0s autopkgtest [09:38:36]: starting date and time: 2024-11-13 09:38:36+0000 0s autopkgtest [09:38:36]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:38:36]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3180ygp8/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-44.secgroup --name adt-plucky-arm64-minimap2-20241113-093835-juju-7f2275-prod-proposed-migration-environment-20-0b74c994-1b5a-463b-97c3-730482c12c8f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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://ftpmaster.internal/ubuntu/ 90s autopkgtest [09:40:06]: testbed dpkg architecture: arm64 90s autopkgtest [09:40:06]: testbed apt version: 2.9.8 90s autopkgtest [09:40:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 91s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 91s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 91s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 91s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 91s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 92s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 92s Fetched 1793 kB in 1s (1997 kB/s) 92s Reading package lists... 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade... 97s The following NEW packages will be installed: 97s python3.13-gdbm 97s The following packages will be upgraded: 97s libpython3-stdlib python3 python3-gdbm python3-minimal 97s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 101 kB of archives. 97s After this operation, 141 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 97s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 97s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 98s Fetched 101 kB in 0s (275 kB/s) 98s (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 ... 79924 files and directories currently installed.) 98s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 98s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 98s Setting up python3-minimal (3.12.7-1) ... 99s (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 ... 79924 files and directories currently installed.) 99s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 99s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 99s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 99s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 99s Selecting previously unselected package python3.13-gdbm. 99s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 99s Unpacking python3.13-gdbm (3.13.0-2) ... 99s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 99s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 99s Setting up python3.13-gdbm (3.13.0-2) ... 99s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 99s Setting up python3 (3.12.7-1) ... 100s Setting up python3-gdbm:arm64 (3.12.7-1) ... 100s Processing triggers for man-db (2.12.1-3) ... 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 103s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Reading package lists... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [09:40:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 112s autopkgtest [09:40:28]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 115s Get:1 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (dsc) [2315 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (tar) [200 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (diff) [11.5 kB] 115s gpgv: Signature made Mon Mar 18 16:37:53 2024 UTC 115s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 115s gpgv: Can't check signature: No public key 115s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: no acceptable signature found 116s autopkgtest [09:40:32]: testing package minimap2 version 2.27+dfsg-1 116s autopkgtest [09:40:32]: build not needed 116s autopkgtest [09:40:32]: test run-unit-test: preparing testbed 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 122s The following additional packages will be installed: 122s libminimap2-dev minimap2 python3-mappy zlib1g-dev 123s The following NEW packages will be installed: 123s autopkgtest-satdep libminimap2-dev minimap2 python3-mappy zlib1g-dev 123s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 123s Need to get 1570 kB/1571 kB of archives. 123s After this operation, 2704 kB of additional disk space will be used. 123s Get:1 /tmp/autopkgtest.IQirtf/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1ubuntu1 [894 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libminimap2-dev arm64 2.27+dfsg-1 [127 kB] 123s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 minimap2 arm64 2.27+dfsg-1 [382 kB] 123s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-mappy arm64 2.27+dfsg-1 [167 kB] 124s Fetched 1570 kB in 1s (2313 kB/s) 124s Selecting previously unselected package zlib1g-dev:arm64. 124s (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 ... 79931 files and directories currently installed.) 124s Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_arm64.deb ... 124s Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 124s Selecting previously unselected package libminimap2-dev. 124s Preparing to unpack .../libminimap2-dev_2.27+dfsg-1_arm64.deb ... 124s Unpacking libminimap2-dev (2.27+dfsg-1) ... 124s Selecting previously unselected package minimap2. 124s Preparing to unpack .../minimap2_2.27+dfsg-1_arm64.deb ... 124s Unpacking minimap2 (2.27+dfsg-1) ... 124s Selecting previously unselected package python3-mappy. 124s Preparing to unpack .../python3-mappy_2.27+dfsg-1_arm64.deb ... 124s Unpacking python3-mappy (2.27+dfsg-1) ... 124s Selecting previously unselected package autopkgtest-satdep. 124s Preparing to unpack .../1-autopkgtest-satdep.deb ... 124s Unpacking autopkgtest-satdep (0) ... 124s Setting up minimap2 (2.27+dfsg-1) ... 124s Setting up python3-mappy (2.27+dfsg-1) ... 124s Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 124s Setting up libminimap2-dev (2.27+dfsg-1) ... 124s Setting up autopkgtest-satdep (0) ... 124s Processing triggers for man-db (2.12.1-3) ... 132s (Reading database ... 80008 files and directories currently installed.) 132s Removing autopkgtest-satdep (0) ... 132s autopkgtest [09:40:48]: test run-unit-test: [----------------------- 133s [M::mm_idx_gen::0.005*1.88] collected minimizers 133s [M::mm_idx_gen::0.007*1.79] sorted minimizers 133s [M::main::0.007*1.78] loaded/built the index for 1 target sequence(s) 133s [M::mm_mapopt_update::0.008*1.75] mid_occ = 10 133s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 133s [M::mm_idx_stat::0.008*1.71] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 133s [M::worker_pipeline::0.016*1.34] mapped 1 sequences 133s [M::main] Version: 2.27-r1193 133s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 133s [M::main] Real time: 0.018 sec; CPU: 0.024 sec; Peak RSS: 0.004 GB 133s [M::mm_idx_gen::0.005*1.34] collected minimizers 133s [M::mm_idx_gen::0.008*1.41] sorted minimizers 133s [M::main::0.011*1.30] loaded/built the index for 1 target sequence(s) 133s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 133s [M::mm_idx_stat::0.012*1.25] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 133s [M::main] Version: 2.27-r1193 133s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 133s [M::main] Real time: 0.014 sec; CPU: 0.017 sec; Peak RSS: 0.003 GB 133s [M::main::0.003*1.47] loaded/built the index for 1 target sequence(s) 133s [M::mm_mapopt_update::0.003*1.29] mid_occ = 10 133s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 133s [M::mm_idx_stat::0.004*1.21] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 133s [M::worker_pipeline::0.013*1.09] mapped 1 sequences 133s [M::main] Version: 2.27-r1193 133s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 133s [M::main] Real time: 0.015 sec; CPU: 0.016 sec; Peak RSS: 0.005 GB 133s autopkgtest [09:40:49]: test run-unit-test: -----------------------] 134s run-unit-test PASS 134s autopkgtest [09:40:50]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 134s autopkgtest [09:40:50]: test command1: preparing testbed 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 142s The following additional packages will be installed: 142s libpython3.13-minimal libpython3.13-stdlib python3-all python3.13 142s python3.13-minimal 142s Suggested packages: 142s python3.13-venv python3.13-doc binfmt-support 142s The following NEW packages will be installed: 142s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 142s python3.13 python3.13-minimal 142s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 142s Need to get 5770 kB/5771 kB of archives. 142s After this operation, 24.1 MB of additional disk space will be used. 142s Get:1 /tmp/autopkgtest.IQirtf/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [728 B] 142s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 143s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 143s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 143s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 143s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 144s Fetched 5770 kB in 1s (6411 kB/s) 144s Selecting previously unselected package libpython3.13-minimal:arm64. 144s (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 ... 80008 files and directories currently installed.) 144s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_arm64.deb ... 144s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 144s Selecting previously unselected package python3.13-minimal. 144s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_arm64.deb ... 144s Unpacking python3.13-minimal (3.13.0-2) ... 144s Selecting previously unselected package libpython3.13-stdlib:arm64. 144s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 144s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 144s Selecting previously unselected package python3.13. 144s Preparing to unpack .../3-python3.13_3.13.0-2_arm64.deb ... 144s Unpacking python3.13 (3.13.0-2) ... 144s Selecting previously unselected package python3-all. 144s Preparing to unpack .../4-python3-all_3.12.7-1_arm64.deb ... 144s Unpacking python3-all (3.12.7-1) ... 144s Selecting previously unselected package autopkgtest-satdep. 144s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 144s Unpacking autopkgtest-satdep (0) ... 144s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 144s Setting up python3.13-minimal (3.13.0-2) ... 146s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 146s Setting up python3.13 (3.13.0-2) ... 148s Setting up python3-all (3.12.7-1) ... 148s Setting up autopkgtest-satdep (0) ... 148s Processing triggers for man-db (2.12.1-3) ... 148s Processing triggers for systemd (256.5-2ubuntu4) ... 154s (Reading database ... 80743 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [09:41:10]: 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 154s autopkgtest [09:41:10]: test command1: [----------------------- 155s Testing with python3.13: 155s Traceback (most recent call last): 155s File "", line 1, in 155s import mappy; print(mappy) 155s ^^^^^^^^^^^^ 155s ModuleNotFoundError: No module named 'mappy' 155s autopkgtest [09:41:11]: test command1: -----------------------] 156s command1 FAIL non-zero exit status 1 156s autopkgtest [09:41:12]: test command1: - - - - - - - - - - results - - - - - - - - - - 156s autopkgtest [09:41:12]: @@@@@@@@@@@@@@@@@@@@ summary 156s run-unit-test PASS 156s command1 FAIL non-zero exit status 1 169s nova [W] Skipping flock in bos03-arm64 169s Creating nova instance adt-plucky-arm64-minimap2-20241113-093835-juju-7f2275-prod-proposed-migration-environment-20-0b74c994-1b5a-463b-97c3-730482c12c8f from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...