0s autopkgtest [11:55:36]: starting date and time: 2024-11-13 11:55:36+0000 0s autopkgtest [11:55:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [11:55:36]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oofm8ehw/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 minimap2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-4.secgroup --name adt-plucky-s390x-minimap2-20241113-115536-juju-7f2275-prod-proposed-migration-environment-15-4ba88272-7251-4ca6-8325-fdc1577c2546 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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://ftpmaster.internal/ubuntu/ 104s autopkgtest [11:57:20]: testbed dpkg architecture: s390x 104s autopkgtest [11:57:20]: testbed apt version: 2.9.8 104s autopkgtest [11:57:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 105s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 105s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 106s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 106s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [85.8 kB] 106s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [565 kB] 106s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [16.6 kB] 106s Fetched 1689 kB in 1s (2146 kB/s) 106s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Calculating upgrade... 108s The following NEW packages will be installed: 108s python3.13-gdbm 108s The following packages will be upgraded: 108s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 109s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 252 kB of archives. 109s After this operation, 98.3 kB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 109s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 109s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 109s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 109s Fetched 252 kB in 0s (536 kB/s) 109s (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 ... 55510 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 109s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Setting up python3-minimal (3.12.7-1) ... 110s (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 ... 55510 files and directories currently installed.) 110s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 110s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 110s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 110s Selecting previously unselected package python3.13-gdbm. 110s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ... 110s Unpacking python3.13-gdbm (3.13.0-2) ... 110s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ... 110s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 110s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 110s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 110s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 110s Setting up python3.13-gdbm (3.13.0-2) ... 110s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 110s Setting up python3 (3.12.7-1) ... 110s Setting up python3-gdbm:s390x (3.12.7-1) ... 110s Processing triggers for man-db (2.12.1-3) ... 110s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 111s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 111s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 112s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [11:57:31]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 116s autopkgtest [11:57:32]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 118s Get:1 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (dsc) [2315 B] 118s Get:2 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (tar) [200 kB] 118s Get:3 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (diff) [11.5 kB] 118s gpgv: Signature made Mon Mar 18 16:37:53 2024 UTC 118s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 118s gpgv: Can't check signature: No public key 118s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: no acceptable signature found 118s autopkgtest [11:57:34]: testing package minimap2 version 2.27+dfsg-1 118s autopkgtest [11:57:34]: build not needed 119s autopkgtest [11:57:35]: test run-unit-test: preparing testbed 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Starting pkgProblemResolver with broken count: 0 122s Starting 2 pkgProblemResolver with broken count: 0 122s Done 122s The following additional packages will be installed: 122s libminimap2-dev minimap2 python3-mappy zlib1g-dev 122s The following NEW packages will be installed: 122s autopkgtest-satdep libminimap2-dev minimap2 python3-mappy zlib1g-dev 122s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 122s Need to get 1650 kB/1651 kB of archives. 122s After this operation, 2818 kB of additional disk space will be used. 122s Get:1 /tmp/autopkgtest.n7dozg/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 122s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-1ubuntu1 [898 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libminimap2-dev s390x 2.27+dfsg-1 [144 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x minimap2 s390x 2.27+dfsg-1 [400 kB] 123s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-mappy s390x 2.27+dfsg-1 [208 kB] 123s Fetched 1650 kB in 1s (2631 kB/s) 123s Selecting previously unselected package zlib1g-dev:s390x. 123s (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 ... 55517 files and directories currently installed.) 123s Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_s390x.deb ... 123s Unpacking zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 123s Selecting previously unselected package libminimap2-dev. 123s Preparing to unpack .../libminimap2-dev_2.27+dfsg-1_s390x.deb ... 123s Unpacking libminimap2-dev (2.27+dfsg-1) ... 123s Selecting previously unselected package minimap2. 123s Preparing to unpack .../minimap2_2.27+dfsg-1_s390x.deb ... 123s Unpacking minimap2 (2.27+dfsg-1) ... 123s Selecting previously unselected package python3-mappy. 123s Preparing to unpack .../python3-mappy_2.27+dfsg-1_s390x.deb ... 123s Unpacking python3-mappy (2.27+dfsg-1) ... 123s Selecting previously unselected package autopkgtest-satdep. 123s Preparing to unpack .../1-autopkgtest-satdep.deb ... 123s Unpacking autopkgtest-satdep (0) ... 123s Setting up minimap2 (2.27+dfsg-1) ... 123s Setting up python3-mappy (2.27+dfsg-1) ... 123s Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 123s Setting up libminimap2-dev (2.27+dfsg-1) ... 123s Setting up autopkgtest-satdep (0) ... 123s Processing triggers for man-db (2.12.1-3) ... 125s (Reading database ... 55594 files and directories currently installed.) 125s Removing autopkgtest-satdep (0) ... 126s autopkgtest [11:57:42]: test run-unit-test: [----------------------- 126s [M::mm_idx_gen::0.001*0.33] collected minimizers 126s [M::mm_idx_gen::0.002*0.53] sorted minimizers 126s [M::main::0.002*0.53] loaded/built the index for 1 target sequence(s) 126s [M::mm_mapopt_update::0.002*0.49] mid_occ = 10 126s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 126s [M::mm_idx_stat::0.002*0.47] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 126s [M::worker_pipeline::0.057*0.97] mapped 1 sequences 126s [M::main] Version: 2.27-r1193 126s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 126s [M::main] Real time: 0.058 sec; CPU: 0.055 sec; Peak RSS: 0.005 GB 126s [M::mm_idx_gen::0.001*0.37] collected minimizers 126s [M::mm_idx_gen::0.002*0.63] sorted minimizers 126s [M::main::0.003*0.45] loaded/built the index for 1 target sequence(s) 126s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 126s [M::mm_idx_stat::0.003*0.43] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 126s [M::main] Version: 2.27-r1193 126s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 126s [M::main] Real time: 0.004 sec; CPU: 0.001 sec; Peak RSS: 0.003 GB 126s [M::main::0.002*0.00] loaded/built the index for 1 target sequence(s) 126s [M::mm_mapopt_update::0.002*0.00] mid_occ = 10 126s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 126s [M::mm_idx_stat::0.002*0.00] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 126s [M::worker_pipeline::0.056*0.97] mapped 1 sequences 126s [M::main] Version: 2.27-r1193 126s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 126s [M::main] Real time: 0.057 sec; CPU: 0.054 sec; Peak RSS: 0.005 GB 127s autopkgtest [11:57:43]: test run-unit-test: -----------------------] 127s autopkgtest [11:57:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 127s run-unit-test PASS 127s autopkgtest [11:57:43]: test command1: preparing testbed 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s Starting pkgProblemResolver with broken count: 0 130s Starting 2 pkgProblemResolver with broken count: 0 130s Done 130s The following additional packages will be installed: 130s libpython3.13-minimal libpython3.13-stdlib python3-all python3.13 130s python3.13-minimal 130s Suggested packages: 130s python3.13-venv python3.13-doc binfmt-support 130s The following NEW packages will be installed: 130s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 130s python3.13 python3.13-minimal 130s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 5856 kB/5856 kB of archives. 130s After this operation, 22.5 MB of additional disk space will be used. 130s Get:1 /tmp/autopkgtest.n7dozg/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 130s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 131s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 131s Fetched 5856 kB in 1s (7070 kB/s) 131s Selecting previously unselected package libpython3.13-minimal:s390x. 131s (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 ... 55594 files and directories currently installed.) 131s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_s390x.deb ... 131s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 131s Selecting previously unselected package python3.13-minimal. 131s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_s390x.deb ... 131s Unpacking python3.13-minimal (3.13.0-2) ... 131s Selecting previously unselected package libpython3.13-stdlib:s390x. 131s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 131s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 132s Selecting previously unselected package python3.13. 132s Preparing to unpack .../3-python3.13_3.13.0-2_s390x.deb ... 132s Unpacking python3.13 (3.13.0-2) ... 132s Selecting previously unselected package python3-all. 132s Preparing to unpack .../4-python3-all_3.12.7-1_s390x.deb ... 132s Unpacking python3-all (3.12.7-1) ... 132s Selecting previously unselected package autopkgtest-satdep. 132s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 132s Unpacking autopkgtest-satdep (0) ... 132s Setting up libpython3.13-minimal:s390x (3.13.0-2) ... 132s Setting up python3.13-minimal (3.13.0-2) ... 133s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 133s Setting up python3.13 (3.13.0-2) ... 134s Setting up python3-all (3.12.7-1) ... 134s Setting up autopkgtest-satdep (0) ... 134s Processing triggers for man-db (2.12.1-3) ... 134s Processing triggers for systemd (256.5-2ubuntu4) ... 136s (Reading database ... 56329 files and directories currently installed.) 136s Removing autopkgtest-satdep (0) ... 137s autopkgtest [11:57:53]: test command1: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import mappy; print(mappy)" ; done 137s autopkgtest [11:57:53]: test command1: [----------------------- 137s Testing with python3.13: 137s Traceback (most recent call last): 137s File "", line 1, in 137s import mappy; print(mappy) 137s ^^^^^^^^^^^^ 137s ModuleNotFoundError: No module named 'mappy' 137s autopkgtest [11:57:53]: test command1: -----------------------] 138s autopkgtest [11:57:54]: test command1: - - - - - - - - - - results - - - - - - - - - - 138s command1 FAIL non-zero exit status 1 138s autopkgtest [11:57:54]: @@@@@@@@@@@@@@@@@@@@ summary 138s run-unit-test PASS 138s command1 FAIL non-zero exit status 1 149s nova [W] Using flock in prodstack6-s390x 149s Creating nova instance adt-plucky-s390x-minimap2-20241113-115536-juju-7f2275-prod-proposed-migration-environment-15-4ba88272-7251-4ca6-8325-fdc1577c2546 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...