0s autopkgtest [23:02:24]: starting date and time: 2025-02-15 23:02:24+0000 0s autopkgtest [23:02:24]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:02:24]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qvxgec6_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade parsnp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-24.secgroup --name adt-plucky-s390x-parsnp-20250215-230224-juju-7f2275-prod-proposed-migration-environment-20-69ab2332-c6c8-4cfe-b191-9fbd7328fc14 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 102s autopkgtest [23:04:06]: testbed dpkg architecture: s390x 102s autopkgtest [23:04:06]: testbed apt version: 2.9.28 103s autopkgtest [23:04:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s autopkgtest [23:04:07]: testbed release detected to be: None 104s autopkgtest [23:04:08]: updating testbed package index (apt update) 104s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 104s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 104s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 104s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 104s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.3 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [828 kB] 105s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 105s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 105s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [163 kB] 105s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [760 B] 105s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [876 kB] 105s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3740 B] 105s Fetched 2073 kB in 1s (2148 kB/s) 105s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Calculating upgrade... 106s The following packages were automatically installed and are no longer required: 106s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 106s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 106s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 106s linux-tools-6.11.0-8-generic 106s Use 'sudo apt autoremove' to remove them. 106s The following packages will be upgraded: 106s dash gcc-14-base libatomic1 libgcc-s1 libstdc++6 libtasn1-6 libxdmcp6 106s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 1155 kB of archives. 106s After this operation, 16.4 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x dash s390x 0.5.12-12ubuntu1 [100 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libatomic1 s390x 14.2.0-17ubuntu1 [9430 B] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x gcc-14-base s390x 14.2.0-17ubuntu1 [53.5 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libstdc++6 s390x 14.2.0-17ubuntu1 [896 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgcc-s1 s390x 14.2.0-17ubuntu1 [35.9 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libtasn1-6 s390x 4.20.0-2 [48.6 kB] 107s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libxdmcp6 s390x 1:1.1.5-1 [11.0 kB] 107s Preconfiguring packages ... 107s Fetched 1155 kB in 1s (1876 kB/s) 107s (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 ... 80969 files and directories currently installed.) 107s Preparing to unpack .../dash_0.5.12-12ubuntu1_s390x.deb ... 107s Unpacking dash (0.5.12-12ubuntu1) over (0.5.12-9ubuntu1) ... 107s Setting up dash (0.5.12-12ubuntu1) ... 107s (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 ... 80969 files and directories currently installed.) 107s Preparing to unpack .../libatomic1_14.2.0-17ubuntu1_s390x.deb ... 107s Unpacking libatomic1:s390x (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 107s Preparing to unpack .../gcc-14-base_14.2.0-17ubuntu1_s390x.deb ... 107s Unpacking gcc-14-base:s390x (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 107s Setting up gcc-14-base:s390x (14.2.0-17ubuntu1) ... 107s (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 ... 80969 files and directories currently installed.) 107s Preparing to unpack .../libstdc++6_14.2.0-17ubuntu1_s390x.deb ... 107s Unpacking libstdc++6:s390x (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 107s Setting up libstdc++6:s390x (14.2.0-17ubuntu1) ... 108s (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 ... 80969 files and directories currently installed.) 108s Preparing to unpack .../libgcc-s1_14.2.0-17ubuntu1_s390x.deb ... 108s Unpacking libgcc-s1:s390x (14.2.0-17ubuntu1) over (14.2.0-16ubuntu1) ... 108s Setting up libgcc-s1:s390x (14.2.0-17ubuntu1) ... 108s (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 ... 80969 files and directories currently installed.) 108s Preparing to unpack .../libtasn1-6_4.20.0-2_s390x.deb ... 108s Unpacking libtasn1-6:s390x (4.20.0-2) over (4.19.0-3build1) ... 108s Preparing to unpack .../libxdmcp6_1%3a1.1.5-1_s390x.deb ... 108s Unpacking libxdmcp6:s390x (1:1.1.5-1) over (1:1.1.3-0ubuntu6) ... 108s Setting up libxdmcp6:s390x (1:1.1.5-1) ... 108s Setting up libatomic1:s390x (14.2.0-17ubuntu1) ... 108s Setting up libtasn1-6:s390x (4.20.0-2) ... 108s Processing triggers for libc-bin (2.40-4ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 108s Processing triggers for debianutils (5.21) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s The following packages will be REMOVED: 109s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 109s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 109s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 109s linux-tools-6.11.0-8-generic* 109s 0 upgraded, 0 newly installed, 9 to remove and 6 not upgraded. 109s After this operation, 167 MB disk space will be freed. 109s (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 ... 80969 files and directories currently installed.) 109s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 109s Removing libpython3.12t64:s390x (3.12.9-1) ... 109s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 109s Removing libnsl2:s390x (1.3.0-3build3) ... 109s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 109s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 109s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 110s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s Processing triggers for libc-bin (2.40-4ubuntu1) ... 110s (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 ... 55869 files and directories currently installed.) 110s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 110s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 110s autopkgtest [23:04:14]: upgrading testbed (apt dist-upgrade and autopurge) 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 111s Entering ResolveByKeep 111s 111s The following packages will be upgraded: 111s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 111s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 10.7 MB of archives. 111s After this operation, 305 kB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu1 [24.3 kB] 111s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu1 [1679 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu1 [4246 kB] 112s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu1 [2891 kB] 112s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu1 [672 kB] 112s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x iproute2 s390x 6.13.0-1ubuntu1 [1174 kB] 112s Preconfiguring packages ... 112s Fetched 10.7 MB in 1s (11.8 MB/s) 112s (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 ... 55867 files and directories currently installed.) 112s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_s390x.deb ... 112s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 112s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_s390x.deb ... 112s Unpacking libc6-dev:s390x (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 112s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 112s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 112s Preparing to unpack .../libc6_2.41-1ubuntu1_s390x.deb ... 112s Checking for services that may need to be restarted... 112s Checking init scripts... 112s Checking for services that may need to be restarted... 112s Checking init scripts... 112s Stopping some services possibly affected by the upgrade (will be restarted later): 112s cron: stopping...done. 112s 112s Unpacking libc6:s390x (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 112s Setting up libc6:s390x (2.41-1ubuntu1) ... 112s Checking for services that may need to be restarted... 112s Checking init scripts... 112s Restarting services possibly affected by the upgrade: 112s cron: restarting...done. 112s 112s Services restarted successfully. 113s (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 ... 55868 files and directories currently installed.) 113s Preparing to unpack .../libc-bin_2.41-1ubuntu1_s390x.deb ... 113s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 113s Setting up libc-bin (2.41-1ubuntu1) ... 113s (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 ... 55868 files and directories currently installed.) 113s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_s390x.deb ... 113s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 113s Setting up iproute2 (6.13.0-1ubuntu1) ... 113s Setting up locales (2.41-1ubuntu1) ... 113s Installing new version of config file /etc/locale.alias ... 113s Generating locales (this might take a while)... 114s en_US.UTF-8... done 114s Generation complete. 114s Setting up libc-dev-bin (2.41-1ubuntu1) ... 114s Setting up libc6-dev:s390x (2.41-1ubuntu1) ... 114s Processing triggers for man-db (2.13.0-1) ... 115s Processing triggers for systemd (257.2-3ubuntu1) ... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 116s Starting pkgProblemResolver with broken count: 0 116s Starting 2 pkgProblemResolver with broken count: 0 116s Done 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s autopkgtest [23:04:20]: rebooting testbed after setup commands that affected boot 135s autopkgtest [23:04:39]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb 4 15:05:57 UTC 2025 138s autopkgtest [23:04:42]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 139s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (dsc) [2258 B] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (tar) [141 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (diff) [10.2 kB] 140s gpgv: Signature made Tue Apr 16 02:55:48 2024 UTC 140s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 140s gpgv: issuer "steve.langasek@ubuntu.com" 140s gpgv: Can't check signature: No public key 140s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1ubuntu1.dsc: no acceptable signature found 140s autopkgtest [23:04:44]: testing package parsnp version 2.0.3+dfsg-1ubuntu1 140s autopkgtest [23:04:44]: build not needed 140s autopkgtest [23:04:44]: test run-unit-test: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s Starting pkgProblemResolver with broken count: 0 141s Starting 2 pkgProblemResolver with broken count: 0 141s Done 141s The following NEW packages will be installed: 141s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono 141s fonts-urw-base35 harvest-tools libblas3 libcairo2 libcapnp-1.1.0 libdeflate0 141s libfontconfig1 libfontenc1 libfreetype6 libgfortran5 libgomp1 libgraphite2-3 141s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 141s liblcms2-2 libmuscle1 libopenjp2-7 libpixman-1-0 libprotobuf32t64 libraqm0 141s libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 141s libxcb-render0 libxcb-shm0 libxrender1 mummer parsnp phipack 141s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 141s python3-pyspoa python3-reportlab python3-rlpycairo python3-tqdm raxml 141s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 141s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 34.1 MB of archives. 141s After this operation, 115 MB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x sgml-base all 1.31 [11.4 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-dejavu-core all 2.37-8 [835 kB] 142s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libfreetype6 s390x 2.13.3+dfsg-1 [431 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x xfonts-utils s390x 1:7.7+7 [101 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] 142s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] 142s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x libcapnp-1.1.0 s390x 1.1.0-2 [1441 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libprotobuf32t64 s390x 3.21.12-10build1 [944 kB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x harvest-tools s390x 1.3-8build6 [132 kB] 142s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 142s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] 142s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x libpixman-1-0 s390x 0.44.0-3 [201 kB] 142s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-render0 s390x 1.17.0-2 [17.0 kB] 142s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x libxcb-shm0 s390x 1.17.0-2 [5862 B] 142s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] 142s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x libcairo2 s390x 1.18.2-2 [580 kB] 142s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 142s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-17ubuntu1 [588 kB] 142s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x libgomp1 s390x 14.2.0-17ubuntu1 [151 kB] 142s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x libgraphite2-3 s390x 1.3.14-2ubuntu1 [79.8 kB] 142s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x libharfbuzz0b s390x 10.2.0-1 [538 kB] 142s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x libimagequant0 s390x 2.18.0-1build1 [43.3 kB] 142s Get:27 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg-turbo8 s390x 2.1.5-3ubuntu2 [147 kB] 142s Get:28 http://ftpmaster.internal/ubuntu plucky/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] 142s Get:29 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 143s Get:30 http://ftpmaster.internal/ubuntu plucky/main s390x liblcms2-2 s390x 2.16-2 [175 kB] 143s Get:31 http://ftpmaster.internal/ubuntu plucky/universe s390x libmuscle1 s390x 3.7+4565-8 [259 kB] 143s Get:32 http://ftpmaster.internal/ubuntu plucky/main s390x libraqm0 s390x 0.10.2-1 [15.8 kB] 143s Get:33 http://ftpmaster.internal/ubuntu plucky/main s390x libsharpyuv0 s390x 1.5.0-0.1 [16.7 kB] 143s Get:34 http://ftpmaster.internal/ubuntu plucky/universe s390x libspoa7.0.0 s390x 4.1.4-2 [82.1 kB] 143s Get:35 http://ftpmaster.internal/ubuntu plucky/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] 143s Get:36 http://ftpmaster.internal/ubuntu plucky/main s390x libwebp7 s390x 1.5.0-0.1 [210 kB] 143s Get:37 http://ftpmaster.internal/ubuntu plucky/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu4 [217 kB] 143s Get:38 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpdemux2 s390x 1.5.0-0.1 [12.6 kB] 143s Get:39 http://ftpmaster.internal/ubuntu plucky/main s390x libwebpmux3 s390x 1.5.0-0.1 [25.8 kB] 143s Get:40 http://ftpmaster.internal/ubuntu plucky/universe s390x mummer s390x 3.23+dfsg-8 [674 kB] 143s Get:41 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-13 [4601 kB] 143s Get:42 http://ftpmaster.internal/ubuntu plucky/main s390x libopenjp2-7 s390x 2.5.0-2ubuntu3 [208 kB] 143s Get:43 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pil s390x 11.1.0-5 [527 kB] 143s Get:44 http://ftpmaster.internal/ubuntu plucky/main s390x python3-cairo s390x 1.26.1-2build1 [138 kB] 143s Get:45 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-freetype all 2.5.1-1 [92.3 kB] 143s Get:46 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-rlpycairo all 0.3.0-3 [9130 B] 143s Get:47 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-reportlab all 4.3.0-1 [1137 kB] 143s Get:48 http://ftpmaster.internal/ubuntu plucky/main s390x xml-core all 0.19 [20.3 kB] 143s Get:49 http://ftpmaster.internal/ubuntu plucky/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] 143s Get:50 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biopython s390x 1.85+dfsg-2 [1756 kB] 143s Get:51 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pyspoa s390x 0.2.1-1 [89.0 kB] 143s Get:52 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-tqdm all 4.67.1-2 [92.5 kB] 143s Get:53 http://ftpmaster.internal/ubuntu plucky/universe s390x fasttree s390x 2.1.11-2 [190 kB] 143s Get:54 http://ftpmaster.internal/ubuntu plucky/universe s390x phipack s390x 0.0.20160614-5 [56.5 kB] 143s Get:55 http://ftpmaster.internal/ubuntu plucky/universe s390x raxml s390x 8.2.13+dfsg-1 [1218 kB] 143s Get:56 http://ftpmaster.internal/ubuntu plucky/universe s390x parsnp s390x 2.0.3+dfsg-1ubuntu1 [193 kB] 143s Fetched 34.1 MB in 2s (18.5 MB/s) 143s Selecting previously unselected package sgml-base. 143s (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 ... 55869 files and directories currently installed.) 143s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 143s Unpacking sgml-base (1.31) ... 143s Selecting previously unselected package fonts-dejavu-mono. 143s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 143s Unpacking fonts-dejavu-mono (2.37-8) ... 143s Selecting previously unselected package fonts-dejavu-core. 143s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 143s Unpacking fonts-dejavu-core (2.37-8) ... 144s Selecting previously unselected package libfontenc1:s390x. 144s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_s390x.deb ... 144s Unpacking libfontenc1:s390x (1:1.1.8-1build1) ... 144s Selecting previously unselected package libfreetype6:s390x. 144s Preparing to unpack .../04-libfreetype6_2.13.3+dfsg-1_s390x.deb ... 144s Unpacking libfreetype6:s390x (2.13.3+dfsg-1) ... 144s Selecting previously unselected package x11-common. 144s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu3_all.deb ... 144s Unpacking x11-common (1:7.7+23ubuntu3) ... 144s Selecting previously unselected package xfonts-encodings. 144s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 144s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 144s Selecting previously unselected package xfonts-utils. 144s Preparing to unpack .../07-xfonts-utils_1%3a7.7+7_s390x.deb ... 144s Unpacking xfonts-utils (1:7.7+7) ... 144s Selecting previously unselected package fonts-urw-base35. 144s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 144s Unpacking fonts-urw-base35 (20200910-8) ... 144s Selecting previously unselected package fontconfig-config. 144s Preparing to unpack .../09-fontconfig-config_2.15.0-1.1ubuntu2_s390x.deb ... 144s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 144s Selecting previously unselected package libcapnp-1.1.0:s390x. 144s Preparing to unpack .../10-libcapnp-1.1.0_1.1.0-2_s390x.deb ... 144s Unpacking libcapnp-1.1.0:s390x (1.1.0-2) ... 144s Selecting previously unselected package libprotobuf32t64:s390x. 144s Preparing to unpack .../11-libprotobuf32t64_3.21.12-10build1_s390x.deb ... 144s Unpacking libprotobuf32t64:s390x (3.21.12-10build1) ... 144s Selecting previously unselected package harvest-tools. 144s Preparing to unpack .../12-harvest-tools_1.3-8build6_s390x.deb ... 144s Unpacking harvest-tools (1.3-8build6) ... 144s Selecting previously unselected package libblas3:s390x. 144s Preparing to unpack .../13-libblas3_3.12.1-2_s390x.deb ... 144s Unpacking libblas3:s390x (3.12.1-2) ... 144s Selecting previously unselected package libfontconfig1:s390x. 144s Preparing to unpack .../14-libfontconfig1_2.15.0-1.1ubuntu2_s390x.deb ... 144s Unpacking libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 144s Selecting previously unselected package libpixman-1-0:s390x. 144s Preparing to unpack .../15-libpixman-1-0_0.44.0-3_s390x.deb ... 144s Unpacking libpixman-1-0:s390x (0.44.0-3) ... 144s Selecting previously unselected package libxcb-render0:s390x. 144s Preparing to unpack .../16-libxcb-render0_1.17.0-2_s390x.deb ... 144s Unpacking libxcb-render0:s390x (1.17.0-2) ... 144s Selecting previously unselected package libxcb-shm0:s390x. 144s Preparing to unpack .../17-libxcb-shm0_1.17.0-2_s390x.deb ... 144s Unpacking libxcb-shm0:s390x (1.17.0-2) ... 144s Selecting previously unselected package libxrender1:s390x. 144s Preparing to unpack .../18-libxrender1_1%3a0.9.10-1.1build1_s390x.deb ... 144s Unpacking libxrender1:s390x (1:0.9.10-1.1build1) ... 144s Selecting previously unselected package libcairo2:s390x. 144s Preparing to unpack .../19-libcairo2_1.18.2-2_s390x.deb ... 144s Unpacking libcairo2:s390x (1.18.2-2) ... 144s Selecting previously unselected package libdeflate0:s390x. 144s Preparing to unpack .../20-libdeflate0_1.23-1_s390x.deb ... 144s Unpacking libdeflate0:s390x (1.23-1) ... 144s Selecting previously unselected package libgfortran5:s390x. 144s Preparing to unpack .../21-libgfortran5_14.2.0-17ubuntu1_s390x.deb ... 144s Unpacking libgfortran5:s390x (14.2.0-17ubuntu1) ... 144s Selecting previously unselected package libgomp1:s390x. 144s Preparing to unpack .../22-libgomp1_14.2.0-17ubuntu1_s390x.deb ... 144s Unpacking libgomp1:s390x (14.2.0-17ubuntu1) ... 144s Selecting previously unselected package libgraphite2-3:s390x. 144s Preparing to unpack .../23-libgraphite2-3_1.3.14-2ubuntu1_s390x.deb ... 144s Unpacking libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 144s Selecting previously unselected package libharfbuzz0b:s390x. 144s Preparing to unpack .../24-libharfbuzz0b_10.2.0-1_s390x.deb ... 144s Unpacking libharfbuzz0b:s390x (10.2.0-1) ... 144s Selecting previously unselected package libimagequant0:s390x. 144s Preparing to unpack .../25-libimagequant0_2.18.0-1build1_s390x.deb ... 144s Unpacking libimagequant0:s390x (2.18.0-1build1) ... 144s Selecting previously unselected package libjpeg-turbo8:s390x. 144s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-3ubuntu2_s390x.deb ... 144s Unpacking libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 144s Selecting previously unselected package libjpeg8:s390x. 144s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_s390x.deb ... 144s Unpacking libjpeg8:s390x (8c-2ubuntu11) ... 144s Selecting previously unselected package liblapack3:s390x. 144s Preparing to unpack .../28-liblapack3_3.12.1-2_s390x.deb ... 144s Unpacking liblapack3:s390x (3.12.1-2) ... 144s Selecting previously unselected package liblcms2-2:s390x. 144s Preparing to unpack .../29-liblcms2-2_2.16-2_s390x.deb ... 144s Unpacking liblcms2-2:s390x (2.16-2) ... 144s Selecting previously unselected package libmuscle1. 144s Preparing to unpack .../30-libmuscle1_3.7+4565-8_s390x.deb ... 144s Unpacking libmuscle1 (3.7+4565-8) ... 144s Selecting previously unselected package libraqm0:s390x. 144s Preparing to unpack .../31-libraqm0_0.10.2-1_s390x.deb ... 144s Unpacking libraqm0:s390x (0.10.2-1) ... 144s Selecting previously unselected package libsharpyuv0:s390x. 144s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_s390x.deb ... 144s Unpacking libsharpyuv0:s390x (1.5.0-0.1) ... 144s Selecting previously unselected package libspoa7.0.0:s390x. 144s Preparing to unpack .../33-libspoa7.0.0_4.1.4-2_s390x.deb ... 144s Unpacking libspoa7.0.0:s390x (4.1.4-2) ... 144s Selecting previously unselected package libjbig0:s390x. 144s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_s390x.deb ... 144s Unpacking libjbig0:s390x (2.1-6.1ubuntu2) ... 144s Selecting previously unselected package libwebp7:s390x. 144s Preparing to unpack .../35-libwebp7_1.5.0-0.1_s390x.deb ... 144s Unpacking libwebp7:s390x (1.5.0-0.1) ... 144s Selecting previously unselected package libtiff6:s390x. 144s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_s390x.deb ... 144s Unpacking libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 144s Selecting previously unselected package libwebpdemux2:s390x. 144s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_s390x.deb ... 144s Unpacking libwebpdemux2:s390x (1.5.0-0.1) ... 144s Selecting previously unselected package libwebpmux3:s390x. 144s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_s390x.deb ... 144s Unpacking libwebpmux3:s390x (1.5.0-0.1) ... 144s Selecting previously unselected package mummer. 144s Preparing to unpack .../39-mummer_3.23+dfsg-8_s390x.deb ... 144s Unpacking mummer (3.23+dfsg-8) ... 144s Selecting previously unselected package python3-numpy. 144s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-13_s390x.deb ... 144s Unpacking python3-numpy (1:1.26.4+ds-13) ... 144s Selecting previously unselected package libopenjp2-7:s390x. 144s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu3_s390x.deb ... 144s Unpacking libopenjp2-7:s390x (2.5.0-2ubuntu3) ... 144s Selecting previously unselected package python3-pil:s390x. 144s Preparing to unpack .../42-python3-pil_11.1.0-5_s390x.deb ... 144s Unpacking python3-pil:s390x (11.1.0-5) ... 144s Selecting previously unselected package python3-cairo. 144s Preparing to unpack .../43-python3-cairo_1.26.1-2build1_s390x.deb ... 144s Unpacking python3-cairo (1.26.1-2build1) ... 144s Selecting previously unselected package python3-freetype. 144s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 144s Unpacking python3-freetype (2.5.1-1) ... 144s Selecting previously unselected package python3-rlpycairo. 144s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 144s Unpacking python3-rlpycairo (0.3.0-3) ... 144s Selecting previously unselected package python3-reportlab. 144s Preparing to unpack .../46-python3-reportlab_4.3.0-1_all.deb ... 144s Unpacking python3-reportlab (4.3.0-1) ... 144s Selecting previously unselected package xml-core. 144s Preparing to unpack .../47-xml-core_0.19_all.deb ... 144s Unpacking xml-core (0.19) ... 144s Selecting previously unselected package w3c-sgml-lib. 144s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 144s Unpacking w3c-sgml-lib (1.3-3) ... 145s Selecting previously unselected package python3-biopython. 145s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2_s390x.deb ... 145s Unpacking python3-biopython (1.85+dfsg-2) ... 145s Selecting previously unselected package python3-pyspoa. 145s Preparing to unpack .../50-python3-pyspoa_0.2.1-1_s390x.deb ... 145s Unpacking python3-pyspoa (0.2.1-1) ... 145s Selecting previously unselected package python3-tqdm. 145s Preparing to unpack .../51-python3-tqdm_4.67.1-2_all.deb ... 145s Unpacking python3-tqdm (4.67.1-2) ... 145s Selecting previously unselected package fasttree. 145s Preparing to unpack .../52-fasttree_2.1.11-2_s390x.deb ... 145s Unpacking fasttree (2.1.11-2) ... 145s Selecting previously unselected package phipack. 145s Preparing to unpack .../53-phipack_0.0.20160614-5_s390x.deb ... 145s Unpacking phipack (0.0.20160614-5) ... 145s Selecting previously unselected package raxml. 145s Preparing to unpack .../54-raxml_8.2.13+dfsg-1_s390x.deb ... 145s Unpacking raxml (8.2.13+dfsg-1) ... 145s Selecting previously unselected package parsnp. 145s Preparing to unpack .../55-parsnp_2.0.3+dfsg-1ubuntu1_s390x.deb ... 145s Unpacking parsnp (2.0.3+dfsg-1ubuntu1) ... 145s Setting up libgraphite2-3:s390x (1.3.14-2ubuntu1) ... 145s Setting up liblcms2-2:s390x (2.16-2) ... 145s Setting up libpixman-1-0:s390x (0.44.0-3) ... 145s Setting up libsharpyuv0:s390x (1.5.0-0.1) ... 145s Setting up libprotobuf32t64:s390x (3.21.12-10build1) ... 145s Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... 145s Setting up libxcb-render0:s390x (1.17.0-2) ... 145s Setting up python3-tqdm (4.67.1-2) ... 145s Setting up x11-common (1:7.7+23ubuntu3) ... 145s Setting up libdeflate0:s390x (1.23-1) ... 145s Setting up libxcb-shm0:s390x (1.17.0-2) ... 145s Setting up libgomp1:s390x (14.2.0-17ubuntu1) ... 145s Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... 145s Setting up libfontenc1:s390x (1:1.1.8-1build1) ... 145s Setting up libblas3:s390x (3.12.1-2) ... 145s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 145s Setting up libfreetype6:s390x (2.13.3+dfsg-1) ... 145s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 145s Setting up libimagequant0:s390x (2.18.0-1build1) ... 145s Setting up fonts-dejavu-mono (2.37-8) ... 145s Setting up libspoa7.0.0:s390x (4.1.4-2) ... 145s Setting up fonts-dejavu-core (2.37-8) ... 145s Setting up libjpeg-turbo8:s390x (2.1.5-3ubuntu2) ... 145s Setting up libgfortran5:s390x (14.2.0-17ubuntu1) ... 145s Setting up libwebp7:s390x (1.5.0-0.1) ... 145s Setting up mummer (3.23+dfsg-8) ... 145s Setting up libopenjp2-7:s390x (2.5.0-2ubuntu3) ... 145s Setting up libharfbuzz0b:s390x (10.2.0-1) ... 145s Setting up phipack (0.0.20160614-5) ... 145s Setting up fasttree (2.1.11-2) ... 145s Setting up sgml-base (1.31) ... 145s Setting up libcapnp-1.1.0:s390x (1.1.0-2) ... 145s Setting up harvest-tools (1.3-8build6) ... 145s Setting up libwebpmux3:s390x (1.5.0-0.1) ... 145s Setting up raxml (8.2.13+dfsg-1) ... 145s Setting up libjpeg8:s390x (8c-2ubuntu11) ... 145s Setting up python3-pyspoa (0.2.1-1) ... 145s Setting up liblapack3:s390x (3.12.1-2) ... 145s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 145s Setting up libmuscle1 (3.7+4565-8) ... 145s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 145s Setting up libwebpdemux2:s390x (1.5.0-0.1) ... 145s Setting up python3-freetype (2.5.1-1) ... 145s Setting up xfonts-utils (1:7.7+7) ... 145s Setting up libraqm0:s390x (0.10.2-1) ... 145s Setting up python3-numpy (1:1.26.4+ds-13) ... 147s Setting up libtiff6:s390x (4.5.1+git230720-4ubuntu4) ... 147s Setting up xml-core (0.19) ... 147s Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... 147s Setting up fonts-urw-base35 (20200910-8) ... 147s Setting up libcairo2:s390x (1.18.2-2) ... 147s Setting up python3-pil:s390x (11.1.0-5) ... 147s Setting up python3-cairo (1.26.1-2build1) ... 147s Setting up python3-rlpycairo (0.3.0-3) ... 147s Setting up python3-reportlab (4.3.0-1) ... 148s Processing triggers for libc-bin (2.41-1ubuntu1) ... 148s Processing triggers for man-db (2.13.0-1) ... 149s Processing triggers for sgml-base (1.31) ... 149s Setting up w3c-sgml-lib (1.3-3) ... 169s Setting up python3-biopython (1.85+dfsg-2) ... 170s Setting up parsnp (2.0.3+dfsg-1ubuntu1) ... 171s autopkgtest [23:05:15]: test run-unit-test: [----------------------- 171s Test 1: With GenBank Annotations 171s 23:05:15 - INFO - |--Parsnp 2.0.3--| 171s 171s 23:05:15 - INFO - 171s ********************************************************************************** 171s SETTINGS: 171s |-refgenome: mers_virus/ref/England1.gbk 171s |-genomes: 171s mers_virus/genomes/Al-Hasa_12_2013.fna 171s mers_virus/genomes/NC_019843.2.fna 171s ...42 more file(s)... 171s mers_virus/genomes/Al-Hasa_2_2013.fna 171s mers_virus/genomes/Hafr-Al-Batin_1_2013.fna 171s |-aligner: muscle 171s |-outdir: /tmp/autopkgtest.AYaDP8/autopkgtest_tmp/P_2025_02_15_230515594226 171s |-OS: Linux 171s |-threads: 1 171s ********************************************************************************** 171s 171s 23:05:15 - INFO - <> 171s 23:05:15 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 172s 23:05:16 - INFO - Reconstructing core genome phylogeny... 175s 23:05:19 - INFO - Aligned 46 genomes in 4.04 seconds 175s 23:05:19 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.AYaDP8/autopkgtest_tmp/P_2025_02_15_230515594226 175s Passed 175s 175s Test 2: Without GenBank Annotations 175s 23:05:19 - INFO - |--Parsnp 2.0.3--| 175s 175s 23:05:19 - INFO - 175s ********************************************************************************** 175s SETTINGS: 175s |-refgenome: mers_virus/ref/England1.fna 175s |-genomes: 175s mers_virus/genomes/Al-Hasa_12_2013.fna 175s mers_virus/genomes/NC_019843.2.fna 175s ...42 more file(s)... 175s mers_virus/genomes/Al-Hasa_2_2013.fna 175s mers_virus/genomes/Hafr-Al-Batin_1_2013.fna 175s |-aligner: muscle 175s |-outdir: /tmp/autopkgtest.AYaDP8/autopkgtest_tmp/P_2025_02_15_230519814037 175s |-OS: Linux 175s |-threads: 1 175s ********************************************************************************** 175s 175s 23:05:19 - INFO - <> 175s 23:05:19 - INFO - No genbank file provided for reference annotations, skipping.. 175s 23:05:19 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 176s 23:05:20 - INFO - Reconstructing core genome phylogeny... 179s 23:05:23 - INFO - Aligned 46 genomes in 4.09 seconds 179s 23:05:23 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.AYaDP8/autopkgtest_tmp/P_2025_02_15_230519814037 179s Passed 179s 180s autopkgtest [23:05:24]: test run-unit-test: -----------------------] 180s run-unit-test PASS 180s autopkgtest [23:05:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 180s autopkgtest [23:05:24]: @@@@@@@@@@@@@@@@@@@@ summary 180s run-unit-test PASS 198s nova [W] Using flock in prodstack6-s390x 198s flock: timeout while waiting to get lock 198s Creating nova instance adt-plucky-s390x-parsnp-20250215-230224-juju-7f2275-prod-proposed-migration-environment-20-69ab2332-c6c8-4cfe-b191-9fbd7328fc14 from image adt/ubuntu-plucky-s390x-server-20250215.img (UUID 099dc609-2061-4009-a65b-d554466baca0)... 198s nova [W] Timed out waiting for 334cc932-a87d-4973-b9d4-5a2303bf2f80 to get deleted.