0s autopkgtest [13:19:53]: starting date and time: 2024-11-04 13:19:53+0000 0s autopkgtest [13:19:53]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:19:53]: host juju-7f2275-prod-proposed-migration-environment-14; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a52bjawx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:htslib --apt-upgrade rna-star --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=htslib/1.20+ds-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-14@lcy02-63.secgroup --name adt-plucky-amd64-rna-star-20241104-124356-juju-7f2275-prod-proposed-migration-environment-14-07c31fa7-e25b-4318-9578-a2e4857c7549 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-14 --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/ 67s autopkgtest [13:21:00]: testbed dpkg architecture: amd64 67s autopkgtest [13:21:00]: testbed apt version: 2.9.8 67s autopkgtest [13:21:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 68s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 68s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 68s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 68s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 68s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [238 kB] 68s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [165 kB] 68s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 68s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [1715 kB] 68s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [833 kB] 68s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [18.1 kB] 68s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [58.6 kB] 68s Fetched 5618 kB in 1s (8201 kB/s) 69s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 72s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 72s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 72s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 73s Reading package lists... 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s autopkgtest [13:21:08]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 75s autopkgtest [13:21:08]: @@@@@@@@@@@@@@@@@@@@ apt-source rna-star 76s Get:1 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (dsc) [2198 B] 76s Get:2 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (tar) [521 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (diff) [379 kB] 76s gpgv: Signature made Sun Apr 14 23:11:04 2024 UTC 76s gpgv: using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B 76s gpgv: Can't check signature: No public key 76s dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-1build1.dsc: no acceptable signature found 76s autopkgtest [13:21:09]: testing package rna-star version 2.7.11b+dfsg-1build1 76s autopkgtest [13:21:09]: build not needed 76s autopkgtest [13:21:09]: test command1: preparing testbed 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 78s The following additional packages will be installed: 78s libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 78s The following NEW packages will be installed: 78s autopkgtest-satdep libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 78s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 2401 kB/2401 kB of archives. 78s After this operation, 18.5 MB of additional disk space will be used. 78s Get:1 /tmp/autopkgtest.vU0pud/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [704 B] 78s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.21-1 [49.8 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.0-1build1 [98.8 kB] 78s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libhts3t64 amd64 1.20+ds-2 [501 kB] 78s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 rna-star amd64 2.7.11b+dfsg-1build1 [1603 kB] 78s Fetched 2401 kB in 0s (13.5 MB/s) 78s Selecting previously unselected package libdeflate0:amd64. 78s (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 ... 75323 files and directories currently installed.) 78s Preparing to unpack .../0-libdeflate0_1.21-1_amd64.deb ... 78s Unpacking libdeflate0:amd64 (1.21-1) ... 78s Selecting previously unselected package libgomp1:amd64. 78s Preparing to unpack .../1-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 78s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 78s Selecting previously unselected package libhtscodecs2:amd64. 78s Preparing to unpack .../2-libhtscodecs2_1.6.0-1build1_amd64.deb ... 78s Unpacking libhtscodecs2:amd64 (1.6.0-1build1) ... 79s Selecting previously unselected package libhts3t64:amd64. 79s Preparing to unpack .../3-libhts3t64_1.20+ds-2_amd64.deb ... 79s Unpacking libhts3t64:amd64 (1.20+ds-2) ... 79s Selecting previously unselected package rna-star. 79s Preparing to unpack .../4-rna-star_2.7.11b+dfsg-1build1_amd64.deb ... 79s Unpacking rna-star (2.7.11b+dfsg-1build1) ... 79s Selecting previously unselected package autopkgtest-satdep. 79s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 79s Unpacking autopkgtest-satdep (0) ... 79s Setting up libhtscodecs2:amd64 (1.6.0-1build1) ... 79s Setting up libdeflate0:amd64 (1.21-1) ... 79s Setting up libgomp1:amd64 (14.2.0-7ubuntu1) ... 79s Setting up libhts3t64:amd64 (1.20+ds-2) ... 79s Setting up rna-star (2.7.11b+dfsg-1build1) ... 79s Setting up autopkgtest-satdep (0) ... 79s Processing triggers for man-db (2.12.1-3) ... 79s Processing triggers for libc-bin (2.40-1ubuntu3) ... 81s (Reading database ... 75376 files and directories currently installed.) 81s Removing autopkgtest-satdep (0) ... 82s autopkgtest [13:21:15]: test command1: debian/tests/run_test.sh STAR 82s autopkgtest [13:21:15]: test command1: [----------------------- 82s /usr/lib/rna-star/bin/STAR-avx2 --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /tmp/autopkgtest.vU0pud/build.3nm/src/debian/tests/foo.gtf 82s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 82s Nov 04 13:21:15 ..... started STAR run 82s Nov 04 13:21:15 ... starting to generate Genome files 82s Nov 04 13:21:15 ..... processing annotations GTF 82s !!!!! WARNING: --genomeSAindexNbases 8 is too large for the genome size=99940, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 7 82s Nov 04 13:21:15 ... starting to sort Suffix Array. This may take a long time... 82s Nov 04 13:21:15 ... sorting Suffix Array chunks and saving them to disk... 82s Nov 04 13:21:15 ... loading chunks from disk, packing SA... 82s Nov 04 13:21:15 ... finished generating suffix array 82s Nov 04 13:21:15 ... generating Suffix Array index 82s Nov 04 13:21:15 ... completed Suffix Array index 82s Nov 04 13:21:15 ... writing Genome to disk ... 82s Nov 04 13:21:15 ... writing Suffix Array to disk ... 82s Nov 04 13:21:15 ... writing SAindex to disk 82s Nov 04 13:21:15 ..... finished successfully 82s /usr/lib/rna-star/bin/STAR-avx2 --runThreadN 1 --genomeDir . --readFilesIn reads.fastq 82s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 82s Nov 04 13:21:15 ..... started STAR run 82s Nov 04 13:21:15 ..... loading genome 82s Nov 04 13:21:15 ..... started mapping 82s Nov 04 13:21:15 ..... finished mapping 82s Nov 04 13:21:15 ..... finished successfully 82s autopkgtest [13:21:15]: test command1: -----------------------] 83s command1 PASS 83s autopkgtest [13:21:16]: test command1: - - - - - - - - - - results - - - - - - - - - - 83s autopkgtest [13:21:16]: @@@@@@@@@@@@@@@@@@@@ summary 83s command1 PASS 95s nova [W] Skipping flock for amd64 95s Creating nova instance adt-plucky-amd64-rna-star-20241104-124356-juju-7f2275-prod-proposed-migration-environment-14-07c31fa7-e25b-4318-9578-a2e4857c7549 from image adt/ubuntu-plucky-amd64-server-20241104.img (UUID 0ab90577-a6b7-4a72-9ab8-957838d495c0)...