0s autopkgtest [01:32:07]: starting date and time: 2024-06-06 01:32:07+0000 0s autopkgtest [01:32:07]: git checkout: 433ed4c Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [01:32:07]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5j1aa17z/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1 astropy/6.0.1-4' -- lxd -r lxd-armhf-10.145.243.48 lxd-armhf-10.145.243.48:autopkgtest/ubuntu/oracular/armhf 36s autopkgtest [01:32:43]: testbed dpkg architecture: armhf 38s autopkgtest [01:32:45]: testbed apt version: 2.9.3 38s autopkgtest [01:32:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 47s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [396 kB] 48s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [4792 B] 48s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [40.1 kB] 48s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2428 B] 48s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [61.5 kB] 48s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [269 kB] 48s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1388 B] 48s Fetched 886 kB in 1s (662 kB/s) 48s Reading package lists... 67s tee: /proc/self/fd/2: Permission denied 92s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 94s Reading package lists... 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade... 97s The following packages will be upgraded: 97s cloud-init dracut-install libperl5.38t64 libsqlite3-0 perl perl-base 97s perl-modules-5.38 python3-typing-extensions 97s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 10.4 MB of archives. 97s After this operation, 30.7 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf libperl5.38t64 armhf 5.38.2-5 [4110 kB] 98s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf perl armhf 5.38.2-5 [231 kB] 98s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf perl-base armhf 5.38.2-5 [1671 kB] 98s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf perl-modules-5.38 all 5.38.2-5 [3110 kB] 98s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libsqlite3-0 armhf 3.46.0-1 [605 kB] 98s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf dracut-install armhf 060+5-8ubuntu2 [34.4 kB] 98s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf python3-typing-extensions all 4.12.1-1 [65.6 kB] 98s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf cloud-init all 24.2~4g5f40426f-0ubuntu1 [609 kB] 99s Preconfiguring packages ... 99s Fetched 10.4 MB in 1s (11.4 MB/s) 99s (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 ... 58338 files and directories currently installed.) 99s Preparing to unpack .../libperl5.38t64_5.38.2-5_armhf.deb ... 99s Unpacking libperl5.38t64:armhf (5.38.2-5) over (5.38.2-4) ... 100s Preparing to unpack .../perl_5.38.2-5_armhf.deb ... 100s Unpacking perl (5.38.2-5) over (5.38.2-4) ... 100s Preparing to unpack .../perl-base_5.38.2-5_armhf.deb ... 100s Unpacking perl-base (5.38.2-5) over (5.38.2-4) ... 100s Setting up perl-base (5.38.2-5) ... 100s (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 ... 58338 files and directories currently installed.) 100s Preparing to unpack .../perl-modules-5.38_5.38.2-5_all.deb ... 100s Unpacking perl-modules-5.38 (5.38.2-5) over (5.38.2-4) ... 101s Preparing to unpack .../libsqlite3-0_3.46.0-1_armhf.deb ... 101s Unpacking libsqlite3-0:armhf (3.46.0-1) over (3.45.3-1) ... 101s Preparing to unpack .../dracut-install_060+5-8ubuntu2_armhf.deb ... 101s Unpacking dracut-install (060+5-8ubuntu2) over (060+5-8ubuntu1) ... 102s Preparing to unpack .../python3-typing-extensions_4.12.1-1_all.deb ... 102s Unpacking python3-typing-extensions (4.12.1-1) over (4.12.0-1) ... 102s Preparing to unpack .../cloud-init_24.2~4g5f40426f-0ubuntu1_all.deb ... 102s Unpacking cloud-init (24.2~4g5f40426f-0ubuntu1) over (24.2~3ge68c8c74-0ubuntu1) ... 102s Setting up cloud-init (24.2~4g5f40426f-0ubuntu1) ... 105s Setting up libsqlite3-0:armhf (3.46.0-1) ... 105s Setting up perl-modules-5.38 (5.38.2-5) ... 105s Setting up python3-typing-extensions (4.12.1-1) ... 105s Setting up dracut-install (060+5-8ubuntu2) ... 105s Setting up libperl5.38t64:armhf (5.38.2-5) ... 105s Setting up perl (5.38.2-5) ... 105s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 106s Processing triggers for man-db (2.12.1-1) ... 106s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [01:33:57]: rebooting testbed after setup commands that affected boot 149s autopkgtest [01:34:36]: testbed running kernel: Linux 5.15.0-107-generic #117-Ubuntu SMP Mon Apr 29 14:37:09 UTC 2024 175s autopkgtest [01:35:02]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 187s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (dsc) [2486 B] 187s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (tar) [420 kB] 187s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (diff) [6696 B] 187s gpgv: Signature made Sat Jun 1 08:34:30 2024 UTC 187s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 187s gpgv: issuer "emollier@debian.org" 187s gpgv: Can't check signature: No public key 187s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.0-1.dsc: no acceptable signature found 187s autopkgtest [01:35:14]: testing package cyvcf2 version 0.31.0-1 189s autopkgtest [01:35:16]: build not needed 192s autopkgtest [01:35:19]: test run-unit-test: preparing testbed 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 203s Starting pkgProblemResolver with broken count: 0 203s Starting 2 pkgProblemResolver with broken count: 0 203s Done 204s The following additional packages will be installed: 204s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 204s python3-all python3-click python3-colorama python3-coloredlogs 204s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 204s python3-packaging python3-pluggy python3-pytest 204s Suggested packages: 204s gcc gfortran python-numpy-doc python3-dev 204s The following NEW packages will be installed: 204s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 204s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 204s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 204s python3-numpy python3-packaging python3-pluggy python3-pytest 204s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 204s Need to get 7922 kB/7922 kB of archives. 204s After this operation, 30.0 MB of additional disk space will be used. 204s Get:1 /tmp/autopkgtest.lbDhex/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 205s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 205s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 205s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 205s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 205s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 205s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 205s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 205s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 205s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 205s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 205s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 205s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 205s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.31.0-1 [827 kB] 205s Get:15 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 205s Get:16 http://ftpmaster.internal/ubuntu oracular/main armhf python3-packaging all 24.0-1 [41.1 kB] 205s Get:17 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 205s Get:18 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf python3-pytest all 8.2.2-1 [250 kB] 206s Fetched 7922 kB in 1s (8383 kB/s) 206s Selecting previously unselected package libblas3:armhf. 206s (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 ... 58338 files and directories currently installed.) 206s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 206s Unpacking libblas3:armhf (3.12.0-3build1) ... 206s Selecting previously unselected package libdeflate0:armhf. 206s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 206s Unpacking libdeflate0:armhf (1.20-1) ... 206s Selecting previously unselected package libgfortran5:armhf. 206s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 206s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 206s Selecting previously unselected package libhtscodecs2:armhf. 206s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 206s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 206s Selecting previously unselected package libhts3t64:armhf. 206s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 206s Unpacking libhts3t64:armhf (1.20+ds-1) ... 206s Selecting previously unselected package liblapack3:armhf. 206s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 206s Unpacking liblapack3:armhf (3.12.0-3build1) ... 206s Selecting previously unselected package python3-all. 206s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 206s Unpacking python3-all (3.12.3-0ubuntu1) ... 206s Selecting previously unselected package python3-colorama. 206s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 206s Unpacking python3-colorama (0.4.6-4) ... 207s Selecting previously unselected package python3-click. 207s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 207s Unpacking python3-click (8.1.7-1) ... 207s Selecting previously unselected package python3-humanfriendly. 207s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 207s Unpacking python3-humanfriendly (10.0-5) ... 207s Selecting previously unselected package python3-coloredlogs. 207s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 207s Unpacking python3-coloredlogs (15.0.1-1) ... 207s Selecting previously unselected package python3-numpy. 207s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 207s Unpacking python3-numpy (1:1.26.4+ds-10) ... 207s Selecting previously unselected package python3-cyvcf2. 207s Preparing to unpack .../12-python3-cyvcf2_0.31.0-1_armhf.deb ... 207s Unpacking python3-cyvcf2 (0.31.0-1) ... 207s Selecting previously unselected package python3-iniconfig. 207s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 207s Unpacking python3-iniconfig (1.1.1-2) ... 207s Selecting previously unselected package python3-packaging. 207s Preparing to unpack .../14-python3-packaging_24.0-1_all.deb ... 207s Unpacking python3-packaging (24.0-1) ... 207s Selecting previously unselected package python3-pluggy. 207s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 207s Unpacking python3-pluggy (1.5.0-1) ... 207s Selecting previously unselected package python3-pytest. 207s Preparing to unpack .../16-python3-pytest_8.2.2-1_all.deb ... 207s Unpacking python3-pytest (8.2.2-1) ... 207s Selecting previously unselected package autopkgtest-satdep. 207s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 207s Unpacking autopkgtest-satdep (0) ... 207s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 207s Setting up python3-iniconfig (1.1.1-2) ... 208s Setting up python3-colorama (0.4.6-4) ... 208s Setting up libdeflate0:armhf (1.20-1) ... 208s Setting up python3-all (3.12.3-0ubuntu1) ... 208s Setting up python3-click (8.1.7-1) ... 208s Setting up libblas3:armhf (3.12.0-3build1) ... 208s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 208s Setting up python3-packaging (24.0-1) ... 208s Setting up python3-humanfriendly (10.0-5) ... 209s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 209s Setting up python3-pluggy (1.5.0-1) ... 209s Setting up libhts3t64:armhf (1.20+ds-1) ... 209s Setting up python3-coloredlogs (15.0.1-1) ... 209s Setting up liblapack3:armhf (3.12.0-3build1) ... 209s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 209s Setting up python3-pytest (8.2.2-1) ... 209s Setting up python3-numpy (1:1.26.4+ds-10) ... 212s Setting up python3-cyvcf2 (0.31.0-1) ... 212s Setting up autopkgtest-satdep (0) ... 212s Processing triggers for man-db (2.12.1-1) ... 213s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 227s (Reading database ... 59605 files and directories currently installed.) 227s Removing autopkgtest-satdep (0) ... 232s autopkgtest [01:35:59]: test run-unit-test: [----------------------- 235s Testing with python3.12 in /tmp/autopkgtest.lbDhex/autopkgtest_tmp: 236s ============================= test session starts ============================== 236s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 -- /usr/bin/python3.12 236s cachedir: .pytest_cache 236s rootdir: /tmp/autopkgtest.lbDhex/autopkgtest_tmp 237s collecting ... collected 112 items 237s 237s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 237s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 237s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 237s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 237s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 237s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 237s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 237s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 237s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 237s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 237s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 237s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 237s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 237s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 237s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 237s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 237s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 237s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 237s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 237s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 237s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 237s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 237s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 237s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 237s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 237s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 237s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 237s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 237s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 237s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 237s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 237s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 237s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 237s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 237s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 237s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 237s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 237s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 238s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 238s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 238s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 238s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 238s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 238s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 238s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 238s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 238s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 238s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 238s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 238s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 238s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 238s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 238s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 238s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 238s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 238s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 238s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 238s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 238s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 238s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 238s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 238s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 238s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 238s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 238s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 238s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 238s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 238s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 238s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 238s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 238s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 238s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 238s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 238s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 238s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 238s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 238s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 238s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 238s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 238s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 238s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 238s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 238s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 238s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 238s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 238s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 238s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 238s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 238s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 238s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 238s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 238s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 238s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 238s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 238s 238s ============================= 112 passed in 2.68s ============================== 239s autopkgtest [01:36:06]: test run-unit-test: -----------------------] 244s autopkgtest [01:36:11]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s run-unit-test PASS 248s autopkgtest [01:36:15]: test autodep8-python3: preparing testbed 284s autopkgtest [01:36:51]: testbed dpkg architecture: armhf 286s autopkgtest [01:36:53]: testbed apt version: 2.9.3 286s autopkgtest [01:36:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 293s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 294s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2428 B] 294s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [4792 B] 294s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [40.1 kB] 294s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [396 kB] 294s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main armhf Packages [61.5 kB] 294s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/universe armhf Packages [269 kB] 294s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse armhf Packages [1388 B] 294s Fetched 886 kB in 1s (910 kB/s) 294s Reading package lists... 309s tee: /proc/self/fd/2: Permission denied 333s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 333s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 333s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 333s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 334s Reading package lists... 334s Reading package lists... 335s Building dependency tree... 335s Reading state information... 336s Calculating upgrade... 337s The following packages will be upgraded: 337s cloud-init dracut-install libperl5.38t64 libsqlite3-0 perl perl-base 337s perl-modules-5.38 python3-typing-extensions 337s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 337s Need to get 10.4 MB of archives. 337s After this operation, 30.7 kB of additional disk space will be used. 337s Get:1 http://ftpmaster.internal/ubuntu oracular/main armhf libperl5.38t64 armhf 5.38.2-5 [4110 kB] 338s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf perl armhf 5.38.2-5 [231 kB] 338s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf perl-base armhf 5.38.2-5 [1671 kB] 338s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf perl-modules-5.38 all 5.38.2-5 [3110 kB] 338s Get:5 http://ftpmaster.internal/ubuntu oracular/main armhf libsqlite3-0 armhf 3.46.0-1 [605 kB] 338s Get:6 http://ftpmaster.internal/ubuntu oracular/main armhf dracut-install armhf 060+5-8ubuntu2 [34.4 kB] 338s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf python3-typing-extensions all 4.12.1-1 [65.6 kB] 338s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf cloud-init all 24.2~4g5f40426f-0ubuntu1 [609 kB] 338s Preconfiguring packages ... 339s Fetched 10.4 MB in 1s (10.2 MB/s) 339s (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 ... 58338 files and directories currently installed.) 339s Preparing to unpack .../libperl5.38t64_5.38.2-5_armhf.deb ... 339s Unpacking libperl5.38t64:armhf (5.38.2-5) over (5.38.2-4) ... 339s Preparing to unpack .../perl_5.38.2-5_armhf.deb ... 339s Unpacking perl (5.38.2-5) over (5.38.2-4) ... 340s Preparing to unpack .../perl-base_5.38.2-5_armhf.deb ... 340s Unpacking perl-base (5.38.2-5) over (5.38.2-4) ... 340s Setting up perl-base (5.38.2-5) ... 340s (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 ... 58338 files and directories currently installed.) 340s Preparing to unpack .../perl-modules-5.38_5.38.2-5_all.deb ... 340s Unpacking perl-modules-5.38 (5.38.2-5) over (5.38.2-4) ... 341s Preparing to unpack .../libsqlite3-0_3.46.0-1_armhf.deb ... 341s Unpacking libsqlite3-0:armhf (3.46.0-1) over (3.45.3-1) ... 341s Preparing to unpack .../dracut-install_060+5-8ubuntu2_armhf.deb ... 341s Unpacking dracut-install (060+5-8ubuntu2) over (060+5-8ubuntu1) ... 341s Preparing to unpack .../python3-typing-extensions_4.12.1-1_all.deb ... 341s Unpacking python3-typing-extensions (4.12.1-1) over (4.12.0-1) ... 341s Preparing to unpack .../cloud-init_24.2~4g5f40426f-0ubuntu1_all.deb ... 342s Unpacking cloud-init (24.2~4g5f40426f-0ubuntu1) over (24.2~3ge68c8c74-0ubuntu1) ... 342s Setting up cloud-init (24.2~4g5f40426f-0ubuntu1) ... 344s Setting up libsqlite3-0:armhf (3.46.0-1) ... 344s Setting up perl-modules-5.38 (5.38.2-5) ... 344s Setting up python3-typing-extensions (4.12.1-1) ... 344s Setting up dracut-install (060+5-8ubuntu2) ... 344s Setting up libperl5.38t64:armhf (5.38.2-5) ... 344s Setting up perl (5.38.2-5) ... 344s Processing triggers for rsyslog (8.2312.0-3ubuntu9) ... 344s Processing triggers for man-db (2.12.1-1) ... 345s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 345s Reading package lists... 346s Building dependency tree... 346s Reading state information... 347s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 349s autopkgtest [01:37:56]: rebooting testbed after setup commands that affected boot 423s Reading package lists... 423s Building dependency tree... 423s Reading state information... 424s Starting pkgProblemResolver with broken count: 0 424s Starting 2 pkgProblemResolver with broken count: 0 424s Done 425s The following additional packages will be installed: 425s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 425s python3-all python3-click python3-colorama python3-coloredlogs 425s python3-cyvcf2 python3-humanfriendly python3-numpy 426s Suggested packages: 426s gcc gfortran python-numpy-doc python3-dev python3-pytest 426s The following NEW packages will be installed: 426s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 426s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 426s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 426s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 426s Need to get 7603 kB/7604 kB of archives. 426s After this operation, 28.4 MB of additional disk space will be used. 426s Get:1 /tmp/autopkgtest.lbDhex/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [712 B] 426s Get:2 http://ftpmaster.internal/ubuntu oracular/main armhf libblas3 armhf 3.12.0-3build1 [123 kB] 426s Get:3 http://ftpmaster.internal/ubuntu oracular/main armhf libdeflate0 armhf 1.20-1 [38.3 kB] 426s Get:4 http://ftpmaster.internal/ubuntu oracular/main armhf libgfortran5 armhf 14.1.0-1ubuntu1 [311 kB] 426s Get:5 http://ftpmaster.internal/ubuntu oracular/universe armhf libhtscodecs2 armhf 1.6.0-1build1 [65.8 kB] 426s Get:6 http://ftpmaster.internal/ubuntu oracular/universe armhf libhts3t64 armhf 1.20+ds-1 [392 kB] 426s Get:7 http://ftpmaster.internal/ubuntu oracular/main armhf liblapack3 armhf 3.12.0-3build1 [2085 kB] 427s Get:8 http://ftpmaster.internal/ubuntu oracular/main armhf python3-all armhf 3.12.3-0ubuntu1 [886 B] 427s Get:9 http://ftpmaster.internal/ubuntu oracular/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 427s Get:10 http://ftpmaster.internal/ubuntu oracular/main armhf python3-click all 8.1.7-1 [79.1 kB] 427s Get:11 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-humanfriendly all 10.0-5 [70.5 kB] 427s Get:12 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 427s Get:13 http://ftpmaster.internal/ubuntu oracular/main armhf python3-numpy armhf 1:1.26.4+ds-10 [3541 kB] 427s Get:14 http://ftpmaster.internal/ubuntu oracular/universe armhf python3-cyvcf2 armhf 0.31.0-1 [827 kB] 428s Fetched 7603 kB in 1s (7528 kB/s) 428s Selecting previously unselected package libblas3:armhf. 428s (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 ... 58338 files and directories currently installed.) 428s Preparing to unpack .../00-libblas3_3.12.0-3build1_armhf.deb ... 428s Unpacking libblas3:armhf (3.12.0-3build1) ... 428s Selecting previously unselected package libdeflate0:armhf. 428s Preparing to unpack .../01-libdeflate0_1.20-1_armhf.deb ... 428s Unpacking libdeflate0:armhf (1.20-1) ... 428s Selecting previously unselected package libgfortran5:armhf. 428s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_armhf.deb ... 428s Unpacking libgfortran5:armhf (14.1.0-1ubuntu1) ... 428s Selecting previously unselected package libhtscodecs2:armhf. 428s Preparing to unpack .../03-libhtscodecs2_1.6.0-1build1_armhf.deb ... 428s Unpacking libhtscodecs2:armhf (1.6.0-1build1) ... 428s Selecting previously unselected package libhts3t64:armhf. 428s Preparing to unpack .../04-libhts3t64_1.20+ds-1_armhf.deb ... 428s Unpacking libhts3t64:armhf (1.20+ds-1) ... 428s Selecting previously unselected package liblapack3:armhf. 428s Preparing to unpack .../05-liblapack3_3.12.0-3build1_armhf.deb ... 428s Unpacking liblapack3:armhf (3.12.0-3build1) ... 428s Selecting previously unselected package python3-all. 428s Preparing to unpack .../06-python3-all_3.12.3-0ubuntu1_armhf.deb ... 428s Unpacking python3-all (3.12.3-0ubuntu1) ... 428s Selecting previously unselected package python3-colorama. 428s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 428s Unpacking python3-colorama (0.4.6-4) ... 428s Selecting previously unselected package python3-click. 428s Preparing to unpack .../08-python3-click_8.1.7-1_all.deb ... 428s Unpacking python3-click (8.1.7-1) ... 428s Selecting previously unselected package python3-humanfriendly. 428s Preparing to unpack .../09-python3-humanfriendly_10.0-5_all.deb ... 428s Unpacking python3-humanfriendly (10.0-5) ... 428s Selecting previously unselected package python3-coloredlogs. 428s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 428s Unpacking python3-coloredlogs (15.0.1-1) ... 428s Selecting previously unselected package python3-numpy. 428s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_armhf.deb ... 428s Unpacking python3-numpy (1:1.26.4+ds-10) ... 429s Selecting previously unselected package python3-cyvcf2. 429s Preparing to unpack .../12-python3-cyvcf2_0.31.0-1_armhf.deb ... 429s Unpacking python3-cyvcf2 (0.31.0-1) ... 429s Selecting previously unselected package autopkgtest-satdep. 429s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 429s Unpacking autopkgtest-satdep (0) ... 429s Setting up libhtscodecs2:armhf (1.6.0-1build1) ... 429s Setting up python3-colorama (0.4.6-4) ... 429s Setting up libdeflate0:armhf (1.20-1) ... 429s Setting up python3-all (3.12.3-0ubuntu1) ... 429s Setting up python3-click (8.1.7-1) ... 430s Setting up libblas3:armhf (3.12.0-3build1) ... 430s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 430s Setting up python3-humanfriendly (10.0-5) ... 430s Setting up libgfortran5:armhf (14.1.0-1ubuntu1) ... 430s Setting up libhts3t64:armhf (1.20+ds-1) ... 430s Setting up python3-coloredlogs (15.0.1-1) ... 430s Setting up liblapack3:armhf (3.12.0-3build1) ... 430s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 430s Setting up python3-numpy (1:1.26.4+ds-10) ... 433s Setting up python3-cyvcf2 (0.31.0-1) ... 433s Setting up autopkgtest-satdep (0) ... 433s Processing triggers for man-db (2.12.1-1) ... 434s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 447s (Reading database ... 59441 files and directories currently installed.) 447s Removing autopkgtest-satdep (0) ... 458s autopkgtest [01:39:45]: 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 458s autopkgtest [01:39:45]: test autodep8-python3: [----------------------- 461s Testing with python3.12: 461s 462s autopkgtest [01:39:49]: test autodep8-python3: -----------------------] 465s autopkgtest [01:39:52]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 465s autodep8-python3 PASS (superficial) 469s autopkgtest [01:39:56]: @@@@@@@@@@@@@@@@@@@@ summary 469s run-unit-test PASS 469s autodep8-python3 PASS (superficial)