0s autopkgtest [00:08:41]: starting date and time: 2024-03-20 00:08:41+0000 0s autopkgtest [00:08:41]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [00:08:41]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9vdtlsxv/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@bos01-ppc64el-11.secgroup --name adt-noble-ppc64el-minimap2-20240320-000841-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-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://us.ports.ubuntu.com/ubuntu-ports/ 154s autopkgtest [00:11:15]: testbed dpkg architecture: ppc64el 154s autopkgtest [00:11:15]: testbed apt version: 2.7.12 154s autopkgtest [00:11:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 155s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.7 kB] 155s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [492 kB] 155s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 155s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3799 kB] 155s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [654 kB] 155s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 155s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 155s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 155s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4104 kB] 156s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 156s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.7 kB] 156s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 159s Fetched 9286 kB in 2s (4107 kB/s) 159s Reading package lists... 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Calculating upgrade... 162s The following packages will be upgraded: 162s ubuntu-minimal ubuntu-standard 162s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Need to get 21.5 kB of archives. 162s After this operation, 0 B of additional disk space will be used. 162s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-minimal ppc64el 1.536build1 [10.7 kB] 162s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-standard ppc64el 1.536build1 [10.7 kB] 163s Fetched 21.5 kB in 0s (76.1 kB/s) 163s (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 ... 70095 files and directories currently installed.) 163s Preparing to unpack .../ubuntu-minimal_1.536build1_ppc64el.deb ... 163s Unpacking ubuntu-minimal (1.536build1) over (1.536) ... 163s Preparing to unpack .../ubuntu-standard_1.536build1_ppc64el.deb ... 163s Unpacking ubuntu-standard (1.536build1) over (1.536) ... 163s Setting up ubuntu-minimal (1.536build1) ... 163s Setting up ubuntu-standard (1.536build1) ... 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 164s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 164s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 164s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 164s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 165s Reading package lists... 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Calculating upgrade... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s autopkgtest [00:11:30]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 169s autopkgtest [00:11:30]: @@@@@@@@@@@@@@@@@@@@ apt-source minimap2 173s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (dsc) [2315 B] 173s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (tar) [199 kB] 173s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe minimap2 2.26+dfsg-1 (diff) [11.5 kB] 173s gpgv: Signature made Thu Feb 29 15:00:20 2024 UTC 173s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 173s gpgv: Can't check signature: No public key 173s dpkg-source: warning: cannot verify inline signature for ./minimap2_2.26+dfsg-1.dsc: no acceptable signature found 173s autopkgtest [00:11:34]: testing package minimap2 version 2.26+dfsg-1 173s autopkgtest [00:11:34]: build not needed 174s autopkgtest [00:11:35]: test run-unit-test: preparing testbed 175s Reading package lists... 175s Building dependency tree... 175s Reading state information... 176s Starting pkgProblemResolver with broken count: 0 176s Starting 2 pkgProblemResolver with broken count: 0 176s Done 176s The following additional packages will be installed: 176s libc-dev-bin libc6-dev libcrypt-dev libminimap2-dev libnsl-dev libtirpc-dev 176s linux-libc-dev minimap2 python3-mappy rpcsvc-proto zlib1g-dev 176s Suggested packages: 176s glibc-doc manpages-dev 176s Recommended packages: 176s manpages manpages-dev libc-devtools 176s The following NEW packages will be installed: 176s autopkgtest-satdep libc-dev-bin libc6-dev libcrypt-dev libminimap2-dev 176s libnsl-dev libtirpc-dev linux-libc-dev minimap2 python3-mappy rpcsvc-proto 176s zlib1g-dev 176s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 5937 kB/5938 kB of archives. 176s After this operation, 25.6 MB of additional disk space will be used. 176s Get:1 /tmp/autopkgtest.ygY201/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 176s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu2 [21.3 kB] 176s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-11.11 [1585 kB] 177s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] 177s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1build1 [262 kB] 177s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libnsl-dev ppc64el 1.3.0-3 [79.2 kB] 177s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el rpcsvc-proto ppc64el 1.4.2-0ubuntu6 [82.3 kB] 177s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libc6-dev ppc64el 2.39-0ubuntu2 [2102 kB] 177s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3ubuntu1 [902 kB] 177s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libminimap2-dev ppc64el 2.26+dfsg-1 [146 kB] 177s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el minimap2 ppc64el 2.26+dfsg-1 [397 kB] 177s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el python3-mappy ppc64el 2.26+dfsg-1 [193 kB] 177s Fetched 5937 kB in 1s (6607 kB/s) 177s Selecting previously unselected package libc-dev-bin. 177s (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 ... 70095 files and directories currently installed.) 177s Preparing to unpack .../00-libc-dev-bin_2.39-0ubuntu2_ppc64el.deb ... 177s Unpacking libc-dev-bin (2.39-0ubuntu2) ... 177s Selecting previously unselected package linux-libc-dev:ppc64el. 177s Preparing to unpack .../01-linux-libc-dev_6.8.0-11.11_ppc64el.deb ... 177s Unpacking linux-libc-dev:ppc64el (6.8.0-11.11) ... 177s Selecting previously unselected package libcrypt-dev:ppc64el. 177s Preparing to unpack .../02-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... 177s Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) ... 177s Selecting previously unselected package libtirpc-dev:ppc64el. 177s Preparing to unpack .../03-libtirpc-dev_1.3.4+ds-1build1_ppc64el.deb ... 177s Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 177s Selecting previously unselected package libnsl-dev:ppc64el. 177s Preparing to unpack .../04-libnsl-dev_1.3.0-3_ppc64el.deb ... 177s Unpacking libnsl-dev:ppc64el (1.3.0-3) ... 177s Selecting previously unselected package rpcsvc-proto. 177s Preparing to unpack .../05-rpcsvc-proto_1.4.2-0ubuntu6_ppc64el.deb ... 177s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ... 177s Selecting previously unselected package libc6-dev:ppc64el. 177s Preparing to unpack .../06-libc6-dev_2.39-0ubuntu2_ppc64el.deb ... 177s Unpacking libc6-dev:ppc64el (2.39-0ubuntu2) ... 177s Selecting previously unselected package zlib1g-dev:ppc64el. 177s Preparing to unpack .../07-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_ppc64el.deb ... 177s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 177s Selecting previously unselected package libminimap2-dev. 177s Preparing to unpack .../08-libminimap2-dev_2.26+dfsg-1_ppc64el.deb ... 177s Unpacking libminimap2-dev (2.26+dfsg-1) ... 178s Selecting previously unselected package minimap2. 178s Preparing to unpack .../09-minimap2_2.26+dfsg-1_ppc64el.deb ... 178s Unpacking minimap2 (2.26+dfsg-1) ... 178s Selecting previously unselected package python3-mappy. 178s Preparing to unpack .../10-python3-mappy_2.26+dfsg-1_ppc64el.deb ... 178s Unpacking python3-mappy (2.26+dfsg-1) ... 178s Selecting previously unselected package autopkgtest-satdep. 178s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 178s Unpacking autopkgtest-satdep (0) ... 178s Setting up minimap2 (2.26+dfsg-1) ... 178s Setting up linux-libc-dev:ppc64el (6.8.0-11.11) ... 178s Setting up python3-mappy (2.26+dfsg-1) ... 178s Setting up libtirpc-dev:ppc64el (1.3.4+ds-1build1) ... 178s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 178s Setting up libnsl-dev:ppc64el (1.3.0-3) ... 178s Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... 178s Setting up libc-dev-bin (2.39-0ubuntu2) ... 178s Setting up libc6-dev:ppc64el (2.39-0ubuntu2) ... 178s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3ubuntu1) ... 178s Setting up libminimap2-dev (2.26+dfsg-1) ... 178s Setting up autopkgtest-satdep (0) ... 178s Processing triggers for man-db (2.12.0-3) ... 181s (Reading database ... 71885 files and directories currently installed.) 181s Removing autopkgtest-satdep (0) ... 181s autopkgtest [00:11:42]: test run-unit-test: [----------------------- 182s [M::mm_idx_gen::0.001*1.17] collected minimizers 182s [M::mm_idx_gen::0.003*1.03] sorted minimizers 182s [M::main::0.003*1.03] loaded/built the index for 1 target sequence(s) 182s [M::mm_mapopt_update::0.003*1.03] mid_occ = 10 182s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 182s [M::mm_idx_stat::0.003*1.03] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 182s [M::worker_pipeline::0.016*1.00] mapped 1 sequences 182s [M::main] Version: 2.26-r1175 182s [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa 182s [M::main] Real time: 0.017 sec; CPU: 0.016 sec; Peak RSS: 0.013 GB 182s [M::mm_idx_gen::0.001*1.27] collected minimizers 182s [M::mm_idx_gen::0.003*0.85] sorted minimizers 182s [M::main::0.006*0.90] loaded/built the index for 1 target sequence(s) 182s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 182s [M::mm_idx_stat::0.006*0.90] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 182s [M::main] Version: 2.26-r1175 182s [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa 182s [M::main] Real time: 0.007 sec; CPU: 0.006 sec; Peak RSS: 0.007 GB 182s [M::main::0.002*1.22] loaded/built the index for 1 target sequence(s) 182s [M::mm_mapopt_update::0.002*1.17] mid_occ = 10 182s [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 182s [M::mm_idx_stat::0.003*1.09] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 182s [M::worker_pipeline::0.015*0.99] mapped 1 sequences 182s [M::main] Version: 2.26-r1175 182s [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa 182s [M::main] Real time: 0.017 sec; CPU: 0.016 sec; Peak RSS: 0.013 GB 182s autopkgtest [00:11:43]: test run-unit-test: -----------------------] 182s autopkgtest [00:11:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 182s run-unit-test PASS 183s autopkgtest [00:11:44]: test command1: preparing testbed 184s Reading package lists... 184s Building dependency tree... 184s Reading state information... 184s Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 185s The following additional packages will be installed: 185s python3-all 185s The following NEW packages will be installed: 185s autopkgtest-satdep python3-all 185s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 185s Need to get 904 B/1632 B of archives. 185s After this operation, 6144 B of additional disk space will be used. 185s Get:1 /tmp/autopkgtest.ygY201/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [728 B] 185s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B] 185s Fetched 904 B in 0s (6008 B/s) 185s Selecting previously unselected package python3-all. 185s (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 ... 71885 files and directories currently installed.) 185s Preparing to unpack .../python3-all_3.12.1-0ubuntu2_ppc64el.deb ... 185s Unpacking python3-all (3.12.1-0ubuntu2) ... 185s Selecting previously unselected package autopkgtest-satdep. 185s Preparing to unpack .../2-autopkgtest-satdep.deb ... 185s Unpacking autopkgtest-satdep (0) ... 185s Setting up python3-all (3.12.1-0ubuntu2) ... 185s Setting up autopkgtest-satdep (0) ... 188s (Reading database ... 71886 files and directories currently installed.) 188s Removing autopkgtest-satdep (0) ... 188s autopkgtest [00:11:49]: 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 188s autopkgtest [00:11:49]: test command1: [----------------------- 188s Testing with python3.12: 188s 189s autopkgtest [00:11:50]: test command1: -----------------------] 189s autopkgtest [00:11:50]: test command1: - - - - - - - - - - results - - - - - - - - - - 189s command1 PASS (superficial) 190s autopkgtest [00:11:51]: @@@@@@@@@@@@@@@@@@@@ summary 190s run-unit-test PASS 190s command1 PASS (superficial) 239s Creating nova instance adt-noble-ppc64el-minimap2-20240320-000841-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240319.img (UUID 9d87beed-6c32-481f-958d-7469e26317f3)...