0s autopkgtest [19:52:47]: starting date and time: 2025-10-20 19:52:47+0000 0s autopkgtest [19:52:47]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [19:52:47]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3h7c0ohr/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-17.secgroup --name adt-resolute-arm64-cyvcf2-20251020-195247-juju-7f2275-prod-proposed-migration-environment-20-ea635ed3-d908-4b01-b031-37a986ab7758 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-cyvcf2-20251020-195247-juju-7f2275-prod-proposed-migration-environment-20-ea635ed3-d908-4b01-b031-37a986ab7758 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 57s autopkgtest [19:53:44]: testbed dpkg architecture: arm64 58s autopkgtest [19:53:45]: testbed apt version: 3.1.8ubuntu1 58s autopkgtest [19:53:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 58s autopkgtest [19:53:45]: testbed release detected to be: None 59s autopkgtest [19:53:46]: updating testbed package index (apt update) 60s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 60s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 60s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 60s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 60s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 60s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 60s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 60s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 60s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 60s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 61s Fetched 1382 kB in 1s (1125 kB/s) 62s Reading package lists... 63s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 63s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 65s Reading package lists... 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 66s Calculating upgrade... 67s The following packages will be upgraded: 67s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 67s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 512 kB of archives. 67s After this operation, 31.7 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 68s dpkg-preconfigure: unable to re-open stdin: No such file or directory 69s Fetched 512 kB in 1s (729 kB/s) 69s (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 ... 83364 files and directories currently installed.) 69s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 69s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 69s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 69s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 70s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 70s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 70s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 70s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 70s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 70s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 71s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 71s Setting up python3-zipp (3.23.0-1) ... 71s Setting up python3-inflect (7.5.0-1) ... 71s Setting up python3-oauthlib (3.3.1-1) ... 72s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 72s Processing triggers for libc-bin (2.42-0ubuntu3) ... 72s autopkgtest [19:53:59]: upgrading testbed (apt dist-upgrade and autopurge) 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 73s Calculating upgrade... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s Solving dependencies... 75s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 78s autopkgtest [19:54:05]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 78s autopkgtest [19:54:05]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 80s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (dsc) [2361 B] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (tar) [420 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (diff) [6888 B] 80s gpgv: Signature made Tue Mar 4 17:10:01 2025 UTC 80s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 80s gpgv: Can't check signature: No public key 80s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2build3.dsc: no acceptable signature found 81s autopkgtest [19:54:08]: testing package cyvcf2 version 0.31.1-2build3 81s autopkgtest [19:54:08]: build not needed 82s autopkgtest [19:54:09]: test run-unit-test: preparing testbed 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Solving dependencies... 84s The following NEW packages will be installed: 84s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 84s python3-all python3-click python3-coloredlogs python3-cyvcf2 84s python3-humanfriendly python3-iniconfig python3-numpy python3-numpy-dev 84s python3-packaging python3-pluggy python3-pytest 84s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 9133 kB of archives. 84s After this operation, 40.0 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 84s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 84s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 85s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 85s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 85s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 85s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.7-1 [884 B] 85s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 85s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 85s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 85s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cyvcf2 arm64 0.31.1-2build3 [917 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 85s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 85s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 85s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 86s Fetched 9133 kB in 1s (6278 kB/s) 86s Selecting previously unselected package python3-numpy-dev:arm64. 86s (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 ... 83374 files and directories currently installed.) 86s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 86s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 86s Selecting previously unselected package libblas3:arm64. 86s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 86s Unpacking libblas3:arm64 (3.12.1-6build1) ... 86s Selecting previously unselected package libgfortran5:arm64. 86s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 86s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 86s Selecting previously unselected package liblapack3:arm64. 86s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 86s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 86s Selecting previously unselected package python3-numpy. 86s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 86s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 87s Selecting previously unselected package libdeflate0:arm64. 87s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 87s Unpacking libdeflate0:arm64 (1.23-2) ... 87s Selecting previously unselected package libhtscodecs2:arm64. 87s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_arm64.deb ... 87s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 87s Selecting previously unselected package libhts3t64:arm64. 87s Preparing to unpack .../07-libhts3t64_1.21+ds-1_arm64.deb ... 87s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 87s Selecting previously unselected package python3-all. 87s Preparing to unpack .../08-python3-all_3.13.7-1_arm64.deb ... 87s Unpacking python3-all (3.13.7-1) ... 87s Selecting previously unselected package python3-click. 87s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 87s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 87s Selecting previously unselected package python3-humanfriendly. 87s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 87s Unpacking python3-humanfriendly (10.0-6) ... 87s Selecting previously unselected package python3-coloredlogs. 87s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 87s Unpacking python3-coloredlogs (15.0.1-1) ... 87s Selecting previously unselected package python3-cyvcf2. 87s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_arm64.deb ... 87s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 87s Selecting previously unselected package python3-iniconfig. 87s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 87s Unpacking python3-iniconfig (1.1.1-2) ... 87s Selecting previously unselected package python3-packaging. 87s Preparing to unpack .../14-python3-packaging_25.0-1_all.deb ... 87s Unpacking python3-packaging (25.0-1) ... 87s Selecting previously unselected package python3-pluggy. 87s Preparing to unpack .../15-python3-pluggy_1.6.0-1_all.deb ... 87s 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:arm64 (1.6.1-2) ... 88s Setting up python3-iniconfig (1.1.1-2) ... 88s Setting up libdeflate0:arm64 (1.23-2) ... 88s Setting up python3-all (3.13.7-1) ... 88s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 88s Setting up libblas3:arm64 (3.12.1-6build1) ... 88s 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 88s Setting up python3-packaging (25.0-1) ... 88s Setting up python3-humanfriendly (10.0-6) ... 89s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 89s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 89s Setting up python3-pluggy (1.6.0-1) ... 89s Setting up libhts3t64:arm64 (1.21+ds-1) ... 89s Setting up python3-coloredlogs (15.0.1-1) ... 89s Setting up liblapack3:arm64 (3.12.1-6build1) ... 89s 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 89s Setting up python3-pytest (8.4.2-1) ... 90s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 93s Setting up python3-cyvcf2 (0.31.1-2build3) ... 93s Processing triggers for man-db (2.13.1-1) ... 94s Processing triggers for libc-bin (2.42-0ubuntu3) ... 95s autopkgtest [19:54:22]: test run-unit-test: [----------------------- 96s Testing with python3.13 in /tmp/autopkgtest.z3lasB/autopkgtest_tmp: 96s ============================= test session starts ============================== 96s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 96s cachedir: .pytest_cache 96s rootdir: /tmp/autopkgtest.z3lasB/autopkgtest_tmp 96s plugins: typeguard-4.4.2 97s collecting ... collected 112 items 97s 97s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 97s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 97s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 97s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 97s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 97s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 97s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 97s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 97s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 97s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 97s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 97s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 97s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 97s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 97s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 97s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 97s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 97s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 97s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 97s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 97s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 97s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 97s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 97s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 97s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 97s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 97s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 97s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 97s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 97s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 97s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 97s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 97s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 97s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 97s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 97s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 97s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 97s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 98s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 98s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 98s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 98s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 98s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 98s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 98s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 98s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 98s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 98s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 98s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 98s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 98s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 98s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 98s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 98s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 98s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 98s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 98s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 98s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 98s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 98s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 98s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 98s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 98s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 98s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 98s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 98s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 98s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 98s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 98s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 98s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 98s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 98s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 98s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 98s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 98s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 98s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 98s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 98s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 98s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 98s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 98s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 98s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 98s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 98s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 98s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 98s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 98s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 98s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 98s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 98s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 98s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 98s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 98s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 98s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 98s 98s ============================= 112 passed in 1.82s ============================== 99s autopkgtest [19:54:26]: test run-unit-test: -----------------------] 100s run-unit-test PASS 100s autopkgtest [19:54:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 100s autopkgtest [19:54:27]: test autodep8-python3: preparing testbed 120s Creating nova instance adt-resolute-arm64-cyvcf2-20251020-195247-juju-7f2275-prod-proposed-migration-environment-20-ea635ed3-d908-4b01-b031-37a986ab7758 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 181s autopkgtest [19:55:48]: testbed dpkg architecture: arm64 182s autopkgtest [19:55:49]: testbed apt version: 3.1.8ubuntu1 182s autopkgtest [19:55:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 182s autopkgtest [19:55:49]: testbed release detected to be: resolute 183s autopkgtest [19:55:50]: updating testbed package index (apt update) 184s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 184s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 184s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 184s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 184s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 184s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 184s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 185s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 185s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 185s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 185s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 185s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 185s Fetched 1382 kB in 1s (1022 kB/s) 187s Reading package lists... 188s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 188s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 188s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 188s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 189s Reading package lists... 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade... 191s The following packages will be upgraded: 191s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 191s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 512 kB of archives. 191s After this operation, 31.7 kB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 191s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 192s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 192s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 192s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 192s dpkg-preconfigure: unable to re-open stdin: No such file or directory 192s Fetched 512 kB in 1s (907 kB/s) 193s (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 ... 83364 files and directories currently installed.) 193s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 193s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 193s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 193s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 193s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 194s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 194s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 194s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 194s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 194s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 194s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 195s Setting up python3-zipp (3.23.0-1) ... 195s Setting up python3-inflect (7.5.0-1) ... 195s Setting up python3-oauthlib (3.3.1-1) ... 196s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 196s Processing triggers for libc-bin (2.42-0ubuntu3) ... 196s autopkgtest [19:56:03]: upgrading testbed (apt dist-upgrade and autopurge) 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Calculating upgrade... 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s Solving dependencies... 199s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 203s Reading package lists... 204s Building dependency tree... 204s Reading state information... 204s Solving dependencies... 204s The following NEW packages will be installed: 204s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 204s python3-all python3-click python3-coloredlogs python3-cyvcf2 204s python3-humanfriendly python3-numpy python3-numpy-dev 205s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 205s Need to get 8785 kB of archives. 205s After this operation, 38.2 MB of additional disk space will be used. 205s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 205s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 205s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 205s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 206s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 207s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libdeflate0 arm64 1.23-2 [46.4 kB] 207s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhtscodecs2 arm64 1.6.1-2 [82.7 kB] 207s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 libhts3t64 arm64 1.21+ds-1 [441 kB] 207s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-all arm64 3.13.7-1 [884 B] 207s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 207s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-humanfriendly all 10.0-6 [70.8 kB] 207s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-coloredlogs all 15.0.1-1 [38.2 kB] 207s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-cyvcf2 arm64 0.31.1-2build3 [917 kB] 208s Fetched 8785 kB in 3s (3329 kB/s) 208s Selecting previously unselected package python3-numpy-dev:arm64. 208s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83374 files and directories currently installed.) 208s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 208s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 208s Selecting previously unselected package libblas3:arm64. 208s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 208s Unpacking libblas3:arm64 (3.12.1-6build1) ... 208s Selecting previously unselected package libgfortran5:arm64. 208s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 208s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 208s Selecting previously unselected package liblapack3:arm64. 208s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 208s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 208s Selecting previously unselected package python3-numpy. 208s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 208s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 209s Selecting previously unselected package libdeflate0:arm64. 209s Preparing to unpack .../05-libdeflate0_1.23-2_arm64.deb ... 209s Unpacking libdeflate0:arm64 (1.23-2) ... 209s Selecting previously unselected package libhtscodecs2:arm64. 209s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_arm64.deb ... 209s Unpacking libhtscodecs2:arm64 (1.6.1-2) ... 209s Selecting previously unselected package libhts3t64:arm64. 209s Preparing to unpack .../07-libhts3t64_1.21+ds-1_arm64.deb ... 209s Unpacking libhts3t64:arm64 (1.21+ds-1) ... 209s Selecting previously unselected package python3-all. 209s Preparing to unpack .../08-python3-all_3.13.7-1_arm64.deb ... 209s Unpacking python3-all (3.13.7-1) ... 209s Selecting previously unselected package python3-click. 209s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 209s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 209s Selecting previously unselected package python3-humanfriendly. 209s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 209s Unpacking python3-humanfriendly (10.0-6) ... 209s Selecting previously unselected package python3-coloredlogs. 209s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 209s Unpacking python3-coloredlogs (15.0.1-1) ... 209s Selecting previously unselected package python3-cyvcf2. 209s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_arm64.deb ... 209s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 209s Setting up libhtscodecs2:arm64 (1.6.1-2) ... 209s Setting up libdeflate0:arm64 (1.23-2) ... 209s Setting up python3-all (3.13.7-1) ... 209s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 210s Setting up libblas3:arm64 (3.12.1-6build1) ... 210s 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 210s Setting up python3-humanfriendly (10.0-6) ... 210s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 210s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 210s Setting up libhts3t64:arm64 (1.21+ds-1) ... 210s Setting up python3-coloredlogs (15.0.1-1) ... 211s Setting up liblapack3:arm64 (3.12.1-6build1) ... 211s 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 211s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 215s Setting up python3-cyvcf2 (0.31.1-2build3) ... 215s Processing triggers for man-db (2.13.1-1) ... 217s Processing triggers for libc-bin (2.42-0ubuntu3) ... 223s autopkgtest [19:56:30]: 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 223s autopkgtest [19:56:30]: test autodep8-python3: [----------------------- 223s Testing with python3.13: 224s 224s autopkgtest [19:56:31]: test autodep8-python3: -----------------------] 225s autodep8-python3 PASS (superficial) 225s autopkgtest [19:56:32]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 226s autopkgtest [19:56:33]: @@@@@@@@@@@@@@@@@@@@ summary 226s run-unit-test PASS 226s autodep8-python3 PASS (superficial)