib/python3/dist-packages/pyensembl/shell.py:74: DeprecationWarning: Nesting argument groups is deprecated. 228s release_group = root_group.add_argument_group() 228s 228s ../../../../usr/lib/python3/dist-packages/pyensembl/shell.py:96 228s /usr/lib/python3/dist-packages/pyensembl/shell.py:96: DeprecationWarning: Nesting argument groups is deprecated. 228s path_group = root_group.add_argument_group() 228s 228s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 228s ================ 28 passed, 98 deselected, 4 warnings in 1.77s ================= 228s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 228s make: *** [/tmp/Nlr7kTFvMF/run:4: pybuild-autopkgtest] Error 25 228s pybuild-autopkgtest: error: /tmp/Nlr7kTFvMF/run pybuild-autopkgtest returned exit code 2 228s autopkgtest [10:01:24]: test pybuild-autopkgtest: -----------------------] 229s autopkgtest [10:01:25]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 229s pybuild-autopkgtest FAIL non-zero exit status 25 229s autopkgtest [10:01:25]: @@@@@@@@@@@@@@@@@@@@ summary 229s run-unit-test FAIL non-zero exit status 2 229s pybuild-autopkgtest FAIL non-zero exit status 25 265s nova [W] Skipping flock in bos03-arm64 265s Creating nova instance adt-plucky-arm64-pyensembl-20241113-095736-juju-7f2275-prod-proposed-migration-environment-15-a5c79e5d-d9d8-485e-8553-4be16e356ed5 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...