0s autopkgtest [08:57:01]: starting date and time: 2024-11-13 08:57:01+0000 0s autopkgtest [08:57:01]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [08:57:01]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a2v87n7e/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-25.secgroup --name adt-plucky-amd64-minimap2-20241113-085700-juju-7f2275-prod-proposed-migration-environment-20-df33d677-9787-4dd4-a334-e7e3e3cc6f1c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 55s autopkgtest [08:57:56]: testbed dpkg architecture: amd64 56s autopkgtest [08:57:57]: testbed apt version: 2.9.8 56s autopkgtest [08:57:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 56s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 57s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 57s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 57s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 57s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 57s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 57s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 57s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 57s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 57s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 57s Fetched 2173 kB in 1s (2750 kB/s) 57s Reading package lists... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 60s Calculating upgrade... 60s The following NEW packages will be installed: 60s python3.13-gdbm 60s The following packages will be upgraded: 60s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 74s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 74s Need to get 253 kB of archives. 74s After this operation, 147 kB of additional disk space will be used. 74s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 82s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 82s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 82s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 82s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 83s Fetched 253 kB in 23s (11.2 kB/s) 83s (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 ... 75541 files and directories currently installed.) 83s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 83s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 83s Setting up python3-minimal (3.12.7-1) ... 83s (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 ... 75541 files and directories currently installed.) 83s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 83s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 83s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 83s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 83s Selecting previously unselected package python3.13-gdbm. 83s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 83s Unpacking python3.13-gdbm (3.13.0-2) ... 83s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 83s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 83s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 83s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 83s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 83s Setting up python3.13-gdbm (3.13.0-2) ... 83s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 83s Setting up python3 (3.12.7-1) ... 83s Setting up python3-gdbm:amd64 (3.12.7-1) ... 83s Processing triggers for man-db (2.12.1-3) ... 84s Processing triggers for libc-bin (2.40-1ubuntu3) ... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 85s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 86s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Calculating upgrade... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [08:58:30]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 89s autopkgtest [08:58:30]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 92s Get:1 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (dsc) [2315 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (tar) [200 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/universe minimap2 2.27+dfsg-1 (diff) [11.5 kB] 92s gpgv: Signature made Mon Mar 18 16:37:53 2024 UTC 92s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.27+dfsg-1.dsc: no acceptable signature found 92s autopkgtest [08:58:33]: testing package minimap2 version 2.27+dfsg-1 92s autopkgtest [08:58:33]: build not needed 93s autopkgtest [08:58:34]: test run-unit-test: preparing testbed 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 96s The following additional packages will be installed: 96s libminimap2-dev minimap2 python3-mappy zlib1g-dev 96s The following NEW packages will be installed: 96s autopkgtest-satdep libminimap2-dev minimap2 python3-mappy zlib1g-dev 96s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 1570 kB/1570 kB of archives. 96s After this operation, 2650 kB of additional disk space will be used. 96s Get:1 /tmp/autopkgtest.my05E3/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 96s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libminimap2-dev amd64 2.27+dfsg-1 [138 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 minimap2 amd64 2.27+dfsg-1 [386 kB] 96s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mappy amd64 2.27+dfsg-1 [150 kB] 97s Fetched 1570 kB in 1s (2496 kB/s) 97s Selecting previously unselected package zlib1g-dev:amd64. 97s (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 ... 75548 files and directories currently installed.) 97s Preparing to unpack .../zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 97s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 97s Selecting previously unselected package libminimap2-dev. 97s Preparing to unpack .../libminimap2-dev_2.27+dfsg-1_amd64.deb ... 97s Unpacking libminimap2-dev (2.27+dfsg-1) ... 97s Selecting previously unselected package minimap2. 97s Preparing to unpack .../minimap2_2.27+dfsg-1_amd64.deb ... 97s Unpacking minimap2 (2.27+dfsg-1) ... 97s Selecting previously unselected package python3-mappy. 97s Preparing to unpack .../python3-mappy_2.27+dfsg-1_amd64.deb ... 97s Unpacking python3-mappy (2.27+dfsg-1) ... 97s Selecting previously unselected package autopkgtest-satdep. 97s Preparing to unpack .../1-autopkgtest-satdep.deb ... 97s Unpacking autopkgtest-satdep (0) ... 97s Setting up minimap2 (2.27+dfsg-1) ... 97s Setting up python3-mappy (2.27+dfsg-1) ... 97s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 97s Setting up libminimap2-dev (2.27+dfsg-1) ... 97s Setting up autopkgtest-satdep (0) ... 97s Processing triggers for man-db (2.12.1-3) ... 99s (Reading database ... 75625 files and directories currently installed.) 99s Removing autopkgtest-satdep (0) ... 100s autopkgtest [08:58:41]: test run-unit-test: [----------------------- 100s [M::mm_idx_gen::0.001*1.13] collected minimizers 100s [M::mm_idx_gen::0.002*1.10] sorted minimizers 100s [M::main::0.002*1.10] loaded/built the index for 1 target sequence(s) 100s [M::mm_mapopt_update::0.002*1.09] mid_occ = 10 100s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 100s [M::mm_idx_stat::0.002*1.08] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 100s [M::worker_pipeline::0.006*0.92] mapped 1 sequences 100s [M::main] Version: 2.27-r1193 100s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 100s [M::main] Real time: 0.007 sec; CPU: 0.006 sec; Peak RSS: 0.005 GB 100s [M::mm_idx_gen::0.001*1.14] collected minimizers 100s [M::mm_idx_gen::0.002*1.28] sorted minimizers 100s [M::main::0.003*1.20] loaded/built the index for 1 target sequence(s) 100s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 100s [M::mm_idx_stat::0.003*1.20] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 100s [M::main] Version: 2.27-r1193 100s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 100s [M::main] Real time: 0.003 sec; CPU: 0.004 sec; Peak RSS: 0.004 GB 100s [M::main::0.002*1.31] loaded/built the index for 1 target sequence(s) 100s [M::mm_mapopt_update::0.002*1.29] mid_occ = 10 100s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 100s [M::mm_idx_stat::0.002*1.25] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 100s [M::worker_pipeline::0.006*1.11] mapped 1 sequences 100s [M::main] Version: 2.27-r1193 100s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 100s [M::main] Real time: 0.006 sec; CPU: 0.007 sec; Peak RSS: 0.005 GB 101s autopkgtest [08:58:42]: test run-unit-test: -----------------------] 101s autopkgtest [08:58:42]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 101s run-unit-test PASS 101s autopkgtest [08:58:42]: test command1: preparing testbed 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 104s The following additional packages will be installed: 104s libpython3.13-minimal libpython3.13-stdlib python3-all python3.13 104s python3.13-minimal 104s Suggested packages: 104s python3.13-venv python3.13-doc binfmt-support 104s The following NEW packages will be installed: 104s autopkgtest-satdep libpython3.13-minimal libpython3.13-stdlib python3-all 104s python3.13 python3.13-minimal 104s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 104s Need to get 5894 kB/5894 kB of archives. 104s After this operation, 22.4 MB of additional disk space will be used. 104s Get:1 /tmp/autopkgtest.my05E3/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [728 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 105s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 105s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 105s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 105s Fetched 5894 kB in 1s (6704 kB/s) 105s Selecting previously unselected package libpython3.13-minimal:amd64. 105s (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 ... 75625 files and directories currently installed.) 105s Preparing to unpack .../0-libpython3.13-minimal_3.13.0-2_amd64.deb ... 105s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 105s Selecting previously unselected package python3.13-minimal. 105s Preparing to unpack .../1-python3.13-minimal_3.13.0-2_amd64.deb ... 105s Unpacking python3.13-minimal (3.13.0-2) ... 105s Selecting previously unselected package libpython3.13-stdlib:amd64. 105s Preparing to unpack .../2-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 105s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 106s Selecting previously unselected package python3.13. 106s Preparing to unpack .../3-python3.13_3.13.0-2_amd64.deb ... 106s Unpacking python3.13 (3.13.0-2) ... 106s Selecting previously unselected package python3-all. 106s Preparing to unpack .../4-python3-all_3.12.7-1_amd64.deb ... 106s Unpacking python3-all (3.12.7-1) ... 106s Selecting previously unselected package autopkgtest-satdep. 106s Preparing to unpack .../5-2-autopkgtest-satdep.deb ... 106s Unpacking autopkgtest-satdep (0) ... 106s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 106s Setting up python3.13-minimal (3.13.0-2) ... 106s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 106s Setting up python3.13 (3.13.0-2) ... 107s Setting up python3-all (3.12.7-1) ... 107s Setting up autopkgtest-satdep (0) ... 107s Processing triggers for man-db (2.12.1-3) ... 107s Processing triggers for systemd (256.5-2ubuntu4) ... 111s (Reading database ... 76360 files and directories currently installed.) 111s Removing autopkgtest-satdep (0) ... 111s autopkgtest [08:58:52]: 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 111s autopkgtest [08:58:52]: test command1: [----------------------- 112s Testing with python3.13: 112s Traceback (most recent call last): 112s File "", line 1, in 112s import mappy; print(mappy) 112s ^^^^^^^^^^^^ 112s ModuleNotFoundError: No module named 'mappy' 112s autopkgtest [08:58:53]: test command1: -----------------------] 112s autopkgtest [08:58:53]: test command1: - - - - - - - - - - results - - - - - - - - - - 112s command1 FAIL non-zero exit status 1 113s autopkgtest [08:58:54]: @@@@@@@@@@@@@@@@@@@@ summary 113s run-unit-test PASS 113s command1 FAIL non-zero exit status 1 127s nova [W] Skipping flock for amd64 127s Creating nova instance adt-plucky-amd64-minimap2-20241113-085700-juju-7f2275-prod-proposed-migration-environment-20-df33d677-9787-4dd4-a334-e7e3e3cc6f1c from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...