0s autopkgtest [15:28:53]: starting date and time: 2025-10-20 15:28:53+0000 0s autopkgtest [15:28:53]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [15:28:53]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.07laoze2/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-8.secgroup --name adt-resolute-s390x-cyvcf2-20251020-152853-juju-7f2275-prod-proposed-migration-environment-15-96eef75f-183f-46f0-8e7f-dc38d533f33c --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-cyvcf2-20251020-152853-juju-7f2275-prod-proposed-migration-environment-15-96eef75f-183f-46f0-8e7f-dc38d533f33c from image adt/ubuntu-resolute-s390x-server-20251020.img (UUID af6042e7-5f94-4102-8fd4-5557e2338897)... 43s autopkgtest [15:29:36]: testbed dpkg architecture: s390x 43s autopkgtest [15:29:36]: testbed apt version: 3.1.8ubuntu1 43s autopkgtest [15:29:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 44s autopkgtest [15:29:37]: testbed release detected to be: None 44s autopkgtest [15:29:37]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 45s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 45s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 45s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 45s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 45s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [56.9 kB] 45s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 45s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 45s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 45s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 45s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [400 kB] 45s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 46s Fetched 1318 kB in 1s (1256 kB/s) 46s Reading package lists... 47s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 47s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Reading package lists... 48s Reading package lists... 48s Building dependency tree... 48s Reading state information... 48s Calculating upgrade... 48s The following packages will be upgraded: 48s libjson-c5 python3-inflect python3-oauthlib python3-zipp 48s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 48s Need to get 175 kB of archives. 48s After this operation, 31.7 kB of additional disk space will be used. 48s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-c5 s390x 0.18+ds-1.1 [36.8 kB] 48s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-inflect all 7.5.0-1 [33.9 kB] 48s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-oauthlib all 3.3.1-1 [93.5 kB] 48s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-zipp all 3.23.0-1 [10.4 kB] 48s dpkg-preconfigure: unable to re-open stdin: No such file or directory 48s Fetched 175 kB in 0s (428 kB/s) 49s (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 ... 56857 files and directories currently installed.) 49s Preparing to unpack .../libjson-c5_0.18+ds-1.1_s390x.deb ... 49s Unpacking libjson-c5:s390x (0.18+ds-1.1) over (0.18+ds-1) ... 49s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 49s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 49s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 49s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 49s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 49s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 49s Setting up python3-zipp (3.23.0-1) ... 49s Setting up python3-inflect (7.5.0-1) ... 49s Setting up python3-oauthlib (3.3.1-1) ... 49s Setting up libjson-c5:s390x (0.18+ds-1.1) ... 49s Processing triggers for libc-bin (2.42-0ubuntu3) ... 49s autopkgtest [15:29:42]: upgrading testbed (apt dist-upgrade and autopurge) 49s Reading package lists... 49s Building dependency tree... 49s Reading state information... 49s Calculating upgrade... 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Solving dependencies... 50s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s autopkgtest [15:29:45]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 52s autopkgtest [15:29:45]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 54s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (dsc) [2361 B] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (tar) [420 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.1-2build3 (diff) [6888 B] 54s gpgv: Signature made Tue Mar 4 17:10:01 2025 UTC 54s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 54s gpgv: Can't check signature: No public key 54s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.1-2build3.dsc: no acceptable signature found 54s autopkgtest [15:29:47]: testing package cyvcf2 version 0.31.1-2build3 55s autopkgtest [15:29:48]: build not needed 58s autopkgtest [15:29:51]: test run-unit-test: preparing testbed 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 58s The following NEW packages will be installed: 58s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 58s python3-all python3-click python3-coloredlogs python3-cyvcf2 58s python3-humanfriendly python3-iniconfig python3-numpy python3-numpy-dev 58s python3-packaging python3-pluggy python3-pytest 58s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 10.4 MB of archives. 58s After this operation, 44.1 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 61s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 62s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 62s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 62s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 62s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 62s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 62s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-humanfriendly all 10.0-6 [70.8 kB] 62s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 62s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cyvcf2 s390x 0.31.1-2build3 [941 kB] 63s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 63s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 63s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 63s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pytest all 8.4.2-1 [268 kB] 63s Fetched 10.4 MB in 4s (2354 kB/s) 63s Selecting previously unselected package python3-numpy-dev:s390x. 63s (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 ... 56867 files and directories currently installed.) 63s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 63s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 63s Selecting previously unselected package libblas3:s390x. 63s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 63s Unpacking libblas3:s390x (3.12.1-6build1) ... 63s Selecting previously unselected package libgfortran5:s390x. 63s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 63s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 63s Selecting previously unselected package liblapack3:s390x. 63s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 63s Unpacking liblapack3:s390x (3.12.1-6build1) ... 63s Selecting previously unselected package python3-numpy. 63s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 63s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 63s Selecting previously unselected package libdeflate0:s390x. 63s Preparing to unpack .../05-libdeflate0_1.23-2_s390x.deb ... 63s Unpacking libdeflate0:s390x (1.23-2) ... 63s Selecting previously unselected package libhtscodecs2:s390x. 63s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_s390x.deb ... 63s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 63s Selecting previously unselected package libhts3t64:s390x. 63s Preparing to unpack .../07-libhts3t64_1.21+ds-1_s390x.deb ... 63s Unpacking libhts3t64:s390x (1.21+ds-1) ... 63s Selecting previously unselected package python3-all. 63s Preparing to unpack .../08-python3-all_3.13.7-1_s390x.deb ... 63s Unpacking python3-all (3.13.7-1) ... 63s Selecting previously unselected package python3-click. 63s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 63s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 63s Selecting previously unselected package python3-humanfriendly. 63s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 63s Unpacking python3-humanfriendly (10.0-6) ... 63s Selecting previously unselected package python3-coloredlogs. 63s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 63s Unpacking python3-coloredlogs (15.0.1-1) ... 63s Selecting previously unselected package python3-cyvcf2. 63s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_s390x.deb ... 63s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 63s Selecting previously unselected package python3-iniconfig. 63s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 63s Unpacking python3-iniconfig (1.1.1-2) ... 63s Selecting previously unselected package python3-packaging. 63s Preparing to unpack .../14-python3-packaging_25.0-1_all.deb ... 63s Unpacking python3-packaging (25.0-1) ... 63s Selecting previously unselected package python3-pluggy. 63s Preparing to unpack .../15-python3-pluggy_1.6.0-1_all.deb ... 63s Unpacking python3-pluggy (1.6.0-1) ... 63s Selecting previously unselected package python3-pytest. 63s Preparing to unpack .../16-python3-pytest_8.4.2-1_all.deb ... 63s Unpacking python3-pytest (8.4.2-1) ... 63s Setting up libhtscodecs2:s390x (1.6.1-2) ... 63s Setting up python3-iniconfig (1.1.1-2) ... 63s Setting up libdeflate0:s390x (1.23-2) ... 63s Setting up python3-all (3.13.7-1) ... 63s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 63s Setting up libblas3:s390x (3.12.1-6build1) ... 63s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 63s Setting up python3-packaging (25.0-1) ... 64s Setting up python3-humanfriendly (10.0-6) ... 64s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 64s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 64s Setting up python3-pluggy (1.6.0-1) ... 64s Setting up libhts3t64:s390x (1.21+ds-1) ... 64s Setting up python3-coloredlogs (15.0.1-1) ... 64s Setting up liblapack3:s390x (3.12.1-6build1) ... 64s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 64s Setting up python3-pytest (8.4.2-1) ... 64s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 65s Setting up python3-cyvcf2 (0.31.1-2build3) ... 65s Processing triggers for man-db (2.13.1-1) ... 66s Processing triggers for libc-bin (2.42-0ubuntu3) ... 67s autopkgtest [15:30:00]: test run-unit-test: [----------------------- 67s Testing with python3.13 in /tmp/autopkgtest.yLFvEF/autopkgtest_tmp: 67s ============================= test session starts ============================== 67s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 67s cachedir: .pytest_cache 67s rootdir: /tmp/autopkgtest.yLFvEF/autopkgtest_tmp 67s plugins: typeguard-4.4.2 67s collecting ... collected 112 items 67s 67s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 67s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 67s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 67s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 67s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 67s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 67s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 67s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 67s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 67s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 67s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 67s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 67s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 67s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 67s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 67s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 67s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 67s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 67s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 67s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 67s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 67s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 67s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 67s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 67s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 67s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 67s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 67s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 68s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 68s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 68s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 68s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 68s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 68s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 68s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 68s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 68s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 68s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 68s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 68s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 68s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 68s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 68s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 68s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 68s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 68s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 68s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 68s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 68s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 68s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 68s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 68s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 68s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 68s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 68s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 68s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 68s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 68s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 68s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 68s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 68s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 68s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 68s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 68s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 68s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 68s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 68s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 68s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 68s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 68s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 68s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 68s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 68s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 68s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 68s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 68s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 68s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 68s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 68s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 68s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 68s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 68s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 68s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 68s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 68s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 68s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 68s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 68s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 68s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 68s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 68s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 68s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 68s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 68s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 68s 68s ============================= 112 passed in 0.83s ============================== 68s autopkgtest [15:30:01]: test run-unit-test: -----------------------] 69s run-unit-test PASS 69s autopkgtest [15:30:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 69s autopkgtest [15:30:02]: test autodep8-python3: preparing testbed 90s Creating nova instance adt-resolute-s390x-cyvcf2-20251020-152853-juju-7f2275-prod-proposed-migration-environment-15-96eef75f-183f-46f0-8e7f-dc38d533f33c from image adt/ubuntu-resolute-s390x-server-20251020.img (UUID af6042e7-5f94-4102-8fd4-5557e2338897)... 129s autopkgtest [15:31:02]: testbed dpkg architecture: s390x 129s autopkgtest [15:31:02]: testbed apt version: 3.1.8ubuntu1 129s autopkgtest [15:31:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 129s autopkgtest [15:31:02]: testbed release detected to be: resolute 130s autopkgtest [15:31:03]: updating testbed package index (apt update) 130s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 131s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 131s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 131s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 131s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 131s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [56.9 kB] 131s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 131s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 131s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 131s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 131s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [400 kB] 131s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 131s Fetched 1318 kB in 1s (1188 kB/s) 132s Reading package lists... 133s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 133s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 133s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 133s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 134s Reading package lists... 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s Calculating upgrade... 134s The following packages will be upgraded: 134s libjson-c5 python3-inflect python3-oauthlib python3-zipp 134s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 175 kB of archives. 134s After this operation, 31.7 kB of additional disk space will be used. 134s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-c5 s390x 0.18+ds-1.1 [36.8 kB] 134s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-inflect all 7.5.0-1 [33.9 kB] 134s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-oauthlib all 3.3.1-1 [93.5 kB] 134s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-zipp all 3.23.0-1 [10.4 kB] 135s dpkg-preconfigure: unable to re-open stdin: No such file or directory 135s Fetched 175 kB in 0s (433 kB/s) 135s (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 ... 56857 files and directories currently installed.) 135s Preparing to unpack .../libjson-c5_0.18+ds-1.1_s390x.deb ... 135s Unpacking libjson-c5:s390x (0.18+ds-1.1) over (0.18+ds-1) ... 135s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 135s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 135s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 135s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 135s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 135s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 135s Setting up python3-zipp (3.23.0-1) ... 135s Setting up python3-inflect (7.5.0-1) ... 135s Setting up python3-oauthlib (3.3.1-1) ... 135s Setting up libjson-c5:s390x (0.18+ds-1.1) ... 135s Processing triggers for libc-bin (2.42-0ubuntu3) ... 135s autopkgtest [15:31:08]: upgrading testbed (apt dist-upgrade and autopurge) 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Calculating upgrade... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s Solving dependencies... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Solving dependencies... 139s The following NEW packages will be installed: 139s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 139s python3-all python3-click python3-coloredlogs python3-cyvcf2 139s python3-humanfriendly python3-numpy python3-numpy-dev 139s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 10.1 MB of archives. 139s After this operation, 42.4 MB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 140s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 140s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 141s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 142s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 143s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 143s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 143s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 143s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 143s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 143s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-humanfriendly all 10.0-6 [70.8 kB] 143s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 143s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cyvcf2 s390x 0.31.1-2build3 [941 kB] 143s Fetched 10.1 MB in 4s (2708 kB/s) 143s Selecting previously unselected package python3-numpy-dev:s390x. 143s (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 ... 56867 files and directories currently installed.) 143s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 143s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 143s Selecting previously unselected package libblas3:s390x. 143s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 143s Unpacking libblas3:s390x (3.12.1-6build1) ... 143s Selecting previously unselected package libgfortran5:s390x. 143s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 143s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 143s Selecting previously unselected package liblapack3:s390x. 143s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 143s Unpacking liblapack3:s390x (3.12.1-6build1) ... 143s Selecting previously unselected package python3-numpy. 143s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 143s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 144s Selecting previously unselected package libdeflate0:s390x. 144s Preparing to unpack .../05-libdeflate0_1.23-2_s390x.deb ... 144s Unpacking libdeflate0:s390x (1.23-2) ... 144s Selecting previously unselected package libhtscodecs2:s390x. 144s Preparing to unpack .../06-libhtscodecs2_1.6.1-2_s390x.deb ... 144s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 144s Selecting previously unselected package libhts3t64:s390x. 144s Preparing to unpack .../07-libhts3t64_1.21+ds-1_s390x.deb ... 144s Unpacking libhts3t64:s390x (1.21+ds-1) ... 144s Selecting previously unselected package python3-all. 144s Preparing to unpack .../08-python3-all_3.13.7-1_s390x.deb ... 144s Unpacking python3-all (3.13.7-1) ... 144s Selecting previously unselected package python3-click. 144s Preparing to unpack .../09-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 144s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 144s Selecting previously unselected package python3-humanfriendly. 144s Preparing to unpack .../10-python3-humanfriendly_10.0-6_all.deb ... 144s Unpacking python3-humanfriendly (10.0-6) ... 144s Selecting previously unselected package python3-coloredlogs. 144s Preparing to unpack .../11-python3-coloredlogs_15.0.1-1_all.deb ... 144s Unpacking python3-coloredlogs (15.0.1-1) ... 144s Selecting previously unselected package python3-cyvcf2. 144s Preparing to unpack .../12-python3-cyvcf2_0.31.1-2build3_s390x.deb ... 144s Unpacking python3-cyvcf2 (0.31.1-2build3) ... 144s Setting up libhtscodecs2:s390x (1.6.1-2) ... 144s Setting up libdeflate0:s390x (1.23-2) ... 144s Setting up python3-all (3.13.7-1) ... 144s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 144s Setting up libblas3:s390x (3.12.1-6build1) ... 144s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 144s Setting up python3-humanfriendly (10.0-6) ... 144s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 144s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 144s Setting up libhts3t64:s390x (1.21+ds-1) ... 144s Setting up python3-coloredlogs (15.0.1-1) ... 144s Setting up liblapack3:s390x (3.12.1-6build1) ... 144s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 144s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 146s Setting up python3-cyvcf2 (0.31.1-2build3) ... 146s Processing triggers for man-db (2.13.1-1) ... 146s Processing triggers for libc-bin (2.42-0ubuntu3) ... 148s autopkgtest [15:31:21]: 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 148s autopkgtest [15:31:21]: test autodep8-python3: [----------------------- 149s Testing with python3.13: 149s 149s autopkgtest [15:31:22]: test autodep8-python3: -----------------------] 149s autodep8-python3 PASS (superficial) 149s autopkgtest [15:31:22]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 150s autopkgtest [15:31:23]: @@@@@@@@@@@@@@@@@@@@ summary 150s run-unit-test PASS 150s autodep8-python3 PASS (superficial)