0s autopkgtest [13:31:25]: starting date and time: 2025-01-11 13:31:25+0000 0s autopkgtest [13:31:25]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:31:25]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2m_3getx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sra-sdk --apt-upgrade sra-sdk --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sra-sdk/3.0.9+dfsg-7ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-2.secgroup --name adt-plucky-amd64-sra-sdk-20250111-133125-juju-7f2275-prod-proposed-migration-environment-2-c7c067c4-aaa6-4fbc-948f-a12d49fb83e1 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 56s autopkgtest [13:32:21]: testbed dpkg architecture: amd64 56s autopkgtest [13:32:21]: testbed apt version: 2.9.18 56s autopkgtest [13:32:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 57s autopkgtest [13:32:22]: testbed release detected to be: None 57s autopkgtest [13:32:22]: updating testbed package index (apt update) 58s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 58s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [774 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.7 kB] 58s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 58s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [131 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [164 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [296 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 58s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [982 kB] 58s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [378 kB] 58s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3516 B] 58s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [13.0 kB] 58s Fetched 2881 kB in 1s (3094 kB/s) 59s Reading package lists... 60s + lsb_release --codename --short 60s + RELEASE=plucky 60s + cat 60s + [ plucky != trusty ] 60s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 61s + /usr/lib/apt/apt-helper analyze-pattern ?true 61s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove ?obsolete 61s 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 + grep -q trusty /etc/lsb-release 61s + [ ! -d /usr/share/doc/unattended-upgrades ] 61s + [ ! -d /usr/share/doc/lxd ] 61s + [ ! -d /usr/share/doc/lxd-client ] 61s + [ ! -d /usr/share/doc/snapd ] 61s + type iptables 61s + cat 61s + chmod 755 /etc/rc.local 61s + . /etc/rc.local 61s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 61s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 61s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 61s + uname -m 61s + [ x86_64 = ppc64le ] 61s + [ -d /run/systemd/system ] 61s + systemd-detect-virt --quiet --vm 61s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 61s + cat 61s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 61s + echo COMPRESS=lz4 61s autopkgtest [13:32:26]: upgrading testbed (apt dist-upgrade and autopurge) 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 62s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 62s Starting 2 pkgProblemResolver with broken count: 0 62s Done 62s Entering ResolveByKeep 63s 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Starting pkgProblemResolver with broken count: 0 63s Starting 2 pkgProblemResolver with broken count: 0 63s Done 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s autopkgtest [13:32:31]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 66s autopkgtest [13:32:31]: @@@@@@@@@@@@@@@@@@@@ apt-source sra-sdk 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (dsc) [2857 B] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (tar) [34.6 MB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe sra-sdk 3.0.9+dfsg-7ubuntu1 (diff) [3792 kB] 73s gpgv: Signature made Wed Oct 30 16:47:11 2024 UTC 73s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 73s gpgv: Can't check signature: No public key 73s dpkg-source: warning: cannot verify inline signature for ./sra-sdk_3.0.9+dfsg-7ubuntu1.dsc: no acceptable signature found 74s autopkgtest [13:32:39]: testing package sra-sdk version 3.0.9+dfsg-7ubuntu1 76s autopkgtest [13:32:41]: build not needed 83s autopkgtest [13:32:48]: test run-unit-test: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 84s The following NEW packages will be installed: 84s libaec0 libhdf5-103-1t64 libmbedcrypto16 libmbedtls21 libmbedx509-7 84s libncbi-ngs-dev libncbi-ngs3 libncbi-vdb3 libncbi-wvdb3 libngs-c++-dev 84s libngs-c++3 libngs-java libngs-java-doc libngs-jni libsz2 ncbi-vdb-data 84s python3-ngs sra-toolkit 85s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 12.7 MB of archives. 85s After this operation, 37.4 MB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-5ubuntu1 [1367 kB] 85s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 85s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 85s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 85s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [67.7 kB] 85s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1409 kB] 85s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libncbi-ngs3 amd64 3.0.9+dfsg-7ubuntu1 [165 kB] 85s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-c++3 amd64 3.0.9+dfsg-7ubuntu1 [131 kB] 85s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-c++-dev amd64 3.0.9+dfsg-7ubuntu1 [186 kB] 85s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libncbi-ngs-dev amd64 3.0.9+dfsg-7ubuntu1 [181 kB] 85s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-2 [1417 kB] 85s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-jni amd64 3.0.9+dfsg-7ubuntu1 [4846 B] 85s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-java amd64 3.0.9+dfsg-7ubuntu1 [91.1 kB] 85s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libngs-java-doc all 3.0.9+dfsg-7ubuntu1 [95.1 kB] 85s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-ngs all 3.0.9+dfsg-7ubuntu1 [24.3 kB] 85s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 sra-toolkit amd64 3.0.9+dfsg-7ubuntu1 [7092 kB] 86s Fetched 12.7 MB in 1s (11.4 MB/s) 86s Selecting previously unselected package libaec0:amd64. 86s (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 ... 75820 files and directories currently installed.) 86s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 86s Unpacking libaec0:amd64 (1.1.3-1) ... 86s Selecting previously unselected package libsz2:amd64. 86s Preparing to unpack .../01-libsz2_1.1.3-1_amd64.deb ... 86s Unpacking libsz2:amd64 (1.1.3-1) ... 86s Selecting previously unselected package libhdf5-103-1t64:amd64. 86s Preparing to unpack .../02-libhdf5-103-1t64_1.10.10+repack-5ubuntu1_amd64.deb ... 86s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 86s Selecting previously unselected package libmbedcrypto16:amd64. 86s Preparing to unpack .../03-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 86s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 86s Selecting previously unselected package libmbedx509-7:amd64. 86s Preparing to unpack .../04-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 86s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 86s Selecting previously unselected package libmbedtls21:amd64. 86s Preparing to unpack .../05-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 86s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 86s Selecting previously unselected package ncbi-vdb-data. 86s Preparing to unpack .../06-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ... 86s Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ... 86s Selecting previously unselected package libncbi-vdb3:amd64. 86s Preparing to unpack .../07-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ... 86s Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 86s Selecting previously unselected package libncbi-ngs3:amd64. 86s Preparing to unpack .../08-libncbi-ngs3_3.0.9+dfsg-7ubuntu1_amd64.deb ... 86s Unpacking libncbi-ngs3:amd64 (3.0.9+dfsg-7ubuntu1) ... 86s Selecting previously unselected package libngs-c++3:amd64. 86s Preparing to unpack .../09-libngs-c++3_3.0.9+dfsg-7ubuntu1_amd64.deb ... 86s Unpacking libngs-c++3:amd64 (3.0.9+dfsg-7ubuntu1) ... 86s Selecting previously unselected package libngs-c++-dev:amd64. 86s Preparing to unpack .../10-libngs-c++-dev_3.0.9+dfsg-7ubuntu1_amd64.deb ... 86s Unpacking libngs-c++-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 86s Selecting previously unselected package libncbi-ngs-dev:amd64. 86s Preparing to unpack .../11-libncbi-ngs-dev_3.0.9+dfsg-7ubuntu1_amd64.deb ... 86s Unpacking libncbi-ngs-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 86s Selecting previously unselected package libncbi-wvdb3:amd64. 86s Preparing to unpack .../12-libncbi-wvdb3_3.0.9+dfsg-2_amd64.deb ... 86s Unpacking libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 87s Selecting previously unselected package libngs-jni:amd64. 87s Preparing to unpack .../13-libngs-jni_3.0.9+dfsg-7ubuntu1_amd64.deb ... 87s Unpacking libngs-jni:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Selecting previously unselected package libngs-java:amd64. 87s Preparing to unpack .../14-libngs-java_3.0.9+dfsg-7ubuntu1_amd64.deb ... 87s Unpacking libngs-java:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Selecting previously unselected package libngs-java-doc. 87s Preparing to unpack .../15-libngs-java-doc_3.0.9+dfsg-7ubuntu1_all.deb ... 87s Unpacking libngs-java-doc (3.0.9+dfsg-7ubuntu1) ... 87s Selecting previously unselected package python3-ngs. 87s Preparing to unpack .../16-python3-ngs_3.0.9+dfsg-7ubuntu1_all.deb ... 87s Unpacking python3-ngs (3.0.9+dfsg-7ubuntu1) ... 87s Selecting previously unselected package sra-toolkit. 87s Preparing to unpack .../17-sra-toolkit_3.0.9+dfsg-7ubuntu1_amd64.deb ... 87s Unpacking sra-toolkit (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libaec0:amd64 (1.1.3-1) ... 87s Setting up libngs-c++3:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up ncbi-vdb-data (3.0.9+dfsg-2) ... 87s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 87s Setting up libsz2:amd64 (1.1.3-1) ... 87s Setting up libngs-java-doc (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libngs-c++-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 87s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 87s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-5ubuntu1) ... 87s Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ... 87s Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ... 87s Setting up libncbi-ngs3:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up sra-toolkit (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libngs-jni:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libngs-java:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up libncbi-ngs-dev:amd64 (3.0.9+dfsg-7ubuntu1) ... 87s Setting up python3-ngs (3.0.9+dfsg-7ubuntu1) ... 87s /usr/lib/python3/dist-packages/ngs/LibManager.py:123: SyntaxWarning: invalid escape sequence '\.' 87s arr = re.split('\.\s*|\-\s*|\s+', version_str) 87s Processing triggers for libc-bin (2.40-4ubuntu1) ... 89s autopkgtest [13:32:54]: test run-unit-test: [----------------------- 90s >>>>>Decompressing test-data archive... 90s dbGaP-0/ 90s dbGaP-0/SRR2042184.fasta 90s meta/ 90s meta/prj_phs710EA_test.ngc 90s meta/SRR6650398_experiment.xml 90s meta/SRR6650398.bam 90s meta/SRR2042184_run.xml 90s meta/SRR2042184_experiment.xml 90s meta/SRR6650398_illumina_run.xml 90s meta/SRR7032226_run.xml 90s meta/SRR7032226_experiment.xml 90s meta/reference.fna 90s meta/SRR6650398_fastq_run.xml 90s public/ 90s public/nannot/ 90s public/wgs/ 90s public/refseq/ 90s public/refseq/NC_000962.3 90s public/sra/ 90s public/sra/SRR7032226.sra 90s public/sra/SRR6650398.sra 90s public/sra/SRR2042184.sra 90s public/files/ 90s >>>>>Running test-sra... 117s 2025-01-11T13:33:22 test-sra.3.0.9 fatal: SIGNAL - Segmentation fault 117s autopkgtest [13:33:22]: test run-unit-test: -----------------------] 118s autopkgtest [13:33:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 118s run-unit-test FAIL non-zero exit status 1 118s autopkgtest [13:33:23]: @@@@@@@@@@@@@@@@@@@@ summary 118s run-unit-test FAIL non-zero exit status 1 136s nova [W] Skipping flock for amd64 136s Creating nova instance adt-plucky-amd64-sra-sdk-20250111-133125-juju-7f2275-prod-proposed-migration-environment-2-c7c067c4-aaa6-4fbc-948f-a12d49fb83e1 from image adt/ubuntu-plucky-amd64-server-20250111.img (UUID 583b1e24-63f4-4305-9a48-aa6a34658dc0)... 136s nova [W] Timed out waiting for 49544289-97ac-4ec6-961b-5aedbc2c3137 to get deleted.