0s autopkgtest [18:32:04]: starting date and time: 2024-11-13 18:32:04+0000 0s autopkgtest [18:32:04]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:32:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.exka7z8v/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-8.secgroup --name adt-plucky-ppc64el-minimap2-20241113-183204-juju-7f2275-prod-proposed-migration-environment-15-93dbc9d3-9605-419f-831d-f1c08ea8efa5 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 133s autopkgtest [18:34:17]: testbed dpkg architecture: ppc64el 133s autopkgtest [18:34:17]: testbed apt version: 2.9.8 133s autopkgtest [18:34:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 135s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 135s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 135s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 135s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 135s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [113 kB] 135s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [672 kB] 135s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB] 135s Fetched 1978 kB in 1s (1778 kB/s) 135s Reading package lists... 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Calculating upgrade... 139s The following NEW packages will be installed: 139s python3.13-gdbm 139s The following packages will be upgraded: 139s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libpython3-stdlib 139s libutempter0 python3 python3-gdbm python3-minimal 139s 8 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 1265 kB of archives. 139s After this operation, 141 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB] 139s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB] 139s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB] 140s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B] 140s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 140s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB] 140s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B] 140s Fetched 1265 kB in 1s (2097 kB/s) 141s (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 ... 73767 files and directories currently installed.) 141s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ... 141s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 141s Setting up python3-minimal (3.12.7-1) ... 141s (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 ... 73767 files and directories currently installed.) 141s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ... 141s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 141s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ... 141s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ... 141s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ... 141s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 141s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ... 141s Selecting previously unselected package python3.13-gdbm. 141s (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 ... 73767 files and directories currently installed.) 141s Preparing to unpack .../python3.13-gdbm_3.13.0-2_ppc64el.deb ... 141s Unpacking python3.13-gdbm (3.13.0-2) ... 141s Preparing to unpack .../python3-gdbm_3.12.7-1_ppc64el.deb ... 141s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ... 141s Preparing to unpack .../libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 141s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 141s Preparing to unpack .../libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ... 141s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ... 141s Preparing to unpack .../libutempter0_1.2.1-4_ppc64el.deb ... 141s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ... 141s Setting up libutempter0:ppc64el (1.2.1-4) ... 141s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 141s Setting up python3.13-gdbm (3.13.0-2) ... 141s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ... 141s Setting up python3 (3.12.7-1) ... 142s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ... 142s Setting up python3-gdbm:ppc64el (3.12.7-1) ... 142s Processing triggers for man-db (2.12.1-3) ... 143s Processing triggers for libc-bin (2.40-1ubuntu3) ... 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 145s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 145s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 145s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 146s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Calculating upgrade... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [18:34:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 151s autopkgtest [18:34:35]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 154s Get:1 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (dsc) [2315 B] 154s Get:2 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (tar) [200 kB] 154s Get:3 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (diff) [11.5 kB] 154s gpgv: Signature made Mon Mar 18 16:37:53 2024 UTC 154s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: no acceptable signature found 154s autopkgtest [18:34:38]: testing package minimap2 version 2.27+dfsg-1 155s autopkgtest [18:34:39]: build not needed 156s autopkgtest [18:34:40]: test run-unit-test: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 161s The following additional packages will be installed: 161s libminimap2-dev minimap2 python3-mappy zlib1g-dev 161s The following NEW packages will be installed: 161s autopkgtest-satdep libminimap2-dev minimap2 python3-mappy zlib1g-dev 161s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 1639 kB/1640 kB of archives. 161s After this operation, 2920 kB of additional disk space will be used. 161s Get:1 /tmp/autopkgtest.1ox3ky/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [728 B] 161s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB] 161s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libminimap2-dev ppc64el 2.27+dfsg-1 [147 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el minimap2 ppc64el 2.27+dfsg-1 [398 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mappy ppc64el 2.27+dfsg-1 [192 kB] 162s Fetched 1639 kB in 1s (2412 kB/s) 162s Selecting previously unselected package zlib1g-dev:ppc64el. 162s (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 ... 73774 files and directories currently installed.) 162s Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ... 162s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 162s Selecting previously unselected package libminimap2-dev. 162s Preparing to unpack .../libminimap2-dev_2.27+dfsg-1_ppc64el.deb ... 162s Unpacking libminimap2-dev (2.27+dfsg-1) ... 162s Selecting previously unselected package minimap2. 162s Preparing to unpack .../minimap2_2.27+dfsg-1_ppc64el.deb ... 162s Unpacking minimap2 (2.27+dfsg-1) ... 162s Selecting previously unselected package python3-mappy. 162s Preparing to unpack .../python3-mappy_2.27+dfsg-1_ppc64el.deb ... 162s Unpacking python3-mappy (2.27+dfsg-1) ... 162s Selecting previously unselected package autopkgtest-satdep. 162s Preparing to unpack .../1-autopkgtest-satdep.deb ... 162s Unpacking autopkgtest-satdep (0) ... 162s Setting up minimap2 (2.27+dfsg-1) ... 162s Setting up python3-mappy (2.27+dfsg-1) ... 162s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 162s Setting up libminimap2-dev (2.27+dfsg-1) ... 162s Setting up autopkgtest-satdep (0) ... 162s Processing triggers for man-db (2.12.1-3) ... 166s (Reading database ... 73851 files and directories currently installed.) 166s Removing autopkgtest-satdep (0) ... 166s autopkgtest [18:34:50]: test run-unit-test: [----------------------- 167s [M::mm_idx_gen::0.002*1.29] collected minimizers 167s [M::mm_idx_gen::0.004*1.05] sorted minimizers 167s [M::main::0.004*1.05] loaded/built the index for 1 target sequence(s) 167s [M::mm_mapopt_update::0.004*1.05] mid_occ = 10 167s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 167s [M::mm_idx_stat::0.004*1.05] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 167s [M::worker_pipeline::0.022*0.69] mapped 1 sequences 167s [M::main] Version: 2.27-r1193 167s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 167s [M::main] Real time: 0.023 sec; CPU: 0.016 sec; Peak RSS: 0.011 GB 167s [M::mm_idx_gen::0.002*1.31] collected minimizers 167s [M::mm_idx_gen::0.003*1.14] sorted minimizers 167s [M::main::0.006*1.04] loaded/built the index for 1 target sequence(s) 167s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 167s [M::mm_idx_stat::0.006*1.04] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 167s [M::main] Version: 2.27-r1193 167s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 167s [M::main] Real time: 0.007 sec; CPU: 0.007 sec; Peak RSS: 0.006 GB 167s [M::main::0.002*1.33] loaded/built the index for 1 target sequence(s) 167s [M::mm_mapopt_update::0.003*1.31] mid_occ = 10 167s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 167s [M::mm_idx_stat::0.003*1.29] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 167s [M::worker_pipeline::0.016*0.85] mapped 1 sequences 167s [M::main] Version: 2.27-r1193 167s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 167s [M::main] Real time: 0.017 sec; CPU: 0.015 sec; Peak RSS: 0.013 GB 167s autopkgtest [18:34:51]: test run-unit-test: -----------------------] 168s run-unit-test PASS 168s autopkgtest [18:34:52]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 168s autopkgtest [18:34:52]: test command1: preparing testbed 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 171s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 172s The following additional packages will be installed: 172s libpython3.13-minimal libpython3.13-stdlib python3-all python3.13 172s python3.13-minimal 172s Suggested packages: 172s python3.13-venv python3.13-doc binfmt-support 172s The following NEW packages will be installed: 172s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 172s python3.13 python3.13-minimal 172s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 6051 kB/6052 kB of archives. 172s After this operation, 25.8 MB of additional disk space will be used. 172s Get:1 /tmp/autopkgtest.1ox3ky/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [736 B] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB] 173s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB] 173s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB] 173s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB] 173s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B] 174s Fetched 6051 kB in 1s (6125 kB/s) 174s Selecting previously unselected package libpython3.13-minimal:ppc64el. 174s (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 ... 73851 files and directories currently installed.) 174s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_ppc64el.deb ... 174s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ... 174s Selecting previously unselected package python3.13-minimal. 174s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_ppc64el.deb ... 174s Unpacking python3.13-minimal (3.13.0-2) ... 174s Selecting previously unselected package libpython3.13-stdlib:ppc64el. 174s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_ppc64el.deb ... 174s Unpacking libpython3.13-stdlib:ppc64el (3.13.0-2) ... 174s Selecting previously unselected package python3.13. 174s Preparing to unpack .../3-python3.13_3.13.0-2_ppc64el.deb ... 174s Unpacking python3.13 (3.13.0-2) ... 174s Selecting previously unselected package python3-all. 174s Preparing to unpack .../4-python3-all_3.12.7-1_ppc64el.deb ... 174s Unpacking python3-all (3.12.7-1) ... 174s Selecting previously unselected package autopkgtest-satdep. 174s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 174s Unpacking autopkgtest-satdep (0) ... 174s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ... 174s Setting up python3.13-minimal (3.13.0-2) ... 176s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ... 176s Setting up python3.13 (3.13.0-2) ... 177s Setting up python3-all (3.12.7-1) ... 177s Setting up autopkgtest-satdep (0) ... 177s Processing triggers for man-db (2.12.1-3) ... 177s Processing triggers for systemd (256.5-2ubuntu4) ... 181s (Reading database ... 74586 files and directories currently installed.) 181s Removing autopkgtest-satdep (0) ... 182s autopkgtest [18:35:06]: 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 182s autopkgtest [18:35:06]: test command1: [----------------------- 182s Testing with python3.13: 182s Traceback (most recent call last): 182s File "", line 1, in 182s import mappy; print(mappy) 182s ^^^^^^^^^^^^ 182s ModuleNotFoundError: No module named 'mappy' 183s autopkgtest [18:35:07]: test command1: -----------------------] 183s autopkgtest [18:35:07]: test command1: - - - - - - - - - - results - - - - - - - - - - 183s command1 FAIL non-zero exit status 1 184s autopkgtest [18:35:08]: @@@@@@@@@@@@@@@@@@@@ summary 184s run-unit-test PASS 184s command1 FAIL non-zero exit status 1 189s nova [W] Using flock in prodstack6-ppc64el 189s Creating nova instance adt-plucky-ppc64el-minimap2-20241113-183204-juju-7f2275-prod-proposed-migration-environment-15-93dbc9d3-9605-419f-831d-f1c08ea8efa5 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...