0s autopkgtest [21:48:14]: starting date and time: 2024-07-20 21:48:14+0000 0s autopkgtest [21:48:14]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [21:48:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.4kz5fma9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.4-1 python3-stdlib-extensions/3.12.4-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-13.secgroup --name adt-oracular-ppc64el-cyvcf2-20240720-214813-juju-7f2275-prod-proposed-migration-environment-2-51e5d10f-bfea-4b18-985f-99af6b02b54e --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 199s autopkgtest [21:51:33]: testbed dpkg architecture: ppc64el 199s autopkgtest [21:51:33]: testbed apt version: 2.9.6 199s autopkgtest [21:51:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 202s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 203s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [401 kB] 203s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4092 B] 203s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [63.1 kB] 203s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 203s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [111 kB] 203s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2116 B] 203s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 203s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 203s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [576 kB] 203s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [8952 B] 203s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1840 B] 203s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 204s Fetched 1304 kB in 1s (1599 kB/s) 204s Reading package lists... 224s Reading package lists... 224s Building dependency tree... 224s Reading state information... 224s Calculating upgrade... 224s The following packages will be upgraded: 224s libbpf1 libpython3-stdlib python3 python3-gdbm python3-minimal 224s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 224s Need to get 298 kB of archives. 224s After this operation, 71.7 kB of additional disk space will be used. 224s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-minimal ppc64el 3.12.4-1 [27.1 kB] 224s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3 ppc64el 3.12.4-1 [24.0 kB] 224s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.4-1 [9818 B] 224s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbpf1 ppc64el 1:1.4.5-1 [218 kB] 225s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-gdbm ppc64el 3.12.4-2 [18.9 kB] 225s Fetched 298 kB in 0s (629 kB/s) 225s (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 ... 72765 files and directories currently installed.) 225s Preparing to unpack .../python3-minimal_3.12.4-1_ppc64el.deb ... 225s Unpacking python3-minimal (3.12.4-1) over (3.12.3-0ubuntu1) ... 225s Setting up python3-minimal (3.12.4-1) ... 225s (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 ... 72765 files and directories currently installed.) 225s Preparing to unpack .../python3_3.12.4-1_ppc64el.deb ... 225s Unpacking python3 (3.12.4-1) over (3.12.3-0ubuntu1) ... 225s Preparing to unpack .../libpython3-stdlib_3.12.4-1_ppc64el.deb ... 225s Unpacking libpython3-stdlib:ppc64el (3.12.4-1) over (3.12.3-0ubuntu1) ... 225s Preparing to unpack .../libbpf1_1%3a1.4.5-1_ppc64el.deb ... 225s Unpacking libbpf1:ppc64el (1:1.4.5-1) over (1:1.4.3-1) ... 225s Preparing to unpack .../python3-gdbm_3.12.4-2_ppc64el.deb ... 225s Unpacking python3-gdbm:ppc64el (3.12.4-2) over (3.12.3-0ubuntu1) ... 225s Setting up libbpf1:ppc64el (1:1.4.5-1) ... 225s Setting up libpython3-stdlib:ppc64el (3.12.4-1) ... 225s Setting up python3 (3.12.4-1) ... 226s Setting up python3-gdbm:ppc64el (3.12.4-2) ... 226s Processing triggers for man-db (2.12.1-2) ... 226s Processing triggers for libc-bin (2.39-0ubuntu9) ... 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 227s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 232s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 232s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 232s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 232s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 233s Reading package lists... 233s Reading package lists... 233s Building dependency tree... 233s Reading state information... 233s Calculating upgrade... 234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 240s autopkgtest [21:52:14]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 240s autopkgtest [21:52:14]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 246s Get:1 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (dsc) [2486 B] 246s Get:2 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (tar) [420 kB] 246s Get:3 http://ftpmaster.internal/ubuntu oracular/universe cyvcf2 0.31.0-1 (diff) [6696 B] 246s gpgv: Signature made Sat Jun 1 08:34:30 2024 UTC 246s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 246s gpgv: issuer "emollier@debian.org" 246s gpgv: Can't check signature: No public key 246s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.0-1.dsc: no acceptable signature found 246s autopkgtest [21:52:20]: testing package cyvcf2 version 0.31.0-1 261s autopkgtest [21:52:35]: build not needed 262s autopkgtest [21:52:36]: test run-unit-test: preparing testbed 263s Reading package lists... 263s Building dependency tree... 263s Reading state information... 263s Starting pkgProblemResolver with broken count: 0 263s Starting 2 pkgProblemResolver with broken count: 0 263s Done 263s The following additional packages will be installed: 263s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 263s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 263s python3-humanfriendly python3-iniconfig python3-numpy python3-packaging 263s python3-pluggy python3-pytest 263s Suggested packages: 263s gcc gfortran python-numpy-doc python3-dev 263s The following NEW packages will be installed: 263s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 263s python3-all python3-click python3-colorama python3-coloredlogs 263s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 263s python3-packaging python3-pluggy python3-pytest 263s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 263s Need to get 10.2 MB/10.2 MB of archives. 263s After this operation, 44.2 MB of additional disk space will be used. 263s Get:1 /tmp/autopkgtest.4zd8W4/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 264s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 264s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-4ubuntu2 [571 kB] 264s Get:4 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 264s Get:5 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB] 264s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 265s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-all ppc64el 3.12.4-1 [884 B] 265s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 265s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-click all 8.1.7-1 [79.1 kB] 265s Get:10 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-humanfriendly all 10.0-5 [70.5 kB] 265s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-coloredlogs all 15.0.1-1 [38.2 kB] 265s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 265s Get:13 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cyvcf2 ppc64el 0.31.0-1 [876 kB] 265s Get:14 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 265s Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.1-1 [41.4 kB] 265s Get:16 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 265s Get:17 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 266s Fetched 10.2 MB in 2s (5305 kB/s) 266s Selecting previously unselected package libblas3:ppc64el. 266s (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 ... 72768 files and directories currently installed.) 266s Preparing to unpack .../00-libblas3_3.12.0-3build1_ppc64el.deb ... 266s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 266s Selecting previously unselected package libgfortran5:ppc64el. 266s Preparing to unpack .../01-libgfortran5_14.1.0-4ubuntu2_ppc64el.deb ... 266s Unpacking libgfortran5:ppc64el (14.1.0-4ubuntu2) ... 266s Selecting previously unselected package libhtscodecs2:ppc64el. 266s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 266s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 266s Selecting previously unselected package libhts3t64:ppc64el. 266s Preparing to unpack .../03-libhts3t64_1.20+ds-1_ppc64el.deb ... 266s Unpacking libhts3t64:ppc64el (1.20+ds-1) ... 266s Selecting previously unselected package liblapack3:ppc64el. 266s Preparing to unpack .../04-liblapack3_3.12.0-3build1_ppc64el.deb ... 266s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 266s Selecting previously unselected package python3-all. 266s Preparing to unpack .../05-python3-all_3.12.4-1_ppc64el.deb ... 266s Unpacking python3-all (3.12.4-1) ... 266s Selecting previously unselected package python3-colorama. 266s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 266s Unpacking python3-colorama (0.4.6-4) ... 266s Selecting previously unselected package python3-click. 266s Preparing to unpack .../07-python3-click_8.1.7-1_all.deb ... 266s Unpacking python3-click (8.1.7-1) ... 266s Selecting previously unselected package python3-humanfriendly. 266s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 266s Unpacking python3-humanfriendly (10.0-5) ... 266s Selecting previously unselected package python3-coloredlogs. 266s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 266s Unpacking python3-coloredlogs (15.0.1-1) ... 266s Selecting previously unselected package python3-numpy. 266s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 266s Unpacking python3-numpy (1:1.26.4+ds-10) ... 266s Selecting previously unselected package python3-cyvcf2. 266s Preparing to unpack .../11-python3-cyvcf2_0.31.0-1_ppc64el.deb ... 266s Unpacking python3-cyvcf2 (0.31.0-1) ... 266s Selecting previously unselected package python3-iniconfig. 266s Preparing to unpack .../12-python3-iniconfig_1.1.1-2_all.deb ... 266s Unpacking python3-iniconfig (1.1.1-2) ... 266s Selecting previously unselected package python3-packaging. 266s Preparing to unpack .../13-python3-packaging_24.1-1_all.deb ... 266s Unpacking python3-packaging (24.1-1) ... 266s Selecting previously unselected package python3-pluggy. 266s Preparing to unpack .../14-python3-pluggy_1.5.0-1_all.deb ... 266s Unpacking python3-pluggy (1.5.0-1) ... 266s Selecting previously unselected package python3-pytest. 266s Preparing to unpack .../15-python3-pytest_7.4.4-1_all.deb ... 266s Unpacking python3-pytest (7.4.4-1) ... 266s Selecting previously unselected package autopkgtest-satdep. 266s Preparing to unpack .../16-1-autopkgtest-satdep.deb ... 266s Unpacking autopkgtest-satdep (0) ... 266s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 266s Setting up python3-iniconfig (1.1.1-2) ... 267s Setting up python3-colorama (0.4.6-4) ... 267s Setting up python3-all (3.12.4-1) ... 267s Setting up python3-click (8.1.7-1) ... 267s Setting up libblas3:ppc64el (3.12.0-3build1) ... 267s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 267s Setting up python3-packaging (24.1-1) ... 267s Setting up python3-humanfriendly (10.0-5) ... 267s Setting up libgfortran5:ppc64el (14.1.0-4ubuntu2) ... 267s Setting up python3-pluggy (1.5.0-1) ... 267s Setting up libhts3t64:ppc64el (1.20+ds-1) ... 267s Setting up python3-coloredlogs (15.0.1-1) ... 268s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 268s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 268s Setting up python3-pytest (7.4.4-1) ... 268s Setting up python3-numpy (1:1.26.4+ds-10) ... 270s Setting up python3-cyvcf2 (0.31.0-1) ... 270s Setting up autopkgtest-satdep (0) ... 270s Processing triggers for man-db (2.12.1-2) ... 271s Processing triggers for libc-bin (2.39-0ubuntu9) ... 273s (Reading database ... 74030 files and directories currently installed.) 273s Removing autopkgtest-satdep (0) ... 274s autopkgtest [21:52:48]: test run-unit-test: [----------------------- 274s Testing with python3.12 in /tmp/autopkgtest.4zd8W4/autopkgtest_tmp: 274s ============================= test session starts ============================== 274s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 -- /usr/bin/python3.12 274s cachedir: .pytest_cache 274s rootdir: /tmp/autopkgtest.4zd8W4/autopkgtest_tmp 275s collecting ... collected 112 items 275s 275s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 275s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 275s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 275s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 275s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 275s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 275s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 275s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 275s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 275s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 275s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 275s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 275s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 275s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 275s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 275s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 275s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 275s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 275s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 275s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 275s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 275s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 275s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 275s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 275s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 275s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 275s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 275s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 275s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 275s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 275s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 275s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 275s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 275s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 275s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 275s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 275s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 275s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 275s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 275s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 275s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 275s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 275s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 275s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 275s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 275s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 275s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 275s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 275s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 275s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 275s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 275s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 275s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 275s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 275s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 275s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 275s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 275s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 275s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 275s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 275s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 275s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 275s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 275s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 275s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 275s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 275s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 275s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 275s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 275s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 275s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 275s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 275s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 275s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 275s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 275s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 275s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 275s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 275s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 275s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 275s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 275s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 275s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 275s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 275s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 275s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 275s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 275s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 275s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 275s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 275s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 275s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 275s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 275s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 275s 275s ============================= 112 passed in 1.26s ============================== 276s autopkgtest [21:52:50]: test run-unit-test: -----------------------] 276s autopkgtest [21:52:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 276s run-unit-test PASS 277s autopkgtest [21:52:51]: test autodep8-python3: preparing testbed 422s autopkgtest [21:55:16]: testbed dpkg architecture: ppc64el 422s autopkgtest [21:55:16]: testbed apt version: 2.9.6 422s autopkgtest [21:55:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 423s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 423s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [63.1 kB] 423s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 423s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4092 B] 423s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [401 kB] 423s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [111 kB] 423s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2116 B] 423s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 423s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 423s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [576 kB] 423s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [8952 B] 423s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1840 B] 423s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 425s Fetched 1304 kB in 1s (1476 kB/s) 425s Reading package lists... 427s Reading package lists... 427s Building dependency tree... 427s Reading state information... 427s Calculating upgrade... 428s The following packages will be upgraded: 428s libbpf1 libpython3-stdlib python3 python3-gdbm python3-minimal 428s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 428s Need to get 298 kB of archives. 428s After this operation, 71.7 kB of additional disk space will be used. 428s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-minimal ppc64el 3.12.4-1 [27.1 kB] 428s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3 ppc64el 3.12.4-1 [24.0 kB] 428s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.4-1 [9818 B] 428s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbpf1 ppc64el 1:1.4.5-1 [218 kB] 428s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-gdbm ppc64el 3.12.4-2 [18.9 kB] 428s Fetched 298 kB in 0s (702 kB/s) 428s (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 ... 72765 files and directories currently installed.) 428s Preparing to unpack .../python3-minimal_3.12.4-1_ppc64el.deb ... 428s Unpacking python3-minimal (3.12.4-1) over (3.12.3-0ubuntu1) ... 428s Setting up python3-minimal (3.12.4-1) ... 429s (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 ... 72765 files and directories currently installed.) 429s Preparing to unpack .../python3_3.12.4-1_ppc64el.deb ... 429s Unpacking python3 (3.12.4-1) over (3.12.3-0ubuntu1) ... 429s Preparing to unpack .../libpython3-stdlib_3.12.4-1_ppc64el.deb ... 429s Unpacking libpython3-stdlib:ppc64el (3.12.4-1) over (3.12.3-0ubuntu1) ... 429s Preparing to unpack .../libbpf1_1%3a1.4.5-1_ppc64el.deb ... 429s Unpacking libbpf1:ppc64el (1:1.4.5-1) over (1:1.4.3-1) ... 429s Preparing to unpack .../python3-gdbm_3.12.4-2_ppc64el.deb ... 429s Unpacking python3-gdbm:ppc64el (3.12.4-2) over (3.12.3-0ubuntu1) ... 429s Setting up libbpf1:ppc64el (1:1.4.5-1) ... 429s Setting up libpython3-stdlib:ppc64el (3.12.4-1) ... 429s Setting up python3 (3.12.4-1) ... 429s Setting up python3-gdbm:ppc64el (3.12.4-2) ... 429s Processing triggers for man-db (2.12.1-2) ... 429s Processing triggers for libc-bin (2.39-0ubuntu9) ... 430s Reading package lists... 430s Building dependency tree... 430s Reading state information... 430s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 430s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 430s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 430s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 430s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 432s Reading package lists... 432s Reading package lists... 432s Building dependency tree... 432s Reading state information... 432s Calculating upgrade... 432s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 432s Reading package lists... 432s Building dependency tree... 432s Reading state information... 432s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 488s Reading package lists... 488s Building dependency tree... 488s Reading state information... 488s Starting pkgProblemResolver with broken count: 0 488s Starting 2 pkgProblemResolver with broken count: 0 488s Done 489s The following additional packages will be installed: 489s libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 python3-all 489s python3-click python3-colorama python3-coloredlogs python3-cyvcf2 489s python3-humanfriendly python3-numpy 489s Suggested packages: 489s gcc gfortran python-numpy-doc python3-dev python3-pytest 489s The following NEW packages will be installed: 489s autopkgtest-satdep libblas3 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 489s python3-all python3-click python3-colorama python3-coloredlogs 489s python3-cyvcf2 python3-humanfriendly python3-numpy 489s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 489s Need to get 9785 kB/9785 kB of archives. 489s After this operation, 42.6 MB of additional disk space will be used. 489s Get:1 /tmp/autopkgtest.4zd8W4/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 489s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 489s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-4ubuntu2 [571 kB] 489s Get:4 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 489s Get:5 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhts3t64 ppc64el 1.20+ds-1 [567 kB] 489s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 489s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el python3-all ppc64el 3.12.4-1 [884 B] 489s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 489s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-click all 8.1.7-1 [79.1 kB] 489s Get:10 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-humanfriendly all 10.0-5 [70.5 kB] 489s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-coloredlogs all 15.0.1-1 [38.2 kB] 489s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 489s Get:13 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-cyvcf2 ppc64el 0.31.0-1 [876 kB] 490s Fetched 9785 kB in 1s (11.2 MB/s) 490s Selecting previously unselected package libblas3:ppc64el. 490s (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 ... 72768 files and directories currently installed.) 490s Preparing to unpack .../00-libblas3_3.12.0-3build1_ppc64el.deb ... 490s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 490s Selecting previously unselected package libgfortran5:ppc64el. 490s Preparing to unpack .../01-libgfortran5_14.1.0-4ubuntu2_ppc64el.deb ... 490s Unpacking libgfortran5:ppc64el (14.1.0-4ubuntu2) ... 490s Selecting previously unselected package libhtscodecs2:ppc64el. 490s Preparing to unpack .../02-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 490s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 490s Selecting previously unselected package libhts3t64:ppc64el. 490s Preparing to unpack .../03-libhts3t64_1.20+ds-1_ppc64el.deb ... 490s Unpacking libhts3t64:ppc64el (1.20+ds-1) ... 490s Selecting previously unselected package liblapack3:ppc64el. 490s Preparing to unpack .../04-liblapack3_3.12.0-3build1_ppc64el.deb ... 490s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 490s Selecting previously unselected package python3-all. 490s Preparing to unpack .../05-python3-all_3.12.4-1_ppc64el.deb ... 490s Unpacking python3-all (3.12.4-1) ... 490s Selecting previously unselected package python3-colorama. 490s Preparing to unpack .../06-python3-colorama_0.4.6-4_all.deb ... 490s Unpacking python3-colorama (0.4.6-4) ... 490s Selecting previously unselected package python3-click. 490s Preparing to unpack .../07-python3-click_8.1.7-1_all.deb ... 490s Unpacking python3-click (8.1.7-1) ... 490s Selecting previously unselected package python3-humanfriendly. 490s Preparing to unpack .../08-python3-humanfriendly_10.0-5_all.deb ... 490s Unpacking python3-humanfriendly (10.0-5) ... 490s Selecting previously unselected package python3-coloredlogs. 490s Preparing to unpack .../09-python3-coloredlogs_15.0.1-1_all.deb ... 490s Unpacking python3-coloredlogs (15.0.1-1) ... 490s Selecting previously unselected package python3-numpy. 490s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 490s Unpacking python3-numpy (1:1.26.4+ds-10) ... 490s Selecting previously unselected package python3-cyvcf2. 490s Preparing to unpack .../11-python3-cyvcf2_0.31.0-1_ppc64el.deb ... 490s Unpacking python3-cyvcf2 (0.31.0-1) ... 490s Selecting previously unselected package autopkgtest-satdep. 490s Preparing to unpack .../12-2-autopkgtest-satdep.deb ... 490s Unpacking autopkgtest-satdep (0) ... 490s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 490s Setting up python3-colorama (0.4.6-4) ... 490s Setting up python3-all (3.12.4-1) ... 490s Setting up python3-click (8.1.7-1) ... 491s Setting up libblas3:ppc64el (3.12.0-3build1) ... 491s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 491s Setting up python3-humanfriendly (10.0-5) ... 491s Setting up libgfortran5:ppc64el (14.1.0-4ubuntu2) ... 491s Setting up libhts3t64:ppc64el (1.20+ds-1) ... 491s Setting up python3-coloredlogs (15.0.1-1) ... 491s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 491s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 491s Setting up python3-numpy (1:1.26.4+ds-10) ... 493s Setting up python3-cyvcf2 (0.31.0-1) ... 493s Setting up autopkgtest-satdep (0) ... 493s Processing triggers for man-db (2.12.1-2) ... 494s Processing triggers for libc-bin (2.39-0ubuntu9) ... 518s (Reading database ... 73866 files and directories currently installed.) 518s Removing autopkgtest-satdep (0) ... 542s autopkgtest [21:57:16]: 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 542s autopkgtest [21:57:16]: test autodep8-python3: [----------------------- 542s Testing with python3.12: 542s 543s autopkgtest [21:57:17]: test autodep8-python3: -----------------------] 544s autodep8-python3 PASS (superficial) 544s autopkgtest [21:57:18]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 545s autopkgtest [21:57:19]: @@@@@@@@@@@@@@@@@@@@ summary 545s run-unit-test PASS 545s autodep8-python3 PASS (superficial) 578s nova [W] Using flock in scalingstack-bos01-ppc64el 578s Creating nova instance adt-oracular-ppc64el-cyvcf2-20240720-214813-juju-7f2275-prod-proposed-migration-environment-2-51e5d10f-bfea-4b18-985f-99af6b02b54e from image adt/ubuntu-oracular-ppc64el-server-20240720.img (UUID 9e0d1223-8d9c-4f47-a977-7dfc1ecc813d)... 578s nova [W] Using flock in scalingstack-bos01-ppc64el 578s Creating nova instance adt-oracular-ppc64el-cyvcf2-20240720-214813-juju-7f2275-prod-proposed-migration-environment-2-51e5d10f-bfea-4b18-985f-99af6b02b54e from image adt/ubuntu-oracular-ppc64el-server-20240720.img (UUID 9e0d1223-8d9c-4f47-a977-7dfc1ecc813d)...