0s autopkgtest [22:17:04]: starting date and time: 2024-03-25 22:17:04+0000 0s autopkgtest [22:17:04]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [22:17:04]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.efqhtd3d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=cyvcf2/0.30.28-1build1 curl/8.5.0-2ubuntu8 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-19.secgroup --name adt-noble-s390x-cyvcf2-20240325-221704-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 138s autopkgtest [22:19:22]: testbed dpkg architecture: s390x 138s autopkgtest [22:19:22]: testbed apt version: 2.7.12 138s autopkgtest [22:19:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 139s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 140s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 140s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 141s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 141s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 141s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 141s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 141s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 141s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 141s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 142s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 142s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 142s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 144s Fetched 9546 kB in 4s (2477 kB/s) 144s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Calculating upgrade... 146s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 147s Unknown architecture, assuming PC-style ttyS0 147s sh: Attempting to set up Debian/Ubuntu apt sources automatically 147s sh: Distribution appears to be Ubuntu 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s eatmydata is already the newest version (131-1). 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 148s Building dependency tree... 148s Reading state information... 148s dbus is already the newest version (1.14.10-4ubuntu1). 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s rng-tools-debian is already the newest version (2.4). 149s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s The following packages will be REMOVED: 149s cloud-init* python3-configobj* python3-debconf* 149s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 149s After this operation, 3256 kB disk space will be freed. 149s (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 ... 52170 files and directories currently installed.) 149s Removing cloud-init (24.1.2-0ubuntu1) ... 150s Removing python3-configobj (5.0.8-3) ... 150s Removing python3-debconf (1.5.86) ... 150s Processing triggers for man-db (2.12.0-3) ... 150s (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 ... 51781 files and directories currently installed.) 150s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 151s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 151s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 151s invoke-rc.d: policy-rc.d denied execution of try-restart. 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s linux-generic is already the newest version (6.8.0-11.11+1). 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 152s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 152s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 152s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 154s Reading package lists... 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Calculating upgrade... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s autopkgtest [22:19:39]: rebooting testbed after setup commands that affected boot 170s autopkgtest [22:19:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 172s autopkgtest [22:19:56]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 174s Get:1 http://ftpmaster.internal/ubuntu noble/universe cyvcf2 0.30.28-1 (dsc) [2426 B] 174s Get:2 http://ftpmaster.internal/ubuntu noble/universe cyvcf2 0.30.28-1 (tar) [420 kB] 174s Get:3 http://ftpmaster.internal/ubuntu noble/universe cyvcf2 0.30.28-1 (diff) [6612 B] 174s gpgv: Signature made Sun Feb 18 08:27:59 2024 UTC 174s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 174s gpgv: Can't check signature: No public key 174s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.30.28-1.dsc: no acceptable signature found 174s autopkgtest [22:19:58]: testing package cyvcf2 version 0.30.28-1 175s autopkgtest [22:19:59]: build not needed 175s autopkgtest [22:19:59]: test run-unit-test: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 178s Starting pkgProblemResolver with broken count: 0 178s Starting 2 pkgProblemResolver with broken count: 0 178s Done 178s The following additional packages will be installed: 178s libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 liblapack3 178s python3-all python3-click python3-colorama python3-coloredlogs 178s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 178s python3-packaging python3-pluggy python3-pytest 178s Suggested packages: 178s gcc gfortran python3-dev 178s The following NEW packages will be installed: 178s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 178s liblapack3 python3-all python3-click python3-colorama python3-coloredlogs 178s python3-cyvcf2 python3-humanfriendly python3-iniconfig python3-numpy 178s python3-packaging python3-pluggy python3-pytest 178s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 11.2 MB/11.2 MB of archives. 178s After this operation, 51.1 MB of additional disk space will be used. 178s Get:1 /tmp/autopkgtest.7XQUTs/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 179s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 180s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 180s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 180s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 180s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 180s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 181s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x python3-all s390x 3.12.1-0ubuntu2 [908 B] 181s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 181s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x python3-click all 8.1.6-1 [79.0 kB] 181s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x python3-humanfriendly all 10.0-4 [70.5 kB] 181s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 181s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 182s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x python3-cyvcf2 s390x 0.30.28-1 [1041 kB] 183s Get:15 http://ftpmaster.internal/ubuntu noble/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 183s Get:16 http://ftpmaster.internal/ubuntu noble/main s390x python3-packaging all 23.2-1 [40.6 kB] 183s Get:17 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pluggy all 1.4.0-1 [20.4 kB] 183s Get:18 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pytest all 7.4.4-1 [305 kB] 183s Fetched 11.2 MB in 5s (2402 kB/s) 183s Selecting previously unselected package libblas3:s390x. 183s (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 ... 51726 files and directories currently installed.) 183s Preparing to unpack .../00-libblas3_3.12.0-3_s390x.deb ... 183s Unpacking libblas3:s390x (3.12.0-3) ... 183s Selecting previously unselected package libdeflate0:s390x. 183s Preparing to unpack .../01-libdeflate0_1.19-1_s390x.deb ... 183s Unpacking libdeflate0:s390x (1.19-1) ... 183s Selecting previously unselected package libgfortran5:s390x. 183s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 183s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 183s Selecting previously unselected package libhtscodecs2:s390x. 183s Preparing to unpack .../03-libhtscodecs2_1.6.0-1_s390x.deb ... 183s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 183s Selecting previously unselected package libhts3:s390x. 183s Preparing to unpack .../04-libhts3_1.18+ds-1_s390x.deb ... 183s Unpacking libhts3:s390x (1.18+ds-1) ... 183s Selecting previously unselected package liblapack3:s390x. 183s Preparing to unpack .../05-liblapack3_3.12.0-3_s390x.deb ... 183s Unpacking liblapack3:s390x (3.12.0-3) ... 183s Selecting previously unselected package python3-all. 183s Preparing to unpack .../06-python3-all_3.12.1-0ubuntu2_s390x.deb ... 183s Unpacking python3-all (3.12.1-0ubuntu2) ... 183s Selecting previously unselected package python3-colorama. 183s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 183s Unpacking python3-colorama (0.4.6-4) ... 183s Selecting previously unselected package python3-click. 183s Preparing to unpack .../08-python3-click_8.1.6-1_all.deb ... 183s Unpacking python3-click (8.1.6-1) ... 183s Selecting previously unselected package python3-humanfriendly. 183s Preparing to unpack .../09-python3-humanfriendly_10.0-4_all.deb ... 183s Unpacking python3-humanfriendly (10.0-4) ... 183s Selecting previously unselected package python3-coloredlogs. 183s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 183s Unpacking python3-coloredlogs (15.0.1-1) ... 183s Selecting previously unselected package python3-numpy. 183s Preparing to unpack .../11-python3-numpy_1%3a1.24.2-2_s390x.deb ... 183s Unpacking python3-numpy (1:1.24.2-2) ... 184s Selecting previously unselected package python3-cyvcf2. 184s Preparing to unpack .../12-python3-cyvcf2_0.30.28-1_s390x.deb ... 184s Unpacking python3-cyvcf2 (0.30.28-1) ... 184s Selecting previously unselected package python3-iniconfig. 184s Preparing to unpack .../13-python3-iniconfig_1.1.1-2_all.deb ... 184s Unpacking python3-iniconfig (1.1.1-2) ... 184s Selecting previously unselected package python3-packaging. 184s Preparing to unpack .../14-python3-packaging_23.2-1_all.deb ... 184s Unpacking python3-packaging (23.2-1) ... 184s Selecting previously unselected package python3-pluggy. 184s Preparing to unpack .../15-python3-pluggy_1.4.0-1_all.deb ... 184s Unpacking python3-pluggy (1.4.0-1) ... 184s Selecting previously unselected package python3-pytest. 184s Preparing to unpack .../16-python3-pytest_7.4.4-1_all.deb ... 184s Unpacking python3-pytest (7.4.4-1) ... 184s Selecting previously unselected package autopkgtest-satdep. 184s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 184s Unpacking autopkgtest-satdep (0) ... 184s Setting up libhtscodecs2:s390x (1.6.0-1) ... 184s Setting up python3-iniconfig (1.1.1-2) ... 184s Setting up python3-colorama (0.4.6-4) ... 184s Setting up libdeflate0:s390x (1.19-1) ... 184s Setting up python3-all (3.12.1-0ubuntu2) ... 184s Setting up python3-click (8.1.6-1) ... 184s Setting up libblas3:s390x (3.12.0-3) ... 184s 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 184s Setting up python3-packaging (23.2-1) ... 184s Setting up python3-humanfriendly (10.0-4) ... 184s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 184s Setting up python3-pluggy (1.4.0-1) ... 185s Setting up python3-coloredlogs (15.0.1-1) ... 185s Setting up liblapack3:s390x (3.12.0-3) ... 185s 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 185s Setting up libhts3:s390x (1.18+ds-1) ... 185s Setting up python3-pytest (7.4.4-1) ... 185s Setting up python3-numpy (1:1.24.2-2) ... 187s Setting up python3-cyvcf2 (0.30.28-1) ... 187s Setting up autopkgtest-satdep (0) ... 187s Processing triggers for man-db (2.12.0-3) ... 187s Processing triggers for libc-bin (2.39-0ubuntu6) ... 190s (Reading database ... 53114 files and directories currently installed.) 190s Removing autopkgtest-satdep (0) ... 190s autopkgtest [22:20:14]: test run-unit-test: [----------------------- 191s Testing with python3.12 in /tmp/autopkgtest.7XQUTs/autopkgtest_tmp: 191s ============================= test session starts ============================== 191s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3.12 191s cachedir: .pytest_cache 191s rootdir: /tmp/autopkgtest.7XQUTs/autopkgtest_tmp 191s collecting ... collected 112 items 191s 191s cyvcf2/tests/test_cli.py::test_version PASSED [ 0%] 191s cyvcf2/tests/test_hemi.py::test_hemi PASSED [ 1%] 191s cyvcf2/tests/test_reader.py::test_init PASSED [ 2%] 191s cyvcf2/tests/test_reader.py::test_type PASSED [ 3%] 191s cyvcf2/tests/test_reader.py::test_type_mnp PASSED [ 4%] 191s cyvcf2/tests/test_reader.py::test_format_str PASSED [ 5%] 191s cyvcf2/tests/test_reader.py::test_missing_samples PASSED [ 6%] 191s cyvcf2/tests/test_reader.py::test_ibd PASSED [ 7%] 191s cyvcf2/tests/test_reader.py::test_relatedness PASSED [ 8%] 191s cyvcf2/tests/test_reader.py::test_pls PASSED [ 8%] 191s cyvcf2/tests/test_reader.py::test_gt_alt_freqs PASSED [ 9%] 191s cyvcf2/tests/test_reader.py::test_str PASSED [ 10%] 191s cyvcf2/tests/test_reader.py::test_region PASSED [ 11%] 191s cyvcf2/tests/test_reader.py::test_empty_info PASSED [ 12%] 191s cyvcf2/tests/test_reader.py::test_phases PASSED [ 13%] 191s cyvcf2/tests/test_reader.py::test_bad_init PASSED [ 14%] 191s cyvcf2/tests/test_reader.py::test_samples PASSED [ 15%] 191s cyvcf2/tests/test_reader.py::test_next PASSED [ 16%] 191s cyvcf2/tests/test_reader.py::test_variant PASSED [ 16%] 191s cyvcf2/tests/test_reader.py::test_info_dict PASSED [ 17%] 191s cyvcf2/tests/test_reader.py::test_attrs PASSED [ 18%] 191s cyvcf2/tests/test_reader.py::test_empty PASSED [ 19%] 191s cyvcf2/tests/test_reader.py::test_format_field PASSED [ 20%] 191s cyvcf2/tests/test_reader.py::test_writer_from_string PASSED [ 21%] 191s cyvcf2/tests/test_reader.py::test_isa PASSED [ 22%] 191s cyvcf2/tests/test_reader.py::test_writer PASSED [ 23%] 191s cyvcf2/tests/test_reader.py::test_filters PASSED [ 24%] 191s cyvcf2/tests/test_reader.py::test_add_info_to_header PASSED [ 25%] 191s cyvcf2/tests/test_reader.py::test_read_flag PASSED [ 25%] 191s cyvcf2/tests/test_reader.py::test_add_flag PASSED [ 26%] 191s cyvcf2/tests/test_reader.py::test_issue198 PASSED [ 27%] 191s cyvcf2/tests/test_reader.py::test_constants PASSED [ 28%] 191s cyvcf2/tests/test_reader.py::test_add_filter_to_header PASSED [ 29%] 191s cyvcf2/tests/test_reader.py::test_seqnames PASSED [ 30%] 191s cyvcf2/tests/test_reader.py::test_different_index PASSED [ 31%] 191s cyvcf2/tests/test_reader.py::test_var_type PASSED [ 32%] 191s cyvcf2/tests/test_reader.py::test_header_info PASSED [ 33%] 191s cyvcf2/tests/test_reader.py::test_snpeff_header PASSED [ 33%] 192s cyvcf2/tests/test_reader.py::test_gt_types PASSED [ 34%] 192s cyvcf2/tests/test_reader.py::test_raw_header PASSED [ 35%] 192s cyvcf2/tests/test_reader.py::test_iterate PASSED [ 36%] 192s cyvcf2/tests/test_reader.py::test_empty_call PASSED [ 37%] 192s cyvcf2/tests/test_reader.py::test_haploid PASSED [ 38%] 192s cyvcf2/tests/test_reader.py::test_diploid PASSED [ 39%] 192s cyvcf2/tests/test_reader.py::test_format PASSED [ 40%] 192s cyvcf2/tests/test_reader.py::test_header_stuff PASSED [ 41%] 192s cyvcf2/tests/test_reader.py::test_bcf PASSED [ 41%] 192s cyvcf2/tests/test_reader.py::test_vcf_no_intervals PASSED [ 42%] 192s cyvcf2/tests/test_reader.py::test_issue12 PASSED [ 43%] 192s cyvcf2/tests/test_reader.py::test_gt_bases_nondiploid PASSED [ 44%] 192s cyvcf2/tests/test_reader.py::test_set_format_float PASSED [ 45%] 192s cyvcf2/tests/test_reader.py::test_set_format_int_a PASSED [ 46%] 192s cyvcf2/tests/test_reader.py::test_set_format_int_b PASSED [ 47%] 192s cyvcf2/tests/test_reader.py::test_set_format_int_c PASSED [ 48%] 192s cyvcf2/tests/test_reader.py::test_set_format_int3 PASSED [ 49%] 192s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_second_longer PASSED [ 50%] 192s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_first_longer PASSED [ 50%] 192s cyvcf2/tests/test_reader.py::test_set_format_str_bytes_number3 PASSED [ 51%] 192s cyvcf2/tests/test_reader.py::test_set_gts PASSED [ 52%] 192s cyvcf2/tests/test_reader.py::test_info_del PASSED [ 53%] 192s cyvcf2/tests/test_reader.py::test_filter_id PASSED [ 54%] 192s cyvcf2/tests/test_reader.py::test_access_gts PASSED [ 55%] 192s cyvcf2/tests/test_reader.py::test_access_genotype PASSED [ 56%] 192s cyvcf2/tests/test_reader.py::test_access_genotype_array PASSED [ 57%] 192s cyvcf2/tests/test_reader.py::test_alt_homozygous_gt PASSED [ 58%] 192s cyvcf2/tests/test_reader.py::test_write_missing_contig PASSED [ 58%] 192s cyvcf2/tests/test_reader.py::test_set_samples PASSED [ 59%] 192s cyvcf2/tests/test_reader.py::test_hrec PASSED [ 60%] 192s cyvcf2/tests/test_reader.py::test_issue44 PASSED [ 61%] 192s cyvcf2/tests/test_reader.py::test_id_field_updates PASSED [ 62%] 192s cyvcf2/tests/test_reader.py::test_set_pos PASSED [ 63%] 192s cyvcf2/tests/test_reader.py::test_set_chrom_when_contig_not_in_header PASSED [ 64%] 192s cyvcf2/tests/test_reader.py::test_set_chrom_after_contig_is_added_to_header PASSED [ 65%] 192s cyvcf2/tests/test_reader.py::test_set_qual PASSED [ 66%] 192s cyvcf2/tests/test_reader.py::test_strict_gt_option_flag PASSED [ 66%] 192s cyvcf2/tests/test_reader.py::test_alt_repr PASSED [ 67%] 192s cyvcf2/tests/test_reader.py::test_closed_iter PASSED [ 68%] 192s cyvcf2/tests/test_reader.py::test_issue72 PASSED [ 69%] 192s cyvcf2/tests/test_reader.py::test_is_transition PASSED [ 70%] 192s cyvcf2/tests/test_reader.py::test_decomposed PASSED [ 71%] 192s cyvcf2/tests/test_reader.py::test_fd PASSED [ 72%] 192s cyvcf2/tests/test_reader.py::test_set_reference PASSED [ 73%] 192s cyvcf2/tests/test_reader.py::test_set_alternates PASSED [ 74%] 192s cyvcf2/tests/test_reader.py::test_no_seqlen PASSED [ 75%] 192s cyvcf2/tests/test_reader.py::test_set_unknown_format PASSED [ 75%] 192s cyvcf2/tests/test_reader.py::test_invalid_header PASSED [ 76%] 192s cyvcf2/tests/test_reader.py::test_genotypes PASSED [ 77%] 192s cyvcf2/tests/test_reader.py::test_issue236 PASSED [ 78%] 192s cyvcf2/tests/test_reader.py::test_issue17_no_gt PASSED [ 79%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.vcf.gz] PASSED [ 80%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-multiallelic-homozygous-alt.vcf.gz] PASSED [ 81%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz0] PASSED [ 82%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[test-strict-gt-option-flag.vcf.gz1] PASSED [ 83%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.vcf.gz] PASSED [ 83%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[multi-contig.bcf] PASSED [ 84%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed[test.snpeff.bcf] PASSED [ 85%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[csi] PASSED [ 86%] 192s cyvcf2/tests/test_reader.py::test_num_records_indexed_csi_tabix[tbi] PASSED [ 87%] 192s cyvcf2/tests/test_reader.py::test_num_records_set_index_multiple_times PASSED [ 88%] 192s cyvcf2/tests/test_reader.py::test_num_records_set_wrong_index PASSED [ 89%] 192s cyvcf2/tests/test_reader.py::test_num_records_no_index[test-genotypes.vcf] PASSED [ 90%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithVcfFname_returnsUncompressedVcf PASSED [ 91%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFname_returnsCompressedBcf PASSED [ 91%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf PASSED [ 92%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedBcfFname_returnsCompressedBcf PASSED [ 93%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithCompressedVcfFname_returnsCompressedVcf PASSED [ 94%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithStdOut_returnsUncompressedVcf PASSED [ 95%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithNonVcfName_returnsUncompressedVcf PASSED [ 96%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithIntFname_returnsUncompressedVcf PASSED [ 97%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithHandle_returnsUncompressedVcf PASSED [ 98%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_defaultModeWithPosixPath_returnsUncompressedVcf PASSED [ 99%] 192s cyvcf2/tests/test_writer.py::TestFileModeInference::test_explicitMode_doesNotInferFromFname PASSED [100%] 192s 192s ============================= 112 passed in 1.16s ============================== 192s autopkgtest [22:20:16]: test run-unit-test: -----------------------] 193s autopkgtest [22:20:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 193s run-unit-test PASS 193s autopkgtest [22:20:17]: test autodep8-python3: preparing testbed 448s autopkgtest [22:24:32]: testbed dpkg architecture: s390x 448s autopkgtest [22:24:32]: testbed apt version: 2.7.12 448s autopkgtest [22:24:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 449s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 449s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7608 B] 449s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB] 449s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3981 kB] 452s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB] 452s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [692 kB] 452s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 452s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 452s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 452s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4136 kB] 453s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 453s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.8 kB] 453s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 455s Fetched 9546 kB in 5s (1863 kB/s) 455s Reading package lists... 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 457s Calculating upgrade... 457s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 458s 0 upgraded, 0 newly installed, 0 to remove and 242 not upgraded. 458s Unknown architecture, assuming PC-style ttyS0 458s sh: Attempting to set up Debian/Ubuntu apt sources automatically 458s sh: Distribution appears to be Ubuntu 459s Reading package lists... 459s Building dependency tree... 459s Reading state information... 459s eatmydata is already the newest version (131-1). 459s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 459s Reading package lists... 459s Building dependency tree... 459s Reading state information... 459s dbus is already the newest version (1.14.10-4ubuntu1). 459s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 459s Reading package lists... 460s Building dependency tree... 460s Reading state information... 460s rng-tools-debian is already the newest version (2.4). 460s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 460s Reading package lists... 460s Building dependency tree... 460s Reading state information... 460s The following packages will be REMOVED: 460s cloud-init* python3-configobj* python3-debconf* 460s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 460s After this operation, 3256 kB disk space will be freed. 460s (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 ... 52170 files and directories currently installed.) 460s Removing cloud-init (24.1.2-0ubuntu1) ... 461s Removing python3-configobj (5.0.8-3) ... 461s Removing python3-debconf (1.5.86) ... 461s Processing triggers for man-db (2.12.0-3) ... 461s (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 ... 51781 files and directories currently installed.) 461s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 462s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 462s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 462s invoke-rc.d: policy-rc.d denied execution of try-restart. 462s Reading package lists... 462s Building dependency tree... 462s Reading state information... 462s linux-generic is already the newest version (6.8.0-11.11+1). 462s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 463s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 463s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 463s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 465s Reading package lists... 465s Reading package lists... 465s Building dependency tree... 465s Reading state information... 465s Calculating upgrade... 465s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 465s Reading package lists... 465s Building dependency tree... 465s Reading state information... 466s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 466s autopkgtest [22:24:50]: rebooting testbed after setup commands that affected boot 505s Reading package lists... 505s Building dependency tree... 505s Reading state information... 506s Starting pkgProblemResolver with broken count: 0 506s Starting 2 pkgProblemResolver with broken count: 0 506s Done 506s The following additional packages will be installed: 506s libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 liblapack3 506s python3-all python3-click python3-colorama python3-coloredlogs 506s python3-cyvcf2 python3-humanfriendly python3-numpy 506s Suggested packages: 506s gcc gfortran python3-dev python3-pytest 506s The following NEW packages will be installed: 506s autopkgtest-satdep libblas3 libdeflate0 libgfortran5 libhts3 libhtscodecs2 506s liblapack3 python3-all python3-click python3-colorama python3-coloredlogs 506s python3-cyvcf2 python3-humanfriendly python3-numpy 506s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 506s Need to get 10.8 MB/10.8 MB of archives. 506s After this operation, 49.6 MB of additional disk space will be used. 506s Get:1 /tmp/autopkgtest.7XQUTs/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 506s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 506s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 506s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 506s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 507s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 507s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 507s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x python3-all s390x 3.12.1-0ubuntu2 [908 B] 507s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 507s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x python3-click all 8.1.6-1 [79.0 kB] 507s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x python3-humanfriendly all 10.0-4 [70.5 kB] 507s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 507s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 508s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x python3-cyvcf2 s390x 0.30.28-1 [1041 kB] 508s Fetched 10.8 MB in 2s (5676 kB/s) 508s Selecting previously unselected package libblas3:s390x. 508s (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 ... 51726 files and directories currently installed.) 508s Preparing to unpack .../00-libblas3_3.12.0-3_s390x.deb ... 508s Unpacking libblas3:s390x (3.12.0-3) ... 508s Selecting previously unselected package libdeflate0:s390x. 508s Preparing to unpack .../01-libdeflate0_1.19-1_s390x.deb ... 508s Unpacking libdeflate0:s390x (1.19-1) ... 508s Selecting previously unselected package libgfortran5:s390x. 508s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 508s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 508s Selecting previously unselected package libhtscodecs2:s390x. 508s Preparing to unpack .../03-libhtscodecs2_1.6.0-1_s390x.deb ... 508s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 508s Selecting previously unselected package libhts3:s390x. 508s Preparing to unpack .../04-libhts3_1.18+ds-1_s390x.deb ... 508s Unpacking libhts3:s390x (1.18+ds-1) ... 508s Selecting previously unselected package liblapack3:s390x. 508s Preparing to unpack .../05-liblapack3_3.12.0-3_s390x.deb ... 508s Unpacking liblapack3:s390x (3.12.0-3) ... 508s Selecting previously unselected package python3-all. 508s Preparing to unpack .../06-python3-all_3.12.1-0ubuntu2_s390x.deb ... 508s Unpacking python3-all (3.12.1-0ubuntu2) ... 508s Selecting previously unselected package python3-colorama. 508s Preparing to unpack .../07-python3-colorama_0.4.6-4_all.deb ... 508s Unpacking python3-colorama (0.4.6-4) ... 508s Selecting previously unselected package python3-click. 508s Preparing to unpack .../08-python3-click_8.1.6-1_all.deb ... 508s Unpacking python3-click (8.1.6-1) ... 508s Selecting previously unselected package python3-humanfriendly. 508s Preparing to unpack .../09-python3-humanfriendly_10.0-4_all.deb ... 508s Unpacking python3-humanfriendly (10.0-4) ... 508s Selecting previously unselected package python3-coloredlogs. 508s Preparing to unpack .../10-python3-coloredlogs_15.0.1-1_all.deb ... 508s Unpacking python3-coloredlogs (15.0.1-1) ... 508s Selecting previously unselected package python3-numpy. 508s Preparing to unpack .../11-python3-numpy_1%3a1.24.2-2_s390x.deb ... 508s Unpacking python3-numpy (1:1.24.2-2) ... 509s Selecting previously unselected package python3-cyvcf2. 509s Preparing to unpack .../12-python3-cyvcf2_0.30.28-1_s390x.deb ... 509s Unpacking python3-cyvcf2 (0.30.28-1) ... 509s Selecting previously unselected package autopkgtest-satdep. 509s Preparing to unpack .../13-2-autopkgtest-satdep.deb ... 509s Unpacking autopkgtest-satdep (0) ... 509s Setting up libhtscodecs2:s390x (1.6.0-1) ... 509s Setting up python3-colorama (0.4.6-4) ... 509s Setting up libdeflate0:s390x (1.19-1) ... 509s Setting up python3-all (3.12.1-0ubuntu2) ... 509s Setting up python3-click (8.1.6-1) ... 509s Setting up libblas3:s390x (3.12.0-3) ... 509s 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 509s Setting up python3-humanfriendly (10.0-4) ... 509s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 509s Setting up python3-coloredlogs (15.0.1-1) ... 509s Setting up liblapack3:s390x (3.12.0-3) ... 509s 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 509s Setting up libhts3:s390x (1.18+ds-1) ... 509s Setting up python3-numpy (1:1.24.2-2) ... 511s Setting up python3-cyvcf2 (0.30.28-1) ... 511s Setting up autopkgtest-satdep (0) ... 511s Processing triggers for man-db (2.12.0-3) ... 512s Processing triggers for libc-bin (2.39-0ubuntu6) ... 514s (Reading database ... 52950 files and directories currently installed.) 514s Removing autopkgtest-satdep (0) ... 516s autopkgtest [22:25:40]: 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 516s autopkgtest [22:25:40]: test autodep8-python3: [----------------------- 516s Testing with python3.12: 517s 517s autopkgtest [22:25:41]: test autodep8-python3: -----------------------] 517s autodep8-python3 PASS (superficial) 517s autopkgtest [22:25:41]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 518s autopkgtest [22:25:42]: @@@@@@@@@@@@@@@@@@@@ summary 518s run-unit-test PASS 518s autodep8-python3 PASS (superficial) 531s Creating nova instance adt-noble-s390x-cyvcf2-20240325-221704-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)... 531s Creating nova instance adt-noble-s390x-cyvcf2-20240325-221704-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240325.img (UUID 9f25d9bc-613c-4979-9452-2ea8e4d84cd0)...