0s autopkgtest [08:58:45]: starting date and time: 2024-11-13 08:58:45+0000 0s autopkgtest [08:58:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:58:45]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.owjt2v0u/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 cyvcf2 --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-arm64-50.secgroup --name adt-plucky-arm64-cyvcf2-20241113-085845-juju-7f2275-prod-proposed-migration-environment-15-7373a0e5-2e6c-44b8-8fa0-2d306182dd22 --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/ 80s autopkgtest [09:00:05]: testbed dpkg architecture: arm64 80s autopkgtest [09:00:05]: testbed apt version: 2.9.8 80s autopkgtest [09:00:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 82s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 82s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 82s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 82s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 82s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 82s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 82s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 82s Fetched 1793 kB in 1s (2112 kB/s) 82s Reading package lists... 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s Calculating upgrade... 86s The following NEW packages will be installed: 86s python3.13-gdbm 86s The following packages will be upgraded: 86s libpython3-stdlib python3 python3-gdbm python3-minimal 86s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 101 kB of archives. 86s After this operation, 141 kB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 86s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 86s Fetched 101 kB in 0s (286 kB/s) 87s (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.) 87s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 87s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 87s Setting up python3-minimal (3.12.7-1) ... 87s (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.) 87s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 87s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 87s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 87s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 87s Selecting previously unselected package python3.13-gdbm. 87s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 87s Unpacking python3.13-gdbm (3.13.0-2) ... 87s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 87s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 87s Setting up python3.13-gdbm (3.13.0-2) ... 87s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 87s Setting up python3 (3.12.7-1) ... 87s Setting up python3-gdbm:arm64 (3.12.7-1) ... 87s Processing triggers for man-db (2.12.1-3) ... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 90s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 90s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 91s Reading package lists... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Calculating upgrade... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s autopkgtest [09:00:20]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 96s autopkgtest [09:00:21]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 97s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (dsc) [2337 B] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (tar) [420 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (diff) [6764 B] 97s gpgv: Signature made Wed Jul 31 09:42:06 2024 UTC 97s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 97s gpgv: Can't check signature: No public key 97s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2.dsc: no acceptable signature found 98s autopkgtest [09:00:23]: testing package cyvcf2 version 0.31.1-2 98s autopkgtest [09:00:23]: build not needed 98s autopkgtest [09:00:23]: test run-unit-test: preparing testbed 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 101s Done 101s The following additional packages will be installed: 101s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 101s libpython3.13-minimal libpython3.13-stdlib python3-all python3-click 101s python3-colorama python3-coloredlogs python3-cyvcf2 python3-humanfriendly 101s python3-iniconfig python3-numpy python3-packaging python3-pluggy 101s python3-pytest python3.13 python3.13-minimal 101s Suggested packages: 101s gcc gfortran python-numpy-doc python3-dev python3.13-venv python3.13-doc 101s binfmt-support 101s The following NEW packages will be installed: 101s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 101s libhtscodecs2 liblapack3 libpython3.13-minimal libpython3.13-stdlib 101s python3-all python3-click python3-colorama python3-coloredlogs 101s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 101s python3-packaging python3-pluggy python3-pytest python3.13 101s python3.13-minimal 101s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 14.3 MB/14.3 MB of archives. 101s After this operation, 61.4 MB of additional disk space will be used. 101s Get:1 /tmp/autopkgtest.zodOLv/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 103s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 103s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 103s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 103s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 103s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 103s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 103s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 104s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 104s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 104s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 104s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 104s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 104s Fetched 14.3 MB in 2s (6041 kB/s) 104s Selecting previously unselected package libpython3.13-minimal:arm64. 104s (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.) 104s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 104s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 104s Selecting previously unselected package python3.13-minimal. 104s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 104s Unpacking python3.13-minimal (3.13.0-2) ... 104s Selecting previously unselected package libblas3:arm64. 104s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ... 104s Unpacking libblas3:arm64 (3.12.0-3build2) ... 104s Selecting previously unselected package libdeflate0:arm64. 104s Preparing to unpack .../03-libdeflate0_1.22-1_arm64.deb ... 104s Unpacking libdeflate0:arm64 (1.22-1) ... 104s Selecting previously unselected package libgfortran5:arm64. 104s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 104s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 104s Selecting previously unselected package libhtscodecs2:arm64. 104s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_arm64.deb ... 104s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 104s Selecting previously unselected package libhts3t64:arm64. 104s Preparing to unpack .../06-libhts3t64_1.20+ds-1_arm64.deb ... 104s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 104s Selecting previously unselected package liblapack3:arm64. 104s Preparing to unpack .../07-liblapack3_3.12.0-3build2_arm64.deb ... 104s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 104s Selecting previously unselected package libpython3.13-stdlib:arm64. 104s Preparing to unpack .../08-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 104s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 105s Selecting previously unselected package python3.13. 105s Preparing to unpack .../09-python3.13_3.13.0-2_arm64.deb ... 105s Unpacking python3.13 (3.13.0-2) ... 105s Selecting previously unselected package python3-all. 105s Preparing to unpack .../10-python3-all_3.12.7-1_arm64.deb ... 105s Unpacking python3-all (3.12.7-1) ... 105s Selecting previously unselected package python3-colorama. 105s Preparing to unpack .../11-python3-colorama_0.4.6-4_all.deb ... 105s Unpacking python3-colorama (0.4.6-4) ... 105s Selecting previously unselected package python3-click. 105s Preparing to unpack .../12-python3-click_8.1.7-2_all.deb ... 105s Unpacking python3-click (8.1.7-2) ... 105s Selecting previously unselected package python3-humanfriendly. 105s Preparing to unpack .../13-python3-humanfriendly_10.0-6_all.deb ... 105s Unpacking python3-humanfriendly (10.0-6) ... 105s Selecting previously unselected package python3-coloredlogs. 105s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1_all.deb ... 105s Unpacking python3-coloredlogs (15.0.1-1) ... 105s Selecting previously unselected package python3-numpy. 105s Preparing to unpack .../15-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 105s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 105s Selecting previously unselected package python3-cyvcf2. 105s Preparing to unpack .../16-python3-cyvcf2_0.31.1-2_arm64.deb ... 105s Unpacking python3-cyvcf2 (0.31.1-2) ... 105s Selecting previously unselected package python3-iniconfig. 105s Preparing to unpack .../17-python3-iniconfig_1.1.1-2_all.deb ... 105s Unpacking python3-iniconfig (1.1.1-2) ... 105s Selecting previously unselected package python3-packaging. 105s Preparing to unpack .../18-python3-packaging_24.1-1_all.deb ... 105s Unpacking python3-packaging (24.1-1) ... 105s Selecting previously unselected package python3-pluggy. 105s Preparing to unpack .../19-python3-pluggy_1.5.0-1_all.deb ... 105s Unpacking python3-pluggy (1.5.0-1) ... 105s Selecting previously unselected package python3-pytest. 105s Preparing to unpack .../20-python3-pytest_8.3.3-1_all.deb ... 105s Unpacking python3-pytest (8.3.3-1) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../21-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 105s Setting up python3-iniconfig (1.1.1-2) ... 106s Setting up python3-colorama (0.4.6-4) ... 106s Setting up libdeflate0:arm64 (1.22-1) ... 106s Setting up python3-click (8.1.7-2) ... 106s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 106s Setting up libblas3:arm64 (3.12.0-3build2) ... 106s 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 106s Setting up python3-packaging (24.1-1) ... 106s Setting up python3-humanfriendly (10.0-6) ... 107s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 107s Setting up python3-pluggy (1.5.0-1) ... 107s Setting up libhts3t64:arm64 (1.20+ds-1) ... 107s Setting up python3.13-minimal (3.13.0-2) ... 108s Setting up python3-coloredlogs (15.0.1-1) ... 108s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 108s Setting up liblapack3:arm64 (3.12.0-3build2) ... 108s 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 108s Setting up python3.13 (3.13.0-2) ... 109s Setting up python3-pytest (8.3.3-1) ... 110s Setting up python3-all (3.12.7-1) ... 110s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 114s Setting up python3-cyvcf2 (0.31.1-2) ... 114s Setting up autopkgtest-satdep (0) ... 114s Processing triggers for systemd (256.5-2ubuntu4) ... 114s Processing triggers for man-db (2.12.1-3) ... 115s Processing triggers for libc-bin (2.40-1ubuntu3) ... 118s (Reading database ... 81931 files and directories currently installed.) 118s Removing autopkgtest-satdep (0) ... 119s autopkgtest [09:00:44]: test run-unit-test: [----------------------- 119s Testing with python3.13 in /tmp/autopkgtest.zodOLv/autopkgtest_tmp: 120s ============================= test session starts ============================== 120s platform linux -- Python 3.13.0, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.13 120s cachedir: .pytest_cache 120s rootdir: /tmp/autopkgtest.zodOLv/autopkgtest_tmp 120s plugins: typeguard-4.4.1 120s collecting ... collected 0 items / 4 errors 120s 120s ==================================== ERRORS ==================================== 120s __________________ ERROR collecting cyvcf2/tests/test_cli.py ___________________ 120s ImportError while importing test module '/tmp/autopkgtest.zodOLv/autopkgtest_tmp/cyvcf2/tests/test_cli.py'. 120s Hint: make sure your test modules/packages have valid Python names. 120s Traceback: 120s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 120s return _bootstrap._gcd_import(name[level:], package, level) 120s cyvcf2/__init__.py:1: in 120s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 120s E ModuleNotFoundError: No module named 'cyvcf2.cyvcf2' 120s __________________ ERROR collecting cyvcf2/tests/test_hemi.py __________________ 120s ImportError while importing test module '/tmp/autopkgtest.zodOLv/autopkgtest_tmp/cyvcf2/tests/test_hemi.py'. 120s Hint: make sure your test modules/packages have valid Python names. 120s Traceback: 120s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 120s return _bootstrap._gcd_import(name[level:], package, level) 120s cyvcf2/__init__.py:1: in 120s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 120s E ModuleNotFoundError: No module named 'cyvcf2.cyvcf2' 120s _________________ ERROR collecting cyvcf2/tests/test_reader.py _________________ 120s ImportError while importing test module '/tmp/autopkgtest.zodOLv/autopkgtest_tmp/cyvcf2/tests/test_reader.py'. 120s Hint: make sure your test modules/packages have valid Python names. 120s Traceback: 120s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 120s return _bootstrap._gcd_import(name[level:], package, level) 120s cyvcf2/__init__.py:1: in 120s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 120s E ModuleNotFoundError: No module named 'cyvcf2.cyvcf2' 120s _________________ ERROR collecting cyvcf2/tests/test_writer.py _________________ 120s ImportError while importing test module '/tmp/autopkgtest.zodOLv/autopkgtest_tmp/cyvcf2/tests/test_writer.py'. 120s Hint: make sure your test modules/packages have valid Python names. 120s Traceback: 120s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 120s return _bootstrap._gcd_import(name[level:], package, level) 120s cyvcf2/__init__.py:1: in 120s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 120s E ModuleNotFoundError: No module named 'cyvcf2.cyvcf2' 120s =========================== short test summary info ============================ 120s ERROR cyvcf2/tests/test_cli.py 120s ERROR cyvcf2/tests/test_hemi.py 120s ERROR cyvcf2/tests/test_reader.py 120s ERROR cyvcf2/tests/test_writer.py 120s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 120s ============================== 4 errors in 0.12s =============================== 120s autopkgtest [09:00:45]: test run-unit-test: -----------------------] 121s run-unit-test FAIL non-zero exit status 2 121s autopkgtest [09:00:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 121s autopkgtest [09:00:46]: test autodep8-python3: preparing testbed 202s autopkgtest [09:02:07]: testbed dpkg architecture: arm64 202s autopkgtest [09:02:07]: testbed apt version: 2.9.8 202s autopkgtest [09:02:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 203s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 203s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 203s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 203s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 203s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 203s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 204s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 204s Fetched 1793 kB in 1s (2289 kB/s) 204s Reading package lists... 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Calculating upgrade... 207s The following NEW packages will be installed: 207s python3.13-gdbm 207s The following packages will be upgraded: 207s libpython3-stdlib python3 python3-gdbm python3-minimal 207s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 207s Need to get 101 kB of archives. 207s After this operation, 141 kB of additional disk space will be used. 207s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 208s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 208s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 208s Fetched 101 kB in 0s (284 kB/s) 208s (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.) 208s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 208s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 208s Setting up python3-minimal (3.12.7-1) ... 209s (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.) 209s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 209s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 209s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 209s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 209s Selecting previously unselected package python3.13-gdbm. 209s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 209s Unpacking python3.13-gdbm (3.13.0-2) ... 209s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 209s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 209s Setting up python3.13-gdbm (3.13.0-2) ... 209s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 209s Setting up python3 (3.12.7-1) ... 209s Setting up python3-gdbm:arm64 (3.12.7-1) ... 209s Processing triggers for man-db (2.12.1-3) ... 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 211s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 211s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 211s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 211s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 212s Reading package lists... 212s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Calculating upgrade... 214s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 214s Reading package lists... 214s Building dependency tree... 214s Reading state information... 215s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s Starting pkgProblemResolver with broken count: 0 226s Starting 2 pkgProblemResolver with broken count: 0 226s Done 227s The following additional packages will be installed: 227s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 227s libpython3.13-minimal libpython3.13-stdlib python3-all python3-click 227s python3-colorama python3-coloredlogs python3-cyvcf2 python3-humanfriendly 227s python3-numpy python3.13 python3.13-minimal 227s Suggested packages: 227s gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv 227s python3.13-doc binfmt-support 227s The following NEW packages will be installed: 227s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 227s libhtscodecs2 liblapack3 libpython3.13-minimal libpython3.13-stdlib 227s python3-all python3-click python3-colorama python3-coloredlogs 227s python3-cyvcf2 python3-humanfriendly python3-numpy python3.13 227s python3.13-minimal 227s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 227s Need to get 14.0 MB/14.0 MB of archives. 227s After this operation, 59.8 MB of additional disk space will be used. 227s Get:1 /tmp/autopkgtest.zodOLv/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 227s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 227s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 227s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 228s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 228s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 228s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 228s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 228s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 228s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 228s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 228s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 228s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 228s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 228s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 228s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 229s Fetched 14.0 MB in 1s (13.7 MB/s) 229s Selecting previously unselected package libpython3.13-minimal:arm64. 229s (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.) 229s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 229s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 229s Selecting previously unselected package python3.13-minimal. 229s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 229s Unpacking python3.13-minimal (3.13.0-2) ... 229s Selecting previously unselected package libblas3:arm64. 229s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ... 229s Unpacking libblas3:arm64 (3.12.0-3build2) ... 229s Selecting previously unselected package libdeflate0:arm64. 229s Preparing to unpack .../03-libdeflate0_1.22-1_arm64.deb ... 229s Unpacking libdeflate0:arm64 (1.22-1) ... 229s Selecting previously unselected package libgfortran5:arm64. 229s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 229s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 229s Selecting previously unselected package libhtscodecs2:arm64. 229s Preparing to unpack .../05-libhtscodecs2_1.6.1-1_arm64.deb ... 229s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 229s Selecting previously unselected package libhts3t64:arm64. 229s Preparing to unpack .../06-libhts3t64_1.20+ds-1_arm64.deb ... 229s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 229s Selecting previously unselected package liblapack3:arm64. 229s Preparing to unpack .../07-liblapack3_3.12.0-3build2_arm64.deb ... 229s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 229s Selecting previously unselected package libpython3.13-stdlib:arm64. 229s Preparing to unpack .../08-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 229s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 229s Selecting previously unselected package python3.13. 229s Preparing to unpack .../09-python3.13_3.13.0-2_arm64.deb ... 229s Unpacking python3.13 (3.13.0-2) ... 229s Selecting previously unselected package python3-all. 229s Preparing to unpack .../10-python3-all_3.12.7-1_arm64.deb ... 229s Unpacking python3-all (3.12.7-1) ... 229s Selecting previously unselected package python3-colorama. 229s Preparing to unpack .../11-python3-colorama_0.4.6-4_all.deb ... 229s Unpacking python3-colorama (0.4.6-4) ... 229s Selecting previously unselected package python3-click. 229s Preparing to unpack .../12-python3-click_8.1.7-2_all.deb ... 229s Unpacking python3-click (8.1.7-2) ... 229s Selecting previously unselected package python3-humanfriendly. 229s Preparing to unpack .../13-python3-humanfriendly_10.0-6_all.deb ... 229s Unpacking python3-humanfriendly (10.0-6) ... 229s Selecting previously unselected package python3-coloredlogs. 229s Preparing to unpack .../14-python3-coloredlogs_15.0.1-1_all.deb ... 229s Unpacking python3-coloredlogs (15.0.1-1) ... 229s Selecting previously unselected package python3-numpy. 229s Preparing to unpack .../15-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 229s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 229s Selecting previously unselected package python3-cyvcf2. 229s Preparing to unpack .../16-python3-cyvcf2_0.31.1-2_arm64.deb ... 229s Unpacking python3-cyvcf2 (0.31.1-2) ... 229s Selecting previously unselected package autopkgtest-satdep. 229s Preparing to unpack .../17-2-autopkgtest-satdep.deb ... 229s Unpacking autopkgtest-satdep (0) ... 229s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 229s Setting up python3-colorama (0.4.6-4) ... 229s Setting up libdeflate0:arm64 (1.22-1) ... 229s Setting up python3-click (8.1.7-2) ... 230s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 230s Setting up libblas3:arm64 (3.12.0-3build2) ... 230s 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 230s Setting up python3-humanfriendly (10.0-6) ... 230s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 230s Setting up libhts3t64:arm64 (1.20+ds-1) ... 230s Setting up python3.13-minimal (3.13.0-2) ... 231s Setting up python3-coloredlogs (15.0.1-1) ... 231s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 231s Setting up liblapack3:arm64 (3.12.0-3build2) ... 231s 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 231s Setting up python3.13 (3.13.0-2) ... 232s Setting up python3-all (3.12.7-1) ... 232s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 236s Setting up python3-cyvcf2 (0.31.1-2) ... 236s Setting up autopkgtest-satdep (0) ... 236s Processing triggers for systemd (256.5-2ubuntu4) ... 236s Processing triggers for man-db (2.12.1-3) ... 237s Processing triggers for libc-bin (2.40-1ubuntu3) ... 240s (Reading database ... 81767 files and directories currently installed.) 240s Removing autopkgtest-satdep (0) ... 242s autopkgtest [09:02:47]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import cyvcf2; print(cyvcf2)" ; done 242s autopkgtest [09:02:47]: test autodep8-python3: [----------------------- 242s Testing with python3.13: 242s Traceback (most recent call last): 242s File "", line 1, in 242s import cyvcf2; print(cyvcf2) 242s ^^^^^^^^^^^^^ 242s File "/usr/lib/python3/dist-packages/cyvcf2/__init__.py", line 1, in 242s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 242s par_het) 242s ModuleNotFoundError: No module named 'cyvcf2.cyvcf2' 243s autopkgtest [09:02:48]: test autodep8-python3: -----------------------] 243s autodep8-python3 FAIL non-zero exit status 1 243s autopkgtest [09:02:48]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 243s autopkgtest [09:02:48]: @@@@@@@@@@@@@@@@@@@@ summary 243s run-unit-test FAIL non-zero exit status 2 243s autodep8-python3 FAIL non-zero exit status 1 270s nova [W] Skipping flock in bos03-arm64 270s Creating nova instance adt-plucky-arm64-cyvcf2-20241113-085845-juju-7f2275-prod-proposed-migration-environment-15-7373a0e5-2e6c-44b8-8fa0-2d306182dd22 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 270s nova [W] Skipping flock in bos03-arm64 270s Creating nova instance adt-plucky-arm64-cyvcf2-20241113-085845-juju-7f2275-prod-proposed-migration-environment-15-7373a0e5-2e6c-44b8-8fa0-2d306182dd22 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...