0s autopkgtest [13:35:45]: starting date and time: 2024-11-14 13:35:45+0000 0s autopkgtest [13:35:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:35:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5ibv4utg/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sra-sdk,src:libxml2 --apt-upgrade sra-sdk --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=sra-sdk/3.0.9+dfsg-7ubuntu1 libxml2/2.12.7+dfsg+really2.9.14-0.2build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-23.secgroup --name adt-plucky-amd64-sra-sdk-20241114-133545-juju-7f2275-prod-proposed-migration-environment-20-a0fe7f64-5414-4516-9b76-9d009a928254 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 52s autopkgtest [13:36:37]: testbed dpkg architecture: amd64 52s autopkgtest [13:36:37]: testbed apt version: 2.9.8 52s autopkgtest [13:36:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 54s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [983 kB] 54s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 54s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 54s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 54s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.9 kB] 54s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [138 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [749 kB] 55s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [291 kB] 55s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B] 55s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B] 55s Fetched 2484 kB in 2s (1387 kB/s) 55s Reading package lists... 57s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 58s The following packages will be upgraded: 58s libxml2 pastebinit 58s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 787 kB of archives. 58s After this operation, 402 kB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2build1 [772 kB] 59s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 59s Fetched 787 kB in 1s (979 kB/s) 60s (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 ... 75542 files and directories currently installed.) 60s Preparing to unpack .../libxml2_2.12.7+dfsg+really2.9.14-0.2build1_amd64.deb ... 60s Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2build1) over (2.12.7+dfsg-3) ... 60s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 60s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 60s Setting up pastebinit (1.7.1-1) ... 60s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2build1) ... 60s Processing triggers for man-db (2.12.1-3) ... 60s Processing triggers for libc-bin (2.40-1ubuntu3) ... 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 61s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 61s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 61s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 62s Reading package lists... 62s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Calculating upgrade... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [13:36:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 66s autopkgtest [13:36:51]: @@@@@@@@@@@@@@@@@@@@ apt-source sra-sdk 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (dsc) [2857 B] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (tar) [34.6 MB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (diff) [3792 kB] 76s gpgv: Signature made Wed Oct 30 16:47:11 2024 UTC 76s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 76s gpgv: Can't check signature: No public key 76s dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.9+dfsg-7ubuntu1.dsc: no acceptable signature found 77s autopkgtest [13:37:02]: testing package sra-sdk version 3.0.9+dfsg-7ubuntu1 80s autopkgtest [13:37:05]: build not needed 98s autopkgtest [13:37:23]: test run-unit-test: preparing testbed 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 101s The following additional packages will be installed: 101s libaec0 libhdf5-103-1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 101s libncbi-ngs-dev libncbi-ngs3 libncbi-vdb3 libncbi-wvdb3 libngs-c++-dev 101s libngs-c++3 libngs-java libngs-java-doc libngs-jni libsz2 ncbi-vdb-data 101s python3-ngs sra-toolkit 101s Recommended packages: 101s med-config 101s The following NEW packages will be installed: 101s autopkgtest-satdep libaec0 libhdf5-103-1t64 libmbedcrypto16 libmbedtls21 101s libmbedx509-7 libncbi-ngs-dev libncbi-ngs3 libncbi-vdb3 libncbi-wvdb3 101s libngs-c++-dev libngs-c++3 libngs-java libngs-java-doc libngs-jni libsz2 101s ncbi-vdb-data python3-ngs sra-toolkit 101s 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 12.6 MB/12.6 MB of archives. 101s After this operation, 37.1 MB of additional disk space will be used. 101s Get:1 /tmp/autopkgtest.Yzs08d/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [764 B] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-2ubuntu1 [275 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-2ubuntu1 [37.1 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-2ubuntu1 [126 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [67.7 kB] 102s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1409 kB] 102s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7ubuntu1 [165 kB] 102s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-c++3 amd64 3.0.9+dfsg-7ubuntu1 [131 kB] 102s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-c++-dev amd64 3.0.9+dfsg-7ubuntu1 [186 kB] 102s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libncbi-ngs-dev amd64 3.0.9+dfsg-7ubuntu1 [181 kB] 102s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-2 [1417 kB] 102s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-jni amd64 3.0.9+dfsg-7ubuntu1 [4846 B] 102s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-java amd64 3.0.9+dfsg-7ubuntu1 [91.1 kB] 102s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-java-doc all 3.0.9+dfsg-7ubuntu1 [95.1 kB] 102s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-ngs all 3.0.9+dfsg-7ubuntu1 [24.3 kB] 102s Get:19 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 sra-toolkit amd64 3.0.9+dfsg-7ubuntu1 [7092 kB] 103s Fetched 12.6 MB in 1s (8789 kB/s) 103s Selecting previously unselected package libaec0:amd64. 103s (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 ... 75542 files and directories currently installed.) 103s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 103s Unpacking libaec0:amd64 (1.1.3-1) ... 103s Selecting previously unselected package libsz2:amd64. 103s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ... 103s Unpacking libsz2:amd64 (1.1.3-1) ... 103s Selecting previously unselected package libhdf5-103-1t64:amd64. 103s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 103s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 103s Selecting previously unselected package libmbedcrypto16:amd64. 103s Preparing to unpack .../03-libmbedcrypto16_3.6.2-2ubuntu1_amd64.deb ... 103s Unpacking libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 103s Selecting previously unselected package libmbedx509-7:amd64. 103s Preparing to unpack .../04-libmbedx509-7_3.6.2-2ubuntu1_amd64.deb ... 103s Unpacking libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 103s Selecting previously unselected package libmbedtls21:amd64. 103s Preparing to unpack .../05-libmbedtls21_3.6.2-2ubuntu1_amd64.deb ... 103s Unpacking libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 103s Selecting previously unselected package ncbi-vdb-data. 103s Preparing to unpack .../06-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ... 103s Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ... 103s Selecting previously unselected package libncbi-vdb3:amd64. 103s Preparing to unpack .../07-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ... 103s Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 103s Selecting previously unselected package libncbi-ngs3:amd64. 103s Preparing to unpack .../08-libncbi-ngs3_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libncbi-ngs3:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libngs-c++3:amd64. 103s Preparing to unpack .../09-libngs-c++3_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libngs-c++3:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libngs-c++-dev:amd64. 103s Preparing to unpack .../10-libngs-c++-dev_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libngs-c++-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libncbi-ngs-dev:amd64. 103s Preparing to unpack .../11-libncbi-ngs-dev_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libncbi-ngs-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libncbi-wvdb3:amd64. 103s Preparing to unpack .../12-libncbi-wvdb3_3.0.9+dfsg-2_amd64.deb ... 103s Unpacking libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 103s Selecting previously unselected package libngs-jni:amd64. 103s Preparing to unpack .../13-libngs-jni_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libngs-jni:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libngs-java:amd64. 103s Preparing to unpack .../14-libngs-java_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking libngs-java:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package libngs-java-doc. 103s Preparing to unpack .../15-libngs-java-doc_3.0.9+dfsg-7ubuntu1_all.deb ... 103s Unpacking libngs-java-doc (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package python3-ngs. 103s Preparing to unpack .../16-python3-ngs_3.0.9+dfsg-7ubuntu1_all.deb ... 103s Unpacking python3-ngs (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package sra-toolkit. 103s Preparing to unpack .../17-sra-toolkit_3.0.9+dfsg-7ubuntu1_amd64.deb ... 103s Unpacking sra-toolkit (3.0.9+dfsg-7ubuntu1) ... 103s Selecting previously unselected package autopkgtest-satdep. 103s Preparing to unpack .../18-1-autopkgtest-satdep.deb ... 103s Unpacking autopkgtest-satdep (0) ... 103s Setting up libaec0:amd64 (1.1.3-1) ... 103s Setting up libngs-c++3:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... 103s Setting up libmbedcrypto16:amd64 (3.6.2-2ubuntu1) ... 103s Setting up libsz2:amd64 (1.1.3-1) ... 103s Setting up libngs-java-doc (3.0.9+dfsg-7ubuntu1) ... 103s Setting up libngs-c++-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up libmbedx509-7:amd64 (3.6.2-2ubuntu1) ... 103s Setting up libmbedtls21:amd64 (3.6.2-2ubuntu1) ... 103s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 103s Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 103s Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 103s Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up sra-toolkit (3.0.9+dfsg-7ubuntu1) ... 103s Setting up libngs-jni:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up libngs-java:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up libncbi-ngs-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 103s Setting up python3-ngs (3.0.9+dfsg-7ubuntu1) ... 104s /usr/lib/python3/dist-packages/ngs/LibManager.py:123: SyntaxWarning: invalid escape sequence '\.' 104s arr = re.split('\.\s*|\-\s*|\s+', version_str) 104s Setting up autopkgtest-satdep (0) ... 104s Processing triggers for libc-bin (2.40-1ubuntu3) ... 108s (Reading database ... 76040 files and directories currently installed.) 108s Removing autopkgtest-satdep (0) ... 109s autopkgtest [13:37:34]: test run-unit-test: [----------------------- 109s >>>>>Decompressing test-data archive... 109s dbGaP-0/ 109s dbGaP-0/SRR2042184.fasta 109s meta/ 109s meta/prj_phs710EA_test.ngc 109s meta/SRR6650398_experiment.xml 109s meta/SRR6650398.bam 109s meta/SRR2042184_run.xml 109s meta/SRR2042184_experiment.xml 109s meta/SRR6650398_illumina_run.xml 109s meta/SRR7032226_run.xml 109s meta/SRR7032226_experiment.xml 109s meta/reference.fna 109s meta/SRR6650398_fastq_run.xml 109s public/ 109s public/nannot/ 109s public/wgs/ 109s public/refseq/ 109s public/refseq/NC_000962.3 109s public/sra/ 109s public/sra/SRR7032226.sra 109s public/sra/SRR6650398.sra 109s public/sra/SRR2042184.sra 109s public/files/ 109s >>>>>Running test-sra... 136s 2024-11-14T13:38:00 test-sra.3.0.9 fatal: SIGNAL - Segmentation fault 136s autopkgtest [13:38:01]: test run-unit-test: -----------------------] 137s autopkgtest [13:38:02]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 137s run-unit-test FAIL non-zero exit status 1 137s autopkgtest [13:38:02]: @@@@@@@@@@@@@@@@@@@@ summary 137s run-unit-test FAIL non-zero exit status 1 149s nova [W] Skipping flock for amd64 149s Creating nova instance adt-plucky-amd64-sra-sdk-20241114-133545-juju-7f2275-prod-proposed-migration-environment-20-a0fe7f64-5414-4516-9b76-9d009a928254 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...