0s autopkgtest [11:02:31]: starting date and time: 2024-03-20 11:02:31+0000 0s autopkgtest [11:02:31]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [11:02:31]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k9wd24wp/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:minimap2 --apt-upgrade minimap2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=minimap2/2.26+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-22.secgroup --name adt-noble-s390x-minimap2-20240320-110231-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 75s autopkgtest [11:03:46]: testbed dpkg architecture: s390x 75s autopkgtest [11:03:46]: testbed apt version: 2.7.12 75s autopkgtest [11:03:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 77s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 77s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3766 kB] 77s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 77s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 77s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [653 kB] 77s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 77s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 77s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 77s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4051 kB] 78s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 78s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [34.4 kB] 78s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 80s Fetched 9188 kB in 3s (3404 kB/s) 80s Reading package lists... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 85s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 85s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 87s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [11:04:01]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 91s autopkgtest [11:04:02]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 93s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (dsc) [2315 B] 93s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (tar) [199 kB] 93s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (diff) [11.5 kB] 94s gpgv: Signature made Thu Feb 29 15:00:20 2024 UTC 94s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 94s gpgv: Can't check signature: No public key 94s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.26+dfsg-1.dsc: no acceptable signature found 94s autopkgtest [11:04:05]: testing package minimap2 version 2.26+dfsg-1 94s autopkgtest [11:04:05]: build not needed 96s autopkgtest [11:04:07]: test run-unit-test: preparing testbed 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Starting pkgProblemResolver with broken count: 0 98s Starting 2 pkgProblemResolver with broken count: 0 98s Done 98s The following additional packages will be installed: 98s libc-dev-bin libc6-dev libcrypt-dev libminimap2-dev libnsl-dev libtirpc-dev 98s linux-libc-dev minimap2 python3-mappy rpcsvc-proto zlib1g-dev 98s Suggested packages: 98s glibc-doc manpages-dev 98s Recommended packages: 98s manpages manpages-dev libc-devtools 98s The following NEW packages will be installed: 98s autopkgtest-satdep libc-dev-bin libc6-dev libcrypt-dev libminimap2-dev 98s libnsl-dev libtirpc-dev linux-libc-dev minimap2 python3-mappy rpcsvc-proto 98s zlib1g-dev 98s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 5395 kB/5395 kB of archives. 98s After this operation, 21.3 MB of additional disk space will be used. 98s Get:1 /tmp/autopkgtest.AL9skN/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 98s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.39-0ubuntu2 [20.2 kB] 98s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-11.11 [1590 kB] 99s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] 99s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1build1 [225 kB] 99s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB] 99s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB] 99s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.39-0ubuntu2 [1629 kB] 99s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] 99s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libminimap2-dev s390x 2.26+dfsg-1 [144 kB] 99s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x minimap2 s390x 2.26+dfsg-1 [399 kB] 99s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x python3-mappy s390x 2.26+dfsg-1 [207 kB] 99s Fetched 5395 kB in 1s (6096 kB/s) 99s Selecting previously unselected package libc-dev-bin. 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 ... 52171 files and directories currently installed.) 99s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_s390x.deb ... 99s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 99s Selecting previously unselected package linux-libc-dev:s390x. 99s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_s390x.deb ... 99s Unpacking linux-libc-dev:s390x (6.8.0-11.11) ... 100s Selecting previously unselected package libcrypt-dev:s390x. 100s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... 100s Unpacking libcrypt-dev:s390x (1:4.4.36-4) ... 100s Selecting previously unselected package libtirpc-dev:s390x. 100s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1build1_s390x.deb ... 100s Unpacking libtirpc-dev:s390x (1.3.4+ds-1build1) ... 100s Selecting previously unselected package libnsl-dev:s390x. 100s Preparing to unpack .../04-libnsl-dev_1.3.0-3_s390x.deb ... 100s Unpacking libnsl-dev:s390x (1.3.0-3) ... 100s Selecting previously unselected package rpcsvc-proto. 100s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ... 100s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 100s Selecting previously unselected package libc6-dev:s390x. 100s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_s390x.deb ... 100s Unpacking libc6-dev:s390x (2.39-0ubuntu2) ... 100s Selecting previously unselected package zlib1g-dev:s390x. 100s Preparing to unpack .../07-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_s390x.deb ... 100s Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 100s Selecting previously unselected package libminimap2-dev. 100s Preparing to unpack .../08-libminimap2-dev_2.26+dfsg-1_s390x.deb ... 100s Unpacking libminimap2-dev (2.26+dfsg-1) ... 100s Selecting previously unselected package minimap2. 100s Preparing to unpack .../09-minimap2_2.26+dfsg-1_s390x.deb ... 100s Unpacking minimap2 (2.26+dfsg-1) ... 100s Selecting previously unselected package python3-mappy. 100s Preparing to unpack .../10-python3-mappy_2.26+dfsg-1_s390x.deb ... 100s Unpacking python3-mappy (2.26+dfsg-1) ... 100s Selecting previously unselected package autopkgtest-satdep. 100s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 100s Unpacking autopkgtest-satdep (0) ... 100s Setting up minimap2 (2.26+dfsg-1) ... 100s Setting up linux-libc-dev:s390x (6.8.0-11.11) ... 100s Setting up python3-mappy (2.26+dfsg-1) ... 100s Setting up libtirpc-dev:s390x (1.3.4+ds-1build1) ... 100s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 100s Setting up libnsl-dev:s390x (1.3.0-3) ... 100s Setting up libcrypt-dev:s390x (1:4.4.36-4) ... 100s Setting up libc-dev-bin (2.39-0ubuntu2) ... 100s Setting up libc6-dev:s390x (2.39-0ubuntu2) ... 100s Setting up zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ... 100s Setting up libminimap2-dev (2.26+dfsg-1) ... 100s Setting up autopkgtest-satdep (0) ... 100s Processing triggers for man-db (2.12.0-3) ... 104s (Reading database ... 53971 files and directories currently installed.) 104s Removing autopkgtest-satdep (0) ... 104s autopkgtest [11:04:15]: test run-unit-test: [----------------------- 105s [M::mm_idx_gen::0.002*1.10] collected minimizers 105s [M::mm_idx_gen::0.003*0.63] sorted minimizers 105s [M::main::0.003*0.63] loaded/built the index for 1 target sequence(s) 105s [M::mm_mapopt_update::0.003*0.60] mid_occ = 10 105s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 105s [M::mm_idx_stat::0.003*0.61] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 105s [M::worker_pipeline::0.095*0.96] mapped 1 sequences 105s [M::main] Version: 2.26-r1175 105s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 105s [M::main] Real time: 0.096 sec; CPU: 0.092 sec; Peak RSS: 0.005 GB 105s [M::mm_idx_gen::0.001*1.18] collected minimizers 105s [M::mm_idx_gen::0.003*0.68] sorted minimizers 105s [M::main::0.004*0.48] loaded/built the index for 1 target sequence(s) 105s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 105s [M::mm_idx_stat::0.004*0.73] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 105s [M::main] Version: 2.26-r1175 105s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 105s [M::main] Real time: 0.005 sec; CPU: 0.004 sec; Peak RSS: 0.004 GB 105s [M::main::0.002*0.61] loaded/built the index for 1 target sequence(s) 105s [M::mm_mapopt_update::0.002*0.57] mid_occ = 10 105s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 105s [M::mm_idx_stat::0.003*0.54] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 105s [M::worker_pipeline::0.099*0.91] mapped 1 sequences 105s [M::main] Version: 2.26-r1175 105s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 105s [M::main] Real time: 0.101 sec; CPU: 0.092 sec; Peak RSS: 0.005 GB 105s autopkgtest [11:04:16]: test run-unit-test: -----------------------] 106s autopkgtest [11:04:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 106s run-unit-test PASS 106s autopkgtest [11:04:17]: test command1: preparing testbed 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 109s The following additional packages will be installed: 109s python3-all 109s The following NEW packages will be installed: 109s autopkgtest-satdep python3-all 109s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 908 B/1636 B of archives. 109s After this operation, 6144 B of additional disk space will be used. 109s Get:1 /tmp/autopkgtest.AL9skN/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B] 109s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-all s390x 3.12.1-0ubuntu2 [908 B] 109s Fetched 908 B in 0s (5627 B/s) 109s Selecting previously unselected package python3-all. 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 ... 53971 files and directories currently installed.) 109s Preparing to unpack .../python3-all_3.12.1-0ubuntu2_s390x.deb ... 109s Unpacking python3-all (3.12.1-0ubuntu2) ... 109s Selecting previously unselected package autopkgtest-satdep. 109s Preparing to unpack .../2-autopkgtest-satdep.deb ... 109s Unpacking autopkgtest-satdep (0) ... 109s Setting up python3-all (3.12.1-0ubuntu2) ... 109s Setting up autopkgtest-satdep (0) ... 112s (Reading database ... 53972 files and directories currently installed.) 112s Removing autopkgtest-satdep (0) ... 113s autopkgtest [11:04:24]: 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 113s autopkgtest [11:04:24]: test command1: [----------------------- 113s Testing with python3.12: 113s 114s autopkgtest [11:04:25]: test command1: -----------------------] 114s autopkgtest [11:04:25]: test command1: - - - - - - - - - - results - - - - - - - - - - 114s command1 PASS (superficial) 115s autopkgtest [11:04:26]: @@@@@@@@@@@@@@@@@@@@ summary 115s run-unit-test PASS 115s command1 PASS (superficial) 126s Creating nova instance adt-noble-s390x-minimap2-20240320-110231-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240320.img (UUID 6569a0ff-4984-4a4c-a4d0-b93f21cb5de9)...