0s autopkgtest [00:18:12]: starting date and time: 2024-06-08 00:18:12+0000 0s autopkgtest [00:18:12]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [00:18:12]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lrwmjhit/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-5.secgroup --name adt-oracular-amd64-cyvcf2-20240608-001812-juju-7f2275-prod-proposed-migration-environment-3-297ea69d-7be9-4298-86e1-e36be7cc28de --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 83s autopkgtest [00:19:35]: testbed dpkg architecture: amd64 83s autopkgtest [00:19:35]: testbed apt version: 2.9.3 83s autopkgtest [00:19:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 83s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 83s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 83s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 83s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 83s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 83s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 83s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 83s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 83s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 83s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 83s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 83s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 83s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 84s Fetched 1081 kB in 0s (3701 kB/s) 84s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 87s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 88s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s autopkgtest [00:19:43]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 91s autopkgtest [00:19:43]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 92s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (dsc) [2486 B] 92s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (tar) [420 kB] 92s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (diff) [6696 B] 93s gpgv: Signature made Sat Jun 1 08:34:30 2024 UTC 93s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 93s gpgv: issuer "emollier@debian.org" 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.0-1.dsc: no acceptable signature found 93s autopkgtest [00:19:45]: testing package cyvcf2 version 0.31.0-1 93s autopkgtest [00:19:45]: build not needed 94s autopkgtest [00:19:46]: test run-unit-test: preparing testbed 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Starting pkgProblemResolver with broken count: 0 95s Starting 2 pkgProblemResolver with broken count: 0 95s Done 96s The following additional packages will be installed: 96s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 96s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 96s python3-humanfriendly python3-iniconfig python3-numpy python3-packaging 96s python3-pluggy python3-pytest 96s Suggested packages: 96s gcc gfortran python-numpy-doc python3-dev 96s The following NEW packages will be installed: 96s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 96s python3-all python3-click python3-colorama python3-coloredlogs 96s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 96s python3-packaging python3-pluggy python3-pytest 96s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 10.2 MB/10.2 MB of archives. 96s After this operation, 43.9 MB of additional disk space will be used. 96s Get:1 /tmp/autopkgtest.StGIl0/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 96s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 96s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 96s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 96s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 96s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 96s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.3-0ubuntu1 [888 B] 96s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 96s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.7-1 [79.1 kB] 96s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-humanfriendly all 10.0-5 [70.5 kB] 96s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 96s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 96s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cyvcf2 amd64 0.31.0-1 [848 kB] 96s Get:14 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 96s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 96s Get:16 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 96s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 96s Fetched 10.2 MB in 0s (69.1 MB/s) 96s Selecting previously unselected package libblas3:amd64. 97s (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 ... 74365 files and directories currently installed.) 97s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 97s Unpacking libblas3:amd64 (3.12.0-3build1) ... 97s Selecting previously unselected package libgfortran5:amd64. 97s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 97s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 97s Selecting previously unselected package libhtscodecs2:amd64. 97s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_amd64.deb ... 97s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 97s Selecting previously unselected package libhts3t64:amd64. 97s Preparing to unpack .../03-libhts3t64_1.20+ds-1_amd64.deb ... 97s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 97s Selecting previously unselected package liblapack3:amd64. 97s Preparing to unpack .../04-liblapack3_3.12.0-3build1_amd64.deb ... 97s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 97s Selecting previously unselected package python3-all. 97s Preparing to unpack .../05-python3-all_3.12.3-0ubuntu1_amd64.deb ... 97s Unpacking python3-all (3.12.3-0ubuntu1) ... 97s Selecting previously unselected package python3-colorama. 97s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 97s Unpacking python3-colorama (0.4.6-4) ... 97s Selecting previously unselected package python3-click. 97s Preparing to unpack .../07-python3-click_8.1.7-1_all.deb ... 97s Unpacking python3-click (8.1.7-1) ... 97s Selecting previously unselected package python3-humanfriendly. 97s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 97s Unpacking python3-humanfriendly (10.0-5) ... 97s Selecting previously unselected package python3-coloredlogs. 97s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 97s Unpacking python3-coloredlogs (15.0.1-1) ... 97s Selecting previously unselected package python3-numpy. 97s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 97s Unpacking python3-numpy (1:1.26.4+ds-10) ... 97s Selecting previously unselected package python3-cyvcf2. 97s Preparing to unpack .../11-python3-cyvcf2_0.31.0-1_amd64.deb ... 97s Unpacking python3-cyvcf2 (0.31.0-1) ... 97s Selecting previously unselected package python3-iniconfig. 97s Preparing to unpack .../12-python3-iniconfig_1.1.1-2_all.deb ... 97s Unpacking python3-iniconfig (1.1.1-2) ... 97s Selecting previously unselected package python3-packaging. 97s Preparing to unpack .../13-python3-packaging_24.0-1_all.deb ... 97s Unpacking python3-packaging (24.0-1) ... 97s Selecting previously unselected package python3-pluggy. 97s Preparing to unpack .../14-python3-pluggy_1.5.0-1_all.deb ... 97s Unpacking python3-pluggy (1.5.0-1) ... 97s Selecting previously unselected package python3-pytest. 97s Preparing to unpack .../15-python3-pytest_8.2.2-1ubuntu1_all.deb ... 97s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 97s Selecting previously unselected package autopkgtest-satdep. 97s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 97s Unpacking autopkgtest-satdep (0) ... 97s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 97s Setting up python3-iniconfig (1.1.1-2) ... 98s Setting up python3-colorama (0.4.6-4) ... 98s Setting up python3-all (3.12.3-0ubuntu1) ... 98s Setting up python3-click (8.1.7-1) ... 98s Setting up libblas3:amd64 (3.12.0-3build1) ... 98s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 98s Setting up python3-packaging (24.0-1) ... 98s Setting up python3-humanfriendly (10.0-5) ... 98s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 98s Setting up python3-pluggy (1.5.0-1) ... 98s Setting up libhts3t64:amd64 (1.20+ds-1) ... 98s Setting up python3-coloredlogs (15.0.1-1) ... 98s Setting up liblapack3:amd64 (3.12.0-3build1) ... 98s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 98s Setting up python3-pytest (8.2.2-1ubuntu1) ... 99s Setting up python3-numpy (1:1.26.4+ds-10) ... 101s Setting up python3-cyvcf2 (0.31.0-1) ... 101s Setting up autopkgtest-satdep (0) ... 101s Processing triggers for man-db (2.12.1-1) ... 102s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 104s (Reading database ... 75627 files and directories currently installed.) 104s Removing autopkgtest-satdep (0) ... 105s autopkgtest [00:19:57]: test run-unit-test: [----------------------- 105s Testing with python3.12 in /tmp/autopkgtest.StGIl0/autopkgtest_tmp: 105s ============================= test session starts ============================== 105s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 -- /usr/bin/python3.12 105s cachedir: .pytest_cache 105s rootdir: /tmp/autopkgtest.StGIl0/autopkgtest_tmp 106s collecting ... collected 112 items 106s 106s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 106s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 106s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 106s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 106s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 106s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 106s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 106s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 106s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 106s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 106s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 106s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 106s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 106s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 106s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 106s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 106s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 106s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 106s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 106s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 106s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 106s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 106s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 106s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 106s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 106s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 106s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 106s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 106s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 106s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 106s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 106s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 106s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 106s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 106s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 106s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 106s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 106s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 106s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 106s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 106s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 106s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 106s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 106s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 106s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 106s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 106s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 106s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 106s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 106s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 106s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 106s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 106s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 106s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 106s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 106s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 106s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 106s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 106s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 106s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 106s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 106s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 106s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 106s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 106s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 106s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 106s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 106s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 106s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 106s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 106s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 106s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 106s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 106s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 106s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 106s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 106s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 106s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 106s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 106s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 106s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 106s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 106s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 106s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 106s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 106s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 106s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 106s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 106s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 106s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 106s 106s ============================= 112 passed in 1.11s ============================== 107s autopkgtest [00:19:59]: test run-unit-test: -----------------------] 107s autopkgtest [00:19:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 107s run-unit-test PASS 107s autopkgtest [00:19:59]: test autodep8-python3: preparing testbed 533s autopkgtest [00:27:05]: testbed dpkg architecture: amd64 533s autopkgtest [00:27:05]: testbed apt version: 2.9.3 533s autopkgtest [00:27:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 534s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 534s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 534s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 534s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 534s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 534s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 534s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 534s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 534s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 534s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 534s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 534s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 534s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 534s Fetched 1081 kB in 0s (4339 kB/s) 534s Reading package lists... 535s Reading package lists... 536s Building dependency tree... 536s Reading state information... 536s Calculating upgrade... 536s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 536s Reading package lists... 537s Building dependency tree... 537s Reading state information... 537s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 537s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 537s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 537s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 537s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 539s Reading package lists... 539s Reading package lists... 539s Building dependency tree... 539s Reading state information... 539s Calculating upgrade... 540s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 540s Reading package lists... 540s Building dependency tree... 540s Reading state information... 540s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 542s Reading package lists... 542s Building dependency tree... 542s Reading state information... 542s Starting pkgProblemResolver with broken count: 0 542s Starting 2 pkgProblemResolver with broken count: 0 542s Done 543s The following additional packages will be installed: 543s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 543s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 543s python3-humanfriendly python3-numpy 543s Suggested packages: 543s gcc gfortran python-numpy-doc python3-dev python3-pytest 543s The following NEW packages will be installed: 543s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 543s python3-all python3-click python3-colorama python3-coloredlogs 543s python3-cyvcf2 python3-humanfriendly python3-numpy 543s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 543s Need to get 9860 kB/9860 kB of archives. 543s After this operation, 42.4 MB of additional disk space will be used. 543s Get:1 /tmp/autopkgtest.StGIl0/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 543s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 543s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 543s Get:4 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 543s Get:5 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhts3t64 amd64 1.20+ds-1 [439 kB] 543s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 543s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-all amd64 3.12.3-0ubuntu1 [888 B] 543s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 543s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.7-1 [79.1 kB] 543s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-humanfriendly all 10.0-5 [70.5 kB] 543s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 543s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 543s Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cyvcf2 amd64 0.31.0-1 [848 kB] 543s Fetched 9860 kB in 0s (84.9 MB/s) 543s Selecting previously unselected package libblas3:amd64. 544s (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 ... 74365 files and directories currently installed.) 544s Preparing to unpack .../00-libblas3_3.12.0-3build1_amd64.deb ... 544s Unpacking libblas3:amd64 (3.12.0-3build1) ... 544s Selecting previously unselected package libgfortran5:amd64. 544s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 544s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 544s Selecting previously unselected package libhtscodecs2:amd64. 544s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_amd64.deb ... 544s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 544s Selecting previously unselected package libhts3t64:amd64. 544s Preparing to unpack .../03-libhts3t64_1.20+ds-1_amd64.deb ... 544s Unpacking libhts3t64:amd64 (1.20+ds-1) ... 544s Selecting previously unselected package liblapack3:amd64. 544s Preparing to unpack .../04-liblapack3_3.12.0-3build1_amd64.deb ... 544s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 544s Selecting previously unselected package python3-all. 544s Preparing to unpack .../05-python3-all_3.12.3-0ubuntu1_amd64.deb ... 544s Unpacking python3-all (3.12.3-0ubuntu1) ... 544s Selecting previously unselected package python3-colorama. 544s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 544s Unpacking python3-colorama (0.4.6-4) ... 544s Selecting previously unselected package python3-click. 544s Preparing to unpack .../07-python3-click_8.1.7-1_all.deb ... 544s Unpacking python3-click (8.1.7-1) ... 544s Selecting previously unselected package python3-humanfriendly. 544s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 544s Unpacking python3-humanfriendly (10.0-5) ... 544s Selecting previously unselected package python3-coloredlogs. 544s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 544s Unpacking python3-coloredlogs (15.0.1-1) ... 544s Selecting previously unselected package python3-numpy. 544s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 544s Unpacking python3-numpy (1:1.26.4+ds-10) ... 544s Selecting previously unselected package python3-cyvcf2. 544s Preparing to unpack .../11-python3-cyvcf2_0.31.0-1_amd64.deb ... 544s Unpacking python3-cyvcf2 (0.31.0-1) ... 544s Selecting previously unselected package autopkgtest-satdep. 544s Preparing to unpack .../12-2-autopkgtest-satdep.deb ... 544s Unpacking autopkgtest-satdep (0) ... 544s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 544s Setting up python3-colorama (0.4.6-4) ... 544s Setting up python3-all (3.12.3-0ubuntu1) ... 544s Setting up python3-click (8.1.7-1) ... 545s Setting up libblas3:amd64 (3.12.0-3build1) ... 545s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 545s Setting up python3-humanfriendly (10.0-5) ... 545s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 545s Setting up libhts3t64:amd64 (1.20+ds-1) ... 545s Setting up python3-coloredlogs (15.0.1-1) ... 545s Setting up liblapack3:amd64 (3.12.0-3build1) ... 545s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 545s Setting up python3-numpy (1:1.26.4+ds-10) ... 547s Setting up python3-cyvcf2 (0.31.0-1) ... 547s Setting up autopkgtest-satdep (0) ... 547s Processing triggers for man-db (2.12.1-1) ... 548s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 550s (Reading database ... 75463 files and directories currently installed.) 550s Removing autopkgtest-satdep (0) ... 551s autopkgtest [00:27:23]: 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 551s autopkgtest [00:27:23]: test autodep8-python3: [----------------------- 551s Testing with python3.12: 551s 551s autopkgtest [00:27:23]: test autodep8-python3: -----------------------] 551s autodep8-python3 PASS (superficial) 551s autopkgtest [00:27:23]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 552s autopkgtest [00:27:24]: @@@@@@@@@@@@@@@@@@@@ summary 552s run-unit-test PASS 552s autodep8-python3 PASS (superficial) 562s nova [W] Skipping flock for amd64 562s Creating nova instance adt-oracular-amd64-cyvcf2-20240608-001812-juju-7f2275-prod-proposed-migration-environment-3-297ea69d-7be9-4298-86e1-e36be7cc28de from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)... 562s nova [W] Skipping flock for amd64 562s Creating nova instance adt-oracular-amd64-cyvcf2-20240608-001812-juju-7f2275-prod-proposed-migration-environment-3-297ea69d-7be9-4298-86e1-e36be7cc28de from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)...