0s autopkgtest [12:20:06]: starting date and time: 2025-10-23 12:20:06+0000 0s autopkgtest [12:20:06]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [12:20:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0fmxy0go/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-3.secgroup --name adt-resolute-amd64-cyvcf2-20251023-122006-juju-7f2275-prod-proposed-migration-environment-15-35a3f126-a8ec-4324-b679-7ee546f889a3 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-cyvcf2-20251023-122006-juju-7f2275-prod-proposed-migration-environment-15-35a3f126-a8ec-4324-b679-7ee546f889a3 from image adt/ubuntu-resolute-amd64-server-20251023.img (UUID edea952f-8f2c-45a6-87ff-4deb46911d29)... 61s autopkgtest [12:21:07]: testbed dpkg architecture: amd64 62s autopkgtest [12:21:08]: testbed apt version: 3.1.8ubuntu1 62s autopkgtest [12:21:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [12:21:08]: testbed release detected to be: None 63s autopkgtest [12:21:09]: updating testbed package index (apt update) 65s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 65s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 65s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 65s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 65s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 65s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.9 kB] 65s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [535 kB] 65s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 65s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [89.5 kB] 65s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [140 kB] 65s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 65s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 65s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [350 kB] 65s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [128 kB] 65s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 65s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 65s Fetched 1447 kB in 1s (1458 kB/s) 65s Reading package lists... 66s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 67s The following packages will be upgraded: 67s python3-yaml 68s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Need to get 188 kB of archives. 68s After this operation, 267 kB of additional disk space will be used. 68s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-yaml amd64 6.0.2-2 [188 kB] 69s dpkg-preconfigure: unable to re-open stdin: No such file or directory 69s Fetched 188 kB in 2s (113 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 ... 78458 files and directories currently installed.) 70s Preparing to unpack .../python3-yaml_6.0.2-2_amd64.deb ... 70s Unpacking python3-yaml (6.0.2-2) over (6.0.2-1build2) ... 70s Setting up python3-yaml (6.0.2-2) ... 70s autopkgtest [12:21:16]: upgrading testbed (apt dist-upgrade and autopurge) 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Solving dependencies... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [12:21:20]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 74s autopkgtest [12:21:20]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 77s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build4 (dsc) [2361 B] 77s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build4 (tar) [420 kB] 77s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build4 (diff) [6924 B] 77s gpgv: Signature made Mon Oct 20 13:59:42 2025 UTC 77s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 77s gpgv: Can't check signature: No public key 77s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2build4.dsc: no acceptable signature found 77s autopkgtest [12:21:23]: testing package cyvcf2 version 0.31.1-2build4 78s autopkgtest [12:21:24]: build not needed 81s autopkgtest [12:21:27]: test run-unit-test: preparing testbed 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 82s python3-all python3-click python3-coloredlogs python3-cyvcf2 82s python3-humanfriendly python3-iniconfig python3-numpy python3-numpy-dev 82s python3-packaging python3-pluggy python3-pytest 82s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 11.8 MB of archives. 82s After this operation, 51.7 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 86s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 87s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 87s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 87s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 87s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 87s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 87s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-humanfriendly all 10.0-6 [70.8 kB] 87s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 87s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cyvcf2 amd64 0.31.1-2build4 [1099 kB] 88s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 88s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 88s Get:16 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 88s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-pytest all 8.4.2-1 [268 kB] 88s Fetched 11.8 MB in 6s (2091 kB/s) 88s Selecting previously unselected package python3-numpy-dev:amd64. 88s (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 ... 78459 files and directories currently installed.) 88s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 88s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 88s Selecting previously unselected package libblas3:amd64. 88s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 88s Unpacking libblas3:amd64 (3.12.1-6build1) ... 88s Selecting previously unselected package libgfortran5:amd64. 88s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 88s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 88s Selecting previously unselected package liblapack3:amd64. 88s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 88s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 88s Selecting previously unselected package python3-numpy. 88s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 88s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 88s Selecting previously unselected package libdeflate0:amd64. 88s Preparing to unpack .../05-libdeflate0_1.23-2_amd64.deb ... 88s Unpacking libdeflate0:amd64 (1.23-2) ... 88s Selecting previously unselected package libhtscodecs2:amd64. 88s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_amd64.deb ... 88s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 88s Selecting previously unselected package libhts3t64:amd64. 88s Preparing to unpack .../07-libhts3t64_1.21+ds-1_amd64.deb ... 88s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 88s Selecting previously unselected package python3-all. 88s Preparing to unpack .../08-python3-all_3.13.7-1_amd64.deb ... 88s Unpacking python3-all (3.13.7-1) ... 88s Selecting previously unselected package python3-click. 88s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 88s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 88s Selecting previously unselected package python3-humanfriendly. 88s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 88s Unpacking python3-humanfriendly (10.0-6) ... 88s Selecting previously unselected package python3-coloredlogs. 88s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 88s Unpacking python3-coloredlogs (15.0.1-1) ... 88s Selecting previously unselected package python3-cyvcf2. 88s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build4_amd64.deb ... 88s Unpacking python3-cyvcf2 (0.31.1-2build4) ... 88s Selecting previously unselected package python3-iniconfig. 88s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 88s Unpacking python3-iniconfig (1.1.1-2) ... 88s Selecting previously unselected package python3-packaging. 88s Preparing to unpack .../14-python3-packaging_25.0-1_all.deb ... 88s Unpacking python3-packaging (25.0-1) ... 88s Selecting previously unselected package python3-pluggy. 88s Preparing to unpack .../15-python3-pluggy_1.6.0-1_all.deb ... 88s Unpacking python3-pluggy (1.6.0-1) ... 88s Selecting previously unselected package python3-pytest. 88s Preparing to unpack .../16-python3-pytest_8.4.2-1_all.deb ... 88s Unpacking python3-pytest (8.4.2-1) ... 88s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 88s Setting up python3-iniconfig (1.1.1-2) ... 89s Setting up libdeflate0:amd64 (1.23-2) ... 89s Setting up python3-all (3.13.7-1) ... 89s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 89s Setting up libblas3:amd64 (3.12.1-6build1) ... 89s 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 89s Setting up python3-packaging (25.0-1) ... 89s Setting up python3-humanfriendly (10.0-6) ... 89s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 89s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 89s Setting up python3-pluggy (1.6.0-1) ... 89s Setting up libhts3t64:amd64 (1.21+ds-1) ... 89s Setting up python3-coloredlogs (15.0.1-1) ... 89s Setting up liblapack3:amd64 (3.12.1-6build1) ... 89s 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 89s Setting up python3-pytest (8.4.2-1) ... 89s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 91s Setting up python3-cyvcf2 (0.31.1-2build4) ... 91s Processing triggers for man-db (2.13.1-1) ... 92s Processing triggers for libc-bin (2.42-0ubuntu3) ... 93s autopkgtest [12:21:39]: test run-unit-test: [----------------------- 93s Testing with python3.13 in /tmp/autopkgtest.1Rz5b5/autopkgtest_tmp: 93s ============================= test session starts ============================== 93s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 93s cachedir: .pytest_cache 93s rootdir: /tmp/autopkgtest.1Rz5b5/autopkgtest_tmp 93s plugins: typeguard-4.4.2 94s collecting ... collected 112 items 94s 94s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 94s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 94s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 94s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 94s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 94s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 94s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 94s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 94s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 94s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 94s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 94s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 94s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 94s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 94s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 94s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 94s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 94s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 94s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 94s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 94s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 94s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 94s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 94s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 94s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 94s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 94s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 94s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 94s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 94s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 94s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 94s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 94s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 94s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 94s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 94s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 94s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 94s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 94s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 94s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 94s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 94s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 94s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 94s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 94s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 94s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 94s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 94s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 94s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 94s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 94s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 94s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 94s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 94s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 94s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 94s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 94s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 94s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 94s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 94s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 94s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 94s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 94s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 94s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 94s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 94s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 94s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 94s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 94s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 94s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 94s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 94s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 94s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 94s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 94s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 94s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 94s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 94s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 94s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 94s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 94s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 94s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 94s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 94s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 94s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 94s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 94s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 94s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 94s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 94s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 94s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 94s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 94s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 95s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 95s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 95s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 95s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 95s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 95s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 95s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 95s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 95s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 95s 95s ============================= 112 passed in 1.04s ============================== 95s autopkgtest [12:21:41]: test run-unit-test: -----------------------] 95s run-unit-test PASS 95s autopkgtest [12:21:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 96s autopkgtest [12:21:42]: test autodep8-python3: preparing testbed 104s Creating nova instance adt-resolute-amd64-cyvcf2-20251023-122006-juju-7f2275-prod-proposed-migration-environment-15-35a3f126-a8ec-4324-b679-7ee546f889a3 from image adt/ubuntu-resolute-amd64-server-20251023.img (UUID edea952f-8f2c-45a6-87ff-4deb46911d29)... 161s autopkgtest [12:22:47]: testbed dpkg architecture: amd64 162s autopkgtest [12:22:48]: testbed apt version: 3.1.8ubuntu1 162s autopkgtest [12:22:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 162s autopkgtest [12:22:48]: testbed release detected to be: resolute 163s autopkgtest [12:22:49]: updating testbed package index (apt update) 163s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 163s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 163s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 164s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 164s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 164s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.9 kB] 164s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [535 kB] 164s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 164s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [89.5 kB] 164s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [140 kB] 164s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 164s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 164s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [350 kB] 164s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [128 kB] 164s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 164s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 164s Fetched 1447 kB in 1s (1311 kB/s) 165s Reading package lists... 166s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 166s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 166s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 166s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 168s Reading package lists... 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s Calculating upgrade... 168s The following packages will be upgraded: 168s python3-yaml 168s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 168s Need to get 188 kB of archives. 168s After this operation, 267 kB of additional disk space will be used. 168s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-yaml amd64 6.0.2-2 [188 kB] 169s dpkg-preconfigure: unable to re-open stdin: No such file or directory 169s Fetched 188 kB in 0s (470 kB/s) 169s (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 ... 78458 files and directories currently installed.) 169s Preparing to unpack .../python3-yaml_6.0.2-2_amd64.deb ... 170s Unpacking python3-yaml (6.0.2-2) over (6.0.2-1build2) ... 170s Setting up python3-yaml (6.0.2-2) ... 170s autopkgtest [12:22:56]: upgrading testbed (apt dist-upgrade and autopurge) 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Calculating upgrade... 171s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 171s Reading package lists... 172s Building dependency tree... 172s Reading state information... 172s Solving dependencies... 172s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Solving dependencies... 176s The following NEW packages will be installed: 176s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 176s python3-all python3-click python3-coloredlogs python3-cyvcf2 176s python3-humanfriendly python3-numpy python3-numpy-dev 176s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 11.5 MB of archives. 176s After this operation, 49.9 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 176s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 176s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 176s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 177s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 177s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2 [49.9 kB] 177s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 177s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 177s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-all amd64 3.13.7-1 [884 B] 177s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 177s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-humanfriendly all 10.0-6 [70.8 kB] 177s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 177s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-cyvcf2 amd64 0.31.1-2build4 [1099 kB] 177s Fetched 11.5 MB in 1s (8751 kB/s) 177s Selecting previously unselected package python3-numpy-dev:amd64. 177s (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 ... 78459 files and directories currently installed.) 177s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 177s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 177s Selecting previously unselected package libblas3:amd64. 177s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 177s Unpacking libblas3:amd64 (3.12.1-6build1) ... 177s Selecting previously unselected package libgfortran5:amd64. 177s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 177s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 177s Selecting previously unselected package liblapack3:amd64. 177s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 177s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 177s Selecting previously unselected package python3-numpy. 177s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 177s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 178s Selecting previously unselected package libdeflate0:amd64. 178s Preparing to unpack .../05-libdeflate0_1.23-2_amd64.deb ... 178s Unpacking libdeflate0:amd64 (1.23-2) ... 178s Selecting previously unselected package libhtscodecs2:amd64. 178s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_amd64.deb ... 178s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 178s Selecting previously unselected package libhts3t64:amd64. 178s Preparing to unpack .../07-libhts3t64_1.21+ds-1_amd64.deb ... 178s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 178s Selecting previously unselected package python3-all. 178s Preparing to unpack .../08-python3-all_3.13.7-1_amd64.deb ... 178s Unpacking python3-all (3.13.7-1) ... 178s Selecting previously unselected package python3-click. 178s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 178s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 178s Selecting previously unselected package python3-humanfriendly. 178s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 178s Unpacking python3-humanfriendly (10.0-6) ... 178s Selecting previously unselected package python3-coloredlogs. 178s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 178s Unpacking python3-coloredlogs (15.0.1-1) ... 178s Selecting previously unselected package python3-cyvcf2. 178s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build4_amd64.deb ... 178s Unpacking python3-cyvcf2 (0.31.1-2build4) ... 178s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 178s Setting up libdeflate0:amd64 (1.23-2) ... 178s Setting up python3-all (3.13.7-1) ... 178s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 178s Setting up libblas3:amd64 (3.12.1-6build1) ... 178s 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 178s Setting up python3-humanfriendly (10.0-6) ... 178s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 178s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 178s Setting up libhts3t64:amd64 (1.21+ds-1) ... 178s Setting up python3-coloredlogs (15.0.1-1) ... 179s Setting up liblapack3:amd64 (3.12.1-6build1) ... 179s 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 179s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 181s Setting up python3-cyvcf2 (0.31.1-2build4) ... 181s Processing triggers for man-db (2.13.1-1) ... 182s Processing triggers for libc-bin (2.42-0ubuntu3) ... 184s autopkgtest [12:23:10]: 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 184s autopkgtest [12:23:10]: test autodep8-python3: [----------------------- 184s Testing with python3.13: 184s 185s autopkgtest [12:23:11]: test autodep8-python3: -----------------------] 185s autodep8-python3 PASS (superficial) 185s autopkgtest [12:23:11]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 186s autopkgtest [12:23:12]: @@@@@@@@@@@@@@@@@@@@ summary 186s run-unit-test PASS 186s autodep8-python3 PASS (superficial)