0s autopkgtest [16:03:10]: starting date and time: 2024-11-14 16:03:10+0000 0s autopkgtest [16:03:10]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:03:10]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._dm5err_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-39.secgroup --name adt-plucky-arm64-cyvcf2-20241114-160310-juju-7f2275-prod-proposed-migration-environment-20-36d1fba8-a02d-4509-bea1-f6ea072c91cb --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 63s autopkgtest [16:04:13]: testbed dpkg architecture: arm64 63s autopkgtest [16:04:13]: testbed apt version: 2.9.8 63s autopkgtest [16:04:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 64s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 64s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 64s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB] 64s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 65s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [724 kB] 65s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6012 B] 65s Fetched 2085 kB in 1s (2207 kB/s) 65s Reading package lists... 67s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s Calculating upgrade... 69s The following packages will be upgraded: 69s pastebinit python3-systemd 69s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Need to get 61.6 kB of archives. 69s After this operation, 347 kB of additional disk space will be used. 69s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 69s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 70s Fetched 61.6 kB in 0s (172 kB/s) 70s (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 ... 79925 files and directories currently installed.) 70s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 70s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 70s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 70s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 70s Setting up pastebinit (1.7.1-1) ... 70s Setting up python3-systemd (235-1build5) ... 70s Processing triggers for man-db (2.12.1-3) ... 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 72s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 73s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 73s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Calculating upgrade... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [16:04:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 78s autopkgtest [16:04:28]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 80s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (dsc) [2337 B] 80s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (tar) [420 kB] 80s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cyvcf2 0.31.1-2 (diff) [6764 B] 80s gpgv: Signature made Wed Jul 31 09:42:06 2024 UTC 80s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 80s gpgv: Can't check signature: No public key 80s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2.dsc: no acceptable signature found 80s autopkgtest [16:04:30]: testing package cyvcf2 version 0.31.1-2 81s autopkgtest [16:04:31]: build not needed 81s autopkgtest [16:04:31]: test run-unit-test: preparing testbed 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Starting pkgProblemResolver with broken count: 0 83s Starting 2 pkgProblemResolver with broken count: 0 83s Done 84s The following additional packages will be installed: 84s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 84s python3-all python3-click python3-colorama python3-coloredlogs 84s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 84s python3-packaging python3-pluggy python3-pytest 84s Suggested packages: 84s gcc gfortran python-numpy-doc python3-dev 84s The following NEW packages will be installed: 84s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 84s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 84s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 84s python3-numpy python3-packaging python3-pluggy python3-pytest 84s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 9040 kB/9041 kB of archives. 84s After this operation, 45.2 MB of additional disk space will be used. 84s Get:1 /tmp/autopkgtest.HedIZY/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 84s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 85s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 85s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 85s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 85s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 85s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 85s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 85s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 85s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 85s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 85s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 85s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 85s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 85s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 85s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 85s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 85s Fetched 9040 kB in 1s (9696 kB/s) 85s Selecting previously unselected package libblas3:arm64. 85s (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 ... 79930 files and directories currently installed.) 85s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 85s Unpacking libblas3:arm64 (3.12.0-3build2) ... 85s Selecting previously unselected package libdeflate0:arm64. 85s Preparing to unpack .../01-libdeflate0_1.22-1_arm64.deb ... 85s Unpacking libdeflate0:arm64 (1.22-1) ... 86s Selecting previously unselected package libgfortran5:arm64. 86s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 86s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 86s Selecting previously unselected package libhtscodecs2:arm64. 86s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_arm64.deb ... 86s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 86s Selecting previously unselected package libhts3t64:arm64. 86s Preparing to unpack .../04-libhts3t64_1.20+ds-1_arm64.deb ... 86s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 86s Selecting previously unselected package liblapack3:arm64. 86s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 86s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 86s Selecting previously unselected package python3-all. 86s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 86s Unpacking python3-all (3.12.6-0ubuntu1) ... 86s Selecting previously unselected package python3-colorama. 86s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 86s Unpacking python3-colorama (0.4.6-4) ... 86s Selecting previously unselected package python3-click. 86s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 86s Unpacking python3-click (8.1.7-2) ... 86s Selecting previously unselected package python3-humanfriendly. 86s Preparing to unpack .../09-python3-humanfriendly_10.0-6_all.deb ... 86s Unpacking python3-humanfriendly (10.0-6) ... 86s Selecting previously unselected package python3-coloredlogs. 86s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 86s Unpacking python3-coloredlogs (15.0.1-1) ... 86s Selecting previously unselected package python3-numpy. 86s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 86s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 86s Selecting previously unselected package python3-cyvcf2. 86s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_arm64.deb ... 86s Unpacking python3-cyvcf2 (0.31.1-2) ... 86s Selecting previously unselected package python3-iniconfig. 86s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 86s Unpacking python3-iniconfig (1.1.1-2) ... 86s Selecting previously unselected package python3-packaging. 86s Preparing to unpack .../14-python3-packaging_24.1-1_all.deb ... 86s Unpacking python3-packaging (24.1-1) ... 86s Selecting previously unselected package python3-pluggy. 86s Preparing to unpack .../15-python3-pluggy_1.5.0-1_all.deb ... 86s Unpacking python3-pluggy (1.5.0-1) ... 86s Selecting previously unselected package python3-pytest. 86s Preparing to unpack .../16-python3-pytest_8.3.3-1_all.deb ... 86s Unpacking python3-pytest (8.3.3-1) ... 86s Selecting previously unselected package autopkgtest-satdep. 86s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 86s Unpacking autopkgtest-satdep (0) ... 86s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 86s Setting up python3-iniconfig (1.1.1-2) ... 87s Setting up python3-colorama (0.4.6-4) ... 87s Setting up libdeflate0:arm64 (1.22-1) ... 87s Setting up python3-all (3.12.6-0ubuntu1) ... 87s Setting up python3-click (8.1.7-2) ... 87s Setting up libblas3:arm64 (3.12.0-3build2) ... 87s 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 87s Setting up python3-packaging (24.1-1) ... 87s Setting up python3-humanfriendly (10.0-6) ... 87s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 87s Setting up python3-pluggy (1.5.0-1) ... 87s Setting up libhts3t64:arm64 (1.20+ds-1) ... 87s Setting up python3-coloredlogs (15.0.1-1) ... 87s Setting up liblapack3:arm64 (3.12.0-3build2) ... 87s 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 87s Setting up python3-pytest (8.3.3-1) ... 88s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 90s Setting up python3-cyvcf2 (0.31.1-2) ... 90s Setting up autopkgtest-satdep (0) ... 90s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for libc-bin (2.40-1ubuntu3) ... 94s (Reading database ... 81216 files and directories currently installed.) 94s Removing autopkgtest-satdep (0) ... 95s autopkgtest [16:04:45]: test run-unit-test: [----------------------- 95s Testing with python3.12 in /tmp/autopkgtest.HedIZY/autopkgtest_tmp: 95s ============================= test session starts ============================== 95s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 95s cachedir: .pytest_cache 95s rootdir: /tmp/autopkgtest.HedIZY/autopkgtest_tmp 95s plugins: typeguard-4.4.1 96s collecting ... collected 112 items 96s 96s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 96s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 96s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 96s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 96s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 96s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 96s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 96s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 96s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 96s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 96s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 96s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 96s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 96s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 96s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 96s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 96s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 96s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 96s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 96s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 96s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 96s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 96s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 96s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 96s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 96s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 96s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 96s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 96s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 96s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 96s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 96s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 96s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 96s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 96s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 96s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 96s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 96s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 96s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 96s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 96s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 96s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 96s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 96s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 96s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 96s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 96s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 96s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 96s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 96s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 96s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 96s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 96s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 96s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 96s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 96s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 96s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 96s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 96s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 96s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 96s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 96s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 96s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 96s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 96s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 96s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 96s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 96s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 96s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 96s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 96s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 96s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 96s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 96s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 96s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 96s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 96s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 96s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 96s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 96s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 96s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 96s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 96s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 96s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 96s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 96s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 96s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 96s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 96s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 96s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 96s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 96s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 96s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 96s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 96s 96s ============================= 112 passed in 1.19s ============================== 97s autopkgtest [16:04:47]: test run-unit-test: -----------------------] 97s run-unit-test PASS 97s autopkgtest [16:04:47]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 98s autopkgtest [16:04:48]: test autodep8-python3: preparing testbed 217s autopkgtest [16:06:47]: testbed dpkg architecture: arm64 217s autopkgtest [16:06:47]: testbed apt version: 2.9.8 217s autopkgtest [16:06:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 218s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 219s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 219s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [966 kB] 219s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 219s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 219s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [138 kB] 219s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 219s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [724 kB] 219s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [6012 B] 219s Fetched 2085 kB in 1s (2133 kB/s) 219s Reading package lists... 222s Reading package lists... 223s Building dependency tree... 223s Reading state information... 224s Calculating upgrade... 224s The following packages will be upgraded: 224s pastebinit python3-systemd 225s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 225s Need to get 61.6 kB of archives. 225s After this operation, 347 kB of additional disk space will be used. 225s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 225s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 225s Fetched 61.6 kB in 0s (174 kB/s) 226s (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 ... 79925 files and directories currently installed.) 226s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 226s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 226s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 226s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 226s Setting up pastebinit (1.7.1-1) ... 226s Setting up python3-systemd (235-1build5) ... 226s Processing triggers for man-db (2.12.1-3) ... 227s Reading package lists... 227s Building dependency tree... 227s Reading state information... 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 229s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 229s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 229s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 229s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 231s Reading package lists... 231s Reading package lists... 231s Building dependency tree... 231s Reading state information... 232s Calculating upgrade... 232s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 232s Reading package lists... 233s Building dependency tree... 233s Reading state information... 234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 239s Reading package lists... 239s Building dependency tree... 239s Reading state information... 240s Starting pkgProblemResolver with broken count: 0 240s Starting 2 pkgProblemResolver with broken count: 0 240s Done 242s The following additional packages will be installed: 242s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 242s python3-all python3-click python3-colorama python3-coloredlogs 242s python3-cyvcf2 python3-humanfriendly python3-numpy 242s Suggested packages: 242s gcc gfortran python-numpy-doc python3-dev python3-pytest 242s The following NEW packages will be installed: 242s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3t64 242s libhtscodecs2 liblapack3 python3-all python3-click python3-colorama 242s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 242s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 242s Need to get 8721 kB/8721 kB of archives. 242s After this operation, 43.6 MB of additional disk space will be used. 242s Get:1 /tmp/autopkgtest.HedIZY/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 242s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 242s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.22-1 [46.2 kB] 242s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 242s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.1-1 [82.5 kB] 242s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhts3t64 arm64 1.20+ds-1 [431 kB] 242s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 243s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 243s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 243s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 243s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 243s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 243s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 243s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-cyvcf2 arm64 0.31.1-2 [908 kB] 243s Fetched 8721 kB in 1s (9362 kB/s) 243s Selecting previously unselected package libblas3:arm64. 243s (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 ... 79930 files and directories currently installed.) 243s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 243s Unpacking libblas3:arm64 (3.12.0-3build2) ... 244s Selecting previously unselected package libdeflate0:arm64. 244s Preparing to unpack .../01-libdeflate0_1.22-1_arm64.deb ... 244s Unpacking libdeflate0:arm64 (1.22-1) ... 244s Selecting previously unselected package libgfortran5:arm64. 244s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 244s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 244s Selecting previously unselected package libhtscodecs2:arm64. 244s Preparing to unpack .../03-libhtscodecs2_1.6.1-1_arm64.deb ... 244s Unpacking libhtscodecs2:arm64 (1.6.1-1) ... 244s Selecting previously unselected package libhts3t64:arm64. 244s Preparing to unpack .../04-libhts3t64_1.20+ds-1_arm64.deb ... 244s Unpacking libhts3t64:arm64 (1.20+ds-1) ... 244s Selecting previously unselected package liblapack3:arm64. 244s Preparing to unpack .../05-liblapack3_3.12.0-3build2_arm64.deb ... 244s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 244s Selecting previously unselected package python3-all. 244s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 244s Unpacking python3-all (3.12.6-0ubuntu1) ... 244s Selecting previously unselected package python3-colorama. 244s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 244s Unpacking python3-colorama (0.4.6-4) ... 244s Selecting previously unselected package python3-click. 244s Preparing to unpack .../08-python3-click_8.1.7-2_all.deb ... 244s Unpacking python3-click (8.1.7-2) ... 244s Selecting previously unselected package python3-humanfriendly. 244s Preparing to unpack .../09-python3-humanfriendly_10.0-6_all.deb ... 244s Unpacking python3-humanfriendly (10.0-6) ... 244s Selecting previously unselected package python3-coloredlogs. 244s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 244s Unpacking python3-coloredlogs (15.0.1-1) ... 244s Selecting previously unselected package python3-numpy. 244s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 244s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 244s Selecting previously unselected package python3-cyvcf2. 244s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2_arm64.deb ... 244s Unpacking python3-cyvcf2 (0.31.1-2) ... 245s Selecting previously unselected package autopkgtest-satdep. 245s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 245s Unpacking autopkgtest-satdep (0) ... 245s Setting up libhtscodecs2:arm64 (1.6.1-1) ... 245s Setting up python3-colorama (0.4.6-4) ... 245s Setting up libdeflate0:arm64 (1.22-1) ... 245s Setting up python3-all (3.12.6-0ubuntu1) ... 245s Setting up python3-click (8.1.7-2) ... 245s Setting up libblas3:arm64 (3.12.0-3build2) ... 245s 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 245s Setting up python3-humanfriendly (10.0-6) ... 246s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 246s Setting up libhts3t64:arm64 (1.20+ds-1) ... 246s Setting up python3-coloredlogs (15.0.1-1) ... 246s Setting up liblapack3:arm64 (3.12.0-3build2) ... 246s 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 246s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 249s Setting up python3-cyvcf2 (0.31.1-2) ... 249s Setting up autopkgtest-satdep (0) ... 249s Processing triggers for man-db (2.12.1-3) ... 249s Processing triggers for libc-bin (2.40-1ubuntu3) ... 254s (Reading database ... 81052 files and directories currently installed.) 254s Removing autopkgtest-satdep (0) ... 256s autopkgtest [16:07:26]: 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 256s autopkgtest [16:07:26]: test autodep8-python3: [----------------------- 256s Testing with python3.12: 256s 257s autopkgtest [16:07:27]: test autodep8-python3: -----------------------] 257s autopkgtest [16:07:27]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 257s autodep8-python3 PASS (superficial) 258s autopkgtest [16:07:28]: @@@@@@@@@@@@@@@@@@@@ summary 258s run-unit-test PASS 258s autodep8-python3 PASS (superficial) 270s nova [W] Skipping flock in bos03-arm64 270s Creating nova instance adt-plucky-arm64-cyvcf2-20241114-160310-juju-7f2275-prod-proposed-migration-environment-20-36d1fba8-a02d-4509-bea1-f6ea072c91cb from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)... 270s nova [W] Skipping flock in bos03-arm64 270s Creating nova instance adt-plucky-arm64-cyvcf2-20241114-160310-juju-7f2275-prod-proposed-migration-environment-20-36d1fba8-a02d-4509-bea1-f6ea072c91cb from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...