0s autopkgtest [07:43:04]: starting date and time: 2024-11-03 07:43:04+0000 0s autopkgtest [07:43:04]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [07:43:04]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.opfh7kwu/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-18.secgroup --name adt-plucky-ppc64el-rna-star-20241103-074304-juju-7f2275-prod-proposed-migration-environment-15-b5321b9d-4ff8-45ba-80fa-3f2bd37eec06 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/ 122s autopkgtest [07:45:06]: testbed dpkg architecture: ppc64el 123s autopkgtest [07:45:07]: testbed apt version: 2.9.8 123s autopkgtest [07:45:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 124s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [177 kB] 125s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2268 kB] 127s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [31.2 kB] 127s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 127s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [213 kB] 127s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1576 kB] 127s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [37.8 kB] 128s Fetched 4384 kB in 4s (1124 kB/s) 128s Reading package lists... 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Calculating upgrade... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 132s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 132s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 133s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Calculating upgrade... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s autopkgtest [07:45:22]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 138s autopkgtest [07:45:22]: @@@@@@@@@@@@@@@@@@@@ apt-source rna-star 140s Get:1 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (dsc) [2198 B] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (tar) [521 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (diff) [379 kB] 141s gpgv: Signature made Sun Apr 14 23:11:04 2024 UTC 141s gpgv: using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B 141s gpgv: Can't check signature: No public key 141s dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-1build1.dsc: no acceptable signature found 141s autopkgtest [07:45:25]: testing package rna-star version 2.7.11b+dfsg-1build1 141s autopkgtest [07:45:25]: build not needed 142s autopkgtest [07:45:26]: test command1: preparing testbed 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 145s The following additional packages will be installed: 145s libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 145s The following NEW packages will be installed: 145s autopkgtest-satdep libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 145s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 1713 kB/1714 kB of archives. 145s After this operation, 5629 kB of additional disk space will be used. 145s Get:1 /tmp/autopkgtest.jO928H/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.21-1 [63.3 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-7ubuntu1 [161 kB] 145s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1build1 [110 kB] 145s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el libhts3t64 ppc64el 1.20+ds-2 [574 kB] 146s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el rna-star ppc64el 2.7.11b+dfsg-1build1 [806 kB] 147s Fetched 1713 kB in 2s (745 kB/s) 147s Selecting previously unselected package libdeflate0:ppc64el. 147s (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 ... 73549 files and directories currently installed.) 147s Preparing to unpack .../0-libdeflate0_1.21-1_ppc64el.deb ... 147s Unpacking libdeflate0:ppc64el (1.21-1) ... 147s Selecting previously unselected package libgomp1:ppc64el. 147s Preparing to unpack .../1-libgomp1_14.2.0-7ubuntu1_ppc64el.deb ... 147s Unpacking libgomp1:ppc64el (14.2.0-7ubuntu1) ... 147s Selecting previously unselected package libhtscodecs2:ppc64el. 147s Preparing to unpack .../2-libhtscodecs2_1.6.0-1build1_ppc64el.deb ... 147s Unpacking libhtscodecs2:ppc64el (1.6.0-1build1) ... 147s Selecting previously unselected package libhts3t64:ppc64el. 147s Preparing to unpack .../3-libhts3t64_1.20+ds-2_ppc64el.deb ... 147s Unpacking libhts3t64:ppc64el (1.20+ds-2) ... 147s Selecting previously unselected package rna-star. 147s Preparing to unpack .../4-rna-star_2.7.11b+dfsg-1build1_ppc64el.deb ... 147s Unpacking rna-star (2.7.11b+dfsg-1build1) ... 147s Selecting previously unselected package autopkgtest-satdep. 147s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 147s Unpacking autopkgtest-satdep (0) ... 147s Setting up libhtscodecs2:ppc64el (1.6.0-1build1) ... 147s Setting up libdeflate0:ppc64el (1.21-1) ... 147s Setting up libgomp1:ppc64el (14.2.0-7ubuntu1) ... 147s Setting up libhts3t64:ppc64el (1.20+ds-2) ... 147s Setting up rna-star (2.7.11b+dfsg-1build1) ... 147s Setting up autopkgtest-satdep (0) ... 147s Processing triggers for man-db (2.12.1-3) ... 148s Processing triggers for libc-bin (2.40-1ubuntu3) ... 151s (Reading database ... 73587 files and directories currently installed.) 151s Removing autopkgtest-satdep (0) ... 152s autopkgtest [07:45:36]: test command1: debian/tests/run_test.sh STAR 152s autopkgtest [07:45:36]: test command1: [----------------------- 152s STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /tmp/autopkgtest.jO928H/build.Tjz/src/debian/tests/foo.gtf 152s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 152s Nov 03 07:45:36 ..... started STAR run 152s Nov 03 07:45:36 ... starting to generate Genome files 152s Nov 03 07:45:36 ..... processing annotations GTF 152s !!!!! 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 152s Nov 03 07:45:36 ... starting to sort Suffix Array. This may take a long time... 152s Nov 03 07:45:36 ... sorting Suffix Array chunks and saving them to disk... 152s Nov 03 07:45:36 ... loading chunks from disk, packing SA... 152s Nov 03 07:45:36 ... finished generating suffix array 152s Nov 03 07:45:36 ... generating Suffix Array index 152s Nov 03 07:45:36 ... completed Suffix Array index 152s Nov 03 07:45:36 ... writing Genome to disk ... 152s Nov 03 07:45:36 ... writing Suffix Array to disk ... 152s Nov 03 07:45:36 ... writing SAindex to disk 152s Nov 03 07:45:36 ..... finished successfully 152s STAR --runThreadN 1 --genomeDir . --readFilesIn reads.fastq 152s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 152s Nov 03 07:45:36 ..... started STAR run 152s Nov 03 07:45:36 ..... loading genome 152s Nov 03 07:45:36 ..... started mapping 152s Nov 03 07:45:36 ..... finished mapping 153s Nov 03 07:45:36 ..... finished successfully 153s autopkgtest [07:45:37]: test command1: -----------------------] 153s autopkgtest [07:45:37]: test command1: - - - - - - - - - - results - - - - - - - - - - 153s command1 PASS 154s autopkgtest [07:45:38]: @@@@@@@@@@@@@@@@@@@@ summary 154s command1 PASS 158s nova [W] Using flock in prodstack6-ppc64el 158s Creating nova instance adt-plucky-ppc64el-rna-star-20241103-074304-juju-7f2275-prod-proposed-migration-environment-15-b5321b9d-4ff8-45ba-80fa-3f2bd37eec06 from image adt/ubuntu-plucky-ppc64el-server-20241103.img (UUID 8938751d-c60c-4749-8c34-7df179962ea5)...