0s autopkgtest [21:32:58]: starting date and time: 2025-02-15 21:32:58+0000 0s autopkgtest [21:32:58]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [21:32:58]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hwkl_j4r/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-30.secgroup --name adt-plucky-amd64-parsnp-20250215-213258-juju-7f2275-prod-proposed-migration-environment-2-681fd2cc-4ad5-4e64-b406-b048ec5b8df8 --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/ 61s autopkgtest [21:33:59]: testbed dpkg architecture: amd64 61s autopkgtest [21:33:59]: testbed apt version: 2.9.28 61s autopkgtest [21:33:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [21:34:00]: testbed release detected to be: None 62s autopkgtest [21:34:00]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 63s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 63s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 63s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [820 kB] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 64s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB] 64s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB] 64s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 64s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 64s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [844 kB] 64s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [303 kB] 64s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 64s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.3 kB] 64s Fetched 2329 kB in 1s (2301 kB/s) 65s Reading package lists... 65s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade... 67s The following packages will be upgraded: 67s libtasn1-6 67s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 51.2 kB of archives. 67s After this operation, 22.5 kB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 68s Fetched 51.2 kB in 1s (73.7 kB/s) 68s (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 ... 108914 files and directories currently installed.) 68s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 68s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 68s Setting up libtasn1-6:amd64 (4.20.0-2) ... 68s Processing triggers for libc-bin (2.40-4ubuntu1) ... 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 69s autopkgtest [21:34:07]: upgrading testbed (apt dist-upgrade and autopurge) 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 69s Entering ResolveByKeep 70s 70s The following packages will be upgraded: 70s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 70s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s Need to get 11.8 MB of archives. 70s After this operation, 746 kB of additional disk space will be used. 70s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 70s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 71s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 71s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 71s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 71s Preconfiguring packages ... 71s Fetched 11.8 MB in 1s (12.8 MB/s) 71s (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 ... 108914 files and directories currently installed.) 71s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 71s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 71s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 71s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 71s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 71s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 72s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 72s Checking for services that may need to be restarted... 72s Checking init scripts... 72s Checking for services that may need to be restarted... 72s Checking init scripts... 72s Stopping some services possibly affected by the upgrade (will be restarted later): 72s cron: stopping...done. 72s 72s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 72s Setting up libc6:amd64 (2.41-1ubuntu1) ... 72s Checking for services that may need to be restarted... 72s Checking init scripts... 72s Restarting services possibly affected by the upgrade: 72s cron: restarting...done. 72s 72s Services restarted successfully. 72s (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 ... 108915 files and directories currently installed.) 72s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 72s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 72s Setting up libc-bin (2.41-1ubuntu1) ... 72s (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 ... 108915 files and directories currently installed.) 72s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 73s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 73s Setting up iproute2 (6.13.0-1ubuntu1) ... 73s Setting up locales (2.41-1ubuntu1) ... 73s Installing new version of config file /etc/locale.alias ... 73s Generating locales (this might take a while)... 75s en_US.UTF-8... done 75s Generation complete. 75s Setting up libc-dev-bin (2.41-1ubuntu1) ... 75s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 75s Processing triggers for man-db (2.13.0-1) ... 76s Processing triggers for systemd (257.2-3ubuntu1) ... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 78s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s autopkgtest [21:34:18]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 80s autopkgtest [21:34:18]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 82s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (dsc) [2258 B] 82s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (tar) [141 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (diff) [10.2 kB] 82s gpgv: Signature made Tue Apr 16 02:55:48 2024 UTC 82s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 82s gpgv: issuer "steve.langasek@ubuntu.com" 82s gpgv: Can't check signature: No public key 82s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1ubuntu1.dsc: no acceptable signature found 82s autopkgtest [21:34:20]: testing package parsnp version 2.0.3+dfsg-1ubuntu1 83s autopkgtest [21:34:21]: build not needed 87s autopkgtest [21:34:25]: test run-unit-test: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Starting pkgProblemResolver with broken count: 0 88s Starting 2 pkgProblemResolver with broken count: 0 88s Done 88s The following NEW packages will be installed: 88s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono 88s fonts-urw-base35 harvest-tools libblas3 libcairo2 libcapnp-1.1.0 libdeflate0 88s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 88s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 88s liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 libprotobuf32t64 88s libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 libwebpdemux2 88s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer parsnp phipack 88s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 88s python3-pyspoa python3-reportlab python3-rlpycairo python3-tqdm raxml 88s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 89s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 36.4 MB of archives. 89s After this operation, 130 MB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 90s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 90s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 90s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 90s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 90s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 90s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] 90s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libcapnp-1.1.0 amd64 1.1.0-2 [1533 kB] 90s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libprotobuf32t64 amd64 3.21.12-10build1 [956 kB] 90s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 harvest-tools amd64 1.3-8build6 [138 kB] 90s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 90s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] 90s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 90s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 90s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 90s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 90s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 90s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 90s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 90s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 90s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 90s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 90s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 90s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 90s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 90s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 90s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 90s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 90s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmuscle1 amd64 3.7+4565-8 [276 kB] 90s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 90s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 90s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libspoa7.0.0 amd64 4.1.4-2 [79.1 kB] 90s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 90s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 90s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 90s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 90s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 90s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 mummer amd64 3.23+dfsg-8 [685 kB] 90s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 91s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.0-2ubuntu3 [217 kB] 91s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5 [589 kB] 91s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build1 [143 kB] 91s Get:45 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 91s Get:46 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 91s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.0-1 [1137 kB] 91s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 91s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 91s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2 [1745 kB] 91s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyspoa amd64 0.2.1-1 [85.8 kB] 91s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-tqdm all 4.67.1-2 [92.5 kB] 91s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 91s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 phipack amd64 0.0.20160614-5 [55.2 kB] 91s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 raxml amd64 8.2.13+dfsg-1 [1640 kB] 91s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 parsnp amd64 2.0.3+dfsg-1ubuntu1 [200 kB] 91s Fetched 36.4 MB in 2s (15.6 MB/s) 91s Selecting previously unselected package sgml-base. 91s (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 ... 108916 files and directories currently installed.) 91s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 91s Unpacking sgml-base (1.31) ... 91s Selecting previously unselected package fonts-dejavu-mono. 91s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 91s Unpacking fonts-dejavu-mono (2.37-8) ... 91s Selecting previously unselected package fonts-dejavu-core. 91s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 91s Unpacking fonts-dejavu-core (2.37-8) ... 91s Selecting previously unselected package libfontenc1:amd64. 91s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 91s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 91s Selecting previously unselected package x11-common. 91s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 91s Unpacking x11-common (1:7.7+23ubuntu3) ... 91s Selecting previously unselected package xfonts-encodings. 91s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 91s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 91s Selecting previously unselected package xfonts-utils. 91s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_amd64.deb ... 91s Unpacking xfonts-utils (1:7.7+7) ... 91s Selecting previously unselected package fonts-urw-base35. 91s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 91s Unpacking fonts-urw-base35 (20200910-8) ... 91s Selecting previously unselected package fontconfig-config. 91s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package libcapnp-1.1.0:amd64. 92s Preparing to unpack .../09-libcapnp-1.1.0_1.1.0-2_amd64.deb ... 92s Unpacking libcapnp-1.1.0:amd64 (1.1.0-2) ... 92s Selecting previously unselected package libprotobuf32t64:amd64. 92s Preparing to unpack .../10-libprotobuf32t64_3.21.12-10build1_amd64.deb ... 92s Unpacking libprotobuf32t64:amd64 (3.21.12-10build1) ... 92s Selecting previously unselected package harvest-tools. 92s Preparing to unpack .../11-harvest-tools_1.3-8build6_amd64.deb ... 92s Unpacking harvest-tools (1.3-8build6) ... 92s Selecting previously unselected package libblas3:amd64. 92s Preparing to unpack .../12-libblas3_3.12.1-2_amd64.deb ... 92s Unpacking libblas3:amd64 (3.12.1-2) ... 92s Selecting previously unselected package libfontconfig1:amd64. 92s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ... 92s Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 92s Selecting previously unselected package libpixman-1-0:amd64. 92s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_amd64.deb ... 92s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 92s Selecting previously unselected package libxcb-render0:amd64. 92s Preparing to unpack .../15-libxcb-render0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxcb-shm0:amd64. 92s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_amd64.deb ... 92s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 92s Selecting previously unselected package libxrender1:amd64. 92s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 92s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 92s Selecting previously unselected package libcairo2:amd64. 92s Preparing to unpack .../18-libcairo2_1.18.2-2_amd64.deb ... 92s Unpacking 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package libimagequant0:amd64. 92s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_amd64.deb ... 92s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 92s Selecting previously unselected package libjpeg-turbo8:amd64. 92s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 92s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 92s Selecting previously unselected package libjpeg8:amd64. 92s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_amd64.deb ... 92s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 92s Selecting previously unselected package liblapack3:amd64. 92s Preparing to unpack .../27-liblapack3_3.12.1-2_amd64.deb ... 92s Unpacking liblapack3:amd64 (3.12.1-2) ... 92s Selecting previously unselected package liblcms2-2:amd64. 92s Preparing to unpack .../28-liblcms2-2_2.16-2_amd64.deb ... 92s Unpacking liblcms2-2:amd64 (2.16-2) ... 92s Selecting previously unselected package liblerc4:amd64. 92s Preparing to unpack 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unselected package libwebp7:amd64. 93s Preparing to unpack .../35-libwebp7_1.5.0-0.1_amd64.deb ... 93s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 93s Selecting previously unselected package libtiff6:amd64. 93s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 93s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 93s Selecting previously unselected package libwebpdemux2:amd64. 93s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_amd64.deb ... 93s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 93s Selecting previously unselected package libwebpmux3:amd64. 93s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_amd64.deb ... 93s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 93s Selecting previously unselected package mummer. 93s Preparing to unpack .../39-mummer_3.23+dfsg-8_amd64.deb ... 93s Unpacking mummer (3.23+dfsg-8) ... 93s Selecting previously unselected package python3-numpy. 93s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 93s 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package fasttree. 94s Preparing to unpack .../52-fasttree_2.1.11-2_amd64.deb ... 94s Unpacking fasttree (2.1.11-2) ... 94s Selecting previously unselected package phipack. 94s Preparing to unpack .../53-phipack_0.0.20160614-5_amd64.deb ... 94s Unpacking phipack (0.0.20160614-5) ... 94s Selecting previously unselected package raxml. 94s Preparing to unpack .../54-raxml_8.2.13+dfsg-1_amd64.deb ... 94s Unpacking raxml (8.2.13+dfsg-1) ... 94s Selecting previously unselected package parsnp. 94s Preparing to unpack .../55-parsnp_2.0.3+dfsg-1ubuntu1_amd64.deb ... 94s Unpacking parsnp (2.0.3+dfsg-1ubuntu1) ... 94s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 94s Setting up liblcms2-2:amd64 (2.16-2) ... 94s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 94s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 94s Setting up libprotobuf32t64:amd64 (3.21.12-10build1) ... 94s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 94s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 94s Setting up libxcb-render0:amd64 (1.17.0-2) ... 94s Setting up python3-tqdm (4.67.1-2) ... 94s Setting up x11-common (1:7.7+23ubuntu3) ... 95s Setting up libdeflate0:amd64 (1.23-1) ... 95s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 95s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ... 95s Setting up python3-freetype (2.5.1-1) ... 95s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 95s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 95s Setting up libblas3:amd64 (3.12.1-2) ... 95s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 95s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 95s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 95s Setting up fonts-dejavu-mono (2.37-8) ... 95s Setting up libspoa7.0.0:amd64 (4.1.4-2) ... 95s Setting up fonts-dejavu-core (2.37-8) ... 95s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 95s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ... 95s Setting up libwebp7:amd64 (1.5.0-0.1) ... 95s Setting up mummer (3.23+dfsg-8) ... 95s Setting up libopenjp2-7:amd64 (2.5.0-2ubuntu3) ... 95s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 95s Setting up phipack (0.0.20160614-5) ... 95s Setting up fasttree (2.1.11-2) ... 95s Setting up sgml-base (1.31) ... 95s Setting up libcapnp-1.1.0:amd64 (1.1.0-2) ... 95s Setting up harvest-tools (1.3-8build6) ... 95s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 95s Setting up raxml (8.2.13+dfsg-1) ... 95s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 95s Setting up python3-pyspoa (0.2.1-1) ... 95s Setting up liblapack3:amd64 (3.12.1-2) ... 95s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 95s Setting up libmuscle1 (3.7+4565-8) ... 95s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 95s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 95s Setting up xfonts-utils (1:7.7+7) ... 95s Setting up libraqm0:amd64 (0.10.2-1) ... 95s Setting up python3-numpy (1:1.26.4+ds-13) ... 96s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 96s Setting up xml-core (0.19) ... 97s Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... 97s Setting up fonts-urw-base35 (20200910-8) ... 97s Setting up libcairo2:amd64 (1.18.2-2) ... 97s Setting up python3-pil:amd64 (11.1.0-5) ... 97s Setting up python3-cairo (1.26.1-2build1) ... 97s Setting up python3-rlpycairo (0.3.0-3) ... 97s Setting up python3-reportlab (4.3.0-1) ... 98s Processing triggers for libc-bin (2.41-1ubuntu1) ... 98s Processing triggers for man-db (2.13.0-1) ... 98s Processing triggers for sgml-base (1.31) ... 99s Setting up w3c-sgml-lib (1.3-3) ... 123s Setting up python3-biopython (1.85+dfsg-2) ... 124s Setting up parsnp (2.0.3+dfsg-1ubuntu1) ... 125s autopkgtest [21:35:03]: test run-unit-test: [----------------------- 125s Test 1: With GenBank Annotations 126s 21:35:04 - INFO - |--Parsnp 2.0.3--| 126s 126s 21:35:04 - INFO - 126s ********************************************************************************** 126s SETTINGS: 126s |-refgenome: mers_virus/ref/England1.gbk 126s |-genomes: 126s mers_virus/genomes/Riyadh_9_2013.fna 126s mers_virus/genomes/Riyadh_2_2012.fna 126s ...42 more file(s)... 126s mers_virus/genomes/England-Qatar_2012.fna 126s mers_virus/genomes/Al-Hasa_4_2013.fna 126s |-aligner: muscle 126s |-outdir: /tmp/autopkgtest.WmoPUR/autopkgtest_tmp/P_2025_02_15_213504206676 126s |-OS: Linux 126s |-threads: 1 126s ********************************************************************************** 126s 126s 21:35:04 - INFO - <> 126s 21:35:04 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 126s 21:35:04 - INFO - Reconstructing core genome phylogeny... 128s 21:35:06 - INFO - Aligned 46 genomes in 2.68 seconds 128s 21:35:06 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.WmoPUR/autopkgtest_tmp/P_2025_02_15_213504206676 128s Passed 128s 128s Test 2: Without GenBank Annotations 129s 21:35:07 - INFO - |--Parsnp 2.0.3--| 129s 129s 21:35:07 - INFO - 129s ********************************************************************************** 129s SETTINGS: 129s |-refgenome: mers_virus/ref/England1.fna 129s |-genomes: 129s mers_virus/genomes/Riyadh_9_2013.fna 129s mers_virus/genomes/Riyadh_2_2012.fna 129s ...42 more file(s)... 129s mers_virus/genomes/England-Qatar_2012.fna 129s mers_virus/genomes/Al-Hasa_4_2013.fna 129s |-aligner: muscle 129s |-outdir: /tmp/autopkgtest.WmoPUR/autopkgtest_tmp/P_2025_02_15_213507194076 129s |-OS: Linux 129s |-threads: 1 129s ********************************************************************************** 129s 129s 21:35:07 - INFO - <> 129s 21:35:07 - INFO - No genbank file provided for reference annotations, skipping.. 129s 21:35:07 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 129s 21:35:07 - INFO - Reconstructing core genome phylogeny... 131s 21:35:09 - INFO - Aligned 46 genomes in 2.61 seconds 131s 21:35:09 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.WmoPUR/autopkgtest_tmp/P_2025_02_15_213507194076 131s Passed 131s 132s autopkgtest [21:35:10]: test run-unit-test: -----------------------] 132s run-unit-test PASS 132s autopkgtest [21:35:10]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 133s autopkgtest [21:35:11]: @@@@@@@@@@@@@@@@@@@@ summary 133s run-unit-test PASS 151s nova [W] Skipping flock for amd64 151s Creating nova instance adt-plucky-amd64-parsnp-20250215-213258-juju-7f2275-prod-proposed-migration-environment-2-681fd2cc-4ad5-4e64-b406-b048ec5b8df8 from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 151s nova [W] Timed out waiting for 1b63b230-ba21-4823-ad92-6c0a7c67a6b6 to get deleted.