0s autopkgtest [17:56:57]: starting date and time: 2024-11-01 17:56:57+0000 0s autopkgtest [17:56:57]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [17:56:57]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m590365i/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-15@bos03-arm64-2.secgroup --name adt-plucky-arm64-rna-star-20241101-175657-juju-7f2275-prod-proposed-migration-environment-15-e87d0b4a-b283-49e0-8824-87f8a04ab5d2 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 84s autopkgtest [17:58:21]: testbed dpkg architecture: arm64 84s autopkgtest [17:58:21]: testbed apt version: 2.9.8 84s autopkgtest [17:58:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 85s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [183 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [44.0 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2775 kB] 86s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 86s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [241 kB] 86s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 86s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [2023 kB] 86s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [36.5 kB] 86s Fetched 5433 kB in 1s (4082 kB/s) 87s Reading package lists... 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Calculating upgrade... 91s The following packages will be upgraded: 91s libevdev2 libftdi1-2 libinih1 nano python3-lazr.uri 91s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 374 kB of archives. 91s After this operation, 17.4 kB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 91s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 91s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 91s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 92s Fetched 374 kB in 0s (837 kB/s) 92s (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 ... 79705 files and directories currently installed.) 92s Preparing to unpack .../libevdev2_1.13.3+dfsg-1_arm64.deb ... 92s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 92s Preparing to unpack .../archives/nano_8.2-1_arm64.deb ... 92s Unpacking nano (8.2-1) over (8.1-1) ... 92s Preparing to unpack .../libftdi1-2_1.5-7_arm64.deb ... 92s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 92s Preparing to unpack .../libinih1_58-1ubuntu1_arm64.deb ... 92s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 92s Preparing to unpack .../python3-lazr.uri_1.0.6-4_all.deb ... 93s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 93s Setting up libinih1:arm64 (58-1ubuntu1) ... 93s Setting up python3-lazr.uri (1.0.6-4) ... 93s Setting up libftdi1-2:arm64 (1.5-7) ... 93s Setting up nano (8.2-1) ... 93s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 93s Processing triggers for man-db (2.12.1-3) ... 94s Processing triggers for install-info (7.1.1-1) ... 94s Processing triggers for libc-bin (2.40-1ubuntu3) ... 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 95s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 97s Reading package lists... 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s Calculating upgrade... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s autopkgtest [17:58:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 102s autopkgtest [17:58:39]: @@@@@@@@@@@@@@@@@@@@ apt-source rna-star 104s Get:1 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (dsc) [2198 B] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (tar) [521 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/universe rna-star 2.7.11b+dfsg-1build1 (diff) [379 kB] 104s gpgv: Signature made Sun Apr 14 23:11:04 2024 UTC 104s gpgv: using RSA key AC0A4FF12611B6FCCF01C111393587D97D86500B 104s gpgv: Can't check signature: No public key 104s dpkg-source: warning: cannot verify inline signature for ./rna-star_2.7.11b+dfsg-1build1.dsc: no acceptable signature found 104s autopkgtest [17:58:41]: testing package rna-star version 2.7.11b+dfsg-1build1 105s autopkgtest [17:58:42]: build not needed 106s autopkgtest [17:58:43]: test command1: preparing testbed 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 110s The following additional packages will be installed: 110s libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 110s The following NEW packages will be installed: 110s autopkgtest-satdep libdeflate0 libgomp1 libhts3t64 libhtscodecs2 rna-star 110s 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 1474 kB/1475 kB of archives. 110s After this operation, 4580 kB of additional disk space will be used. 110s Get:1 /tmp/autopkgtest.tZ0ayE/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.21-1 [46.2 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhtscodecs2 arm64 1.6.0-1build1 [78.0 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libhts3t64 arm64 1.20+ds-2 [437 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 rna-star arm64 2.7.11b+dfsg-1build1 [769 kB] 111s Fetched 1474 kB in 1s (2213 kB/s) 111s Selecting previously unselected package libdeflate0:arm64. 111s (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 ... 79705 files and directories currently installed.) 111s Preparing to unpack .../0-libdeflate0_1.21-1_arm64.deb ... 111s Unpacking libdeflate0:arm64 (1.21-1) ... 111s Selecting previously unselected package libgomp1:arm64. 111s Preparing to unpack .../1-libgomp1_14.2.0-7ubuntu1_arm64.deb ... 111s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ... 111s Selecting previously unselected package libhtscodecs2:arm64. 111s Preparing to unpack .../2-libhtscodecs2_1.6.0-1build1_arm64.deb ... 111s Unpacking libhtscodecs2:arm64 (1.6.0-1build1) ... 111s Selecting previously unselected package libhts3t64:arm64. 111s Preparing to unpack .../3-libhts3t64_1.20+ds-2_arm64.deb ... 111s Unpacking libhts3t64:arm64 (1.20+ds-2) ... 111s Selecting previously unselected package rna-star. 111s Preparing to unpack .../4-rna-star_2.7.11b+dfsg-1build1_arm64.deb ... 111s Unpacking rna-star (2.7.11b+dfsg-1build1) ... 111s Selecting previously unselected package autopkgtest-satdep. 111s Preparing to unpack .../5-1-autopkgtest-satdep.deb ... 111s Unpacking autopkgtest-satdep (0) ... 111s Setting up libhtscodecs2:arm64 (1.6.0-1build1) ... 111s Setting up libdeflate0:arm64 (1.21-1) ... 111s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ... 111s Setting up libhts3t64:arm64 (1.20+ds-2) ... 111s Setting up rna-star (2.7.11b+dfsg-1build1) ... 111s Setting up autopkgtest-satdep (0) ... 111s Processing triggers for man-db (2.12.1-3) ... 112s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s (Reading database ... 79743 files and directories currently installed.) 116s Removing autopkgtest-satdep (0) ... 116s autopkgtest [17:58:53]: test command1: debian/tests/run_test.sh STAR 116s autopkgtest [17:58:53]: test command1: [----------------------- 116s STAR --runThreadN 1 --runMode genomeGenerate --genomeDir . --genomeSAindexNbases 8 --genomeFastaFiles foo.fa --sjdbGTFfile /tmp/autopkgtest.tZ0ayE/build.Gjj/src/debian/tests/foo.gtf 116s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 116s Nov 01 17:58:53 ..... started STAR run 116s Nov 01 17:58:53 ... starting to generate Genome files 116s Nov 01 17:58:53 ..... processing annotations GTF 116s !!!!! 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 116s Nov 01 17:58:53 ... starting to sort Suffix Array. This may take a long time... 116s Nov 01 17:58:53 ... sorting Suffix Array chunks and saving them to disk... 116s Nov 01 17:58:53 ... loading chunks from disk, packing SA... 116s Nov 01 17:58:53 ... finished generating suffix array 116s Nov 01 17:58:53 ... generating Suffix Array index 116s Nov 01 17:58:53 ... completed Suffix Array index 116s Nov 01 17:58:53 ... writing Genome to disk ... 116s Nov 01 17:58:53 ... writing Suffix Array to disk ... 116s Nov 01 17:58:53 ... writing SAindex to disk 116s Nov 01 17:58:53 ..... finished successfully 117s STAR --runThreadN 1 --genomeDir . --readFilesIn reads.fastq 117s STAR version: 2.7.11b compiled: 2024-04-14T23:10:25+00:00 117s Nov 01 17:58:53 ..... started STAR run 117s Nov 01 17:58:53 ..... loading genome 117s Nov 01 17:58:53 ..... started mapping 117s Nov 01 17:58:54 ..... finished mapping 117s Nov 01 17:58:54 ..... finished successfully 117s autopkgtest [17:58:54]: test command1: -----------------------] 118s autopkgtest [17:58:55]: test command1: - - - - - - - - - - results - - - - - - - - - - 118s command1 PASS 118s autopkgtest [17:58:55]: @@@@@@@@@@@@@@@@@@@@ summary 118s command1 PASS 137s nova [W] Skipping flock in bos03-arm64 137s Creating nova instance adt-plucky-arm64-rna-star-20241101-175657-juju-7f2275-prod-proposed-migration-environment-15-e87d0b4a-b283-49e0-8824-87f8a04ab5d2 from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...