0s autopkgtest [08:09:03]: starting date and time: 2025-02-16 08:09:03+0000 0s autopkgtest [08:09:03]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [08:09:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u7d9xvq8/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-16.secgroup --name adt-plucky-arm64-parsnp-20250216-080903-juju-7f2275-prod-proposed-migration-environment-2-3c2e07f3-1357-41f3-b3b9-41ebd04e76ea --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 159s autopkgtest [08:11:42]: testbed dpkg architecture: arm64 160s autopkgtest [08:11:43]: testbed apt version: 2.9.28 160s autopkgtest [08:11:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 160s autopkgtest [08:11:43]: testbed release detected to be: None 161s autopkgtest [08:11:44]: updating testbed package index (apt update) 161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 162s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 162s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 162s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 162s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.1 kB] 162s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [812 kB] 162s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 162s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [74.8 kB] 162s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [167 kB] 162s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 162s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [921 kB] 162s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [10.0 kB] 162s Fetched 2119 kB in 1s (2175 kB/s) 163s Reading package lists... 164s Reading package lists... 165s Building dependency tree... 165s Reading state information... 165s Calculating upgrade... 166s The following packages will be upgraded: 166s pci.ids 166s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 166s Need to get 284 kB of archives. 166s After this operation, 1024 B of additional disk space will be used. 166s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 pci.ids all 0.0~2025.02.12-1 [284 kB] 167s Fetched 284 kB in 0s (680 kB/s) 167s (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 ... 116609 files and directories currently installed.) 167s Preparing to unpack .../pci.ids_0.0~2025.02.12-1_all.deb ... 167s Unpacking pci.ids (0.0~2025.02.12-1) over (0.0~2025.02.05-1) ... 167s Setting up pci.ids (0.0~2025.02.12-1) ... 167s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 169s autopkgtest [08:11:52]: upgrading testbed (apt dist-upgrade and autopurge) 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 171s Entering ResolveByKeep 171s 172s The following packages will be upgraded: 172s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 172s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 10.7 MB of archives. 172s After this operation, 358 kB of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu1 [24.0 kB] 172s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu1 [1750 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu1 [4246 kB] 172s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu1 [2910 kB] 172s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu1 [600 kB] 172s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 iproute2 arm64 6.13.0-1ubuntu1 [1158 kB] 173s Preconfiguring packages ... 173s Fetched 10.7 MB in 1s (11.5 MB/s) 173s (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 ... 116609 files and directories currently installed.) 173s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_arm64.deb ... 173s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 173s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_arm64.deb ... 173s Unpacking libc6-dev:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 174s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 174s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 174s Preparing to unpack .../libc6_2.41-1ubuntu1_arm64.deb ... 174s Checking for services that may need to be restarted... 174s Checking init scripts... 174s Checking for services that may need to be restarted... 174s Checking init scripts... 174s Stopping some services possibly affected by the upgrade (will be restarted later): 174s cron: stopping...done. 174s 174s Unpacking libc6:arm64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 175s Setting up libc6:arm64 (2.41-1ubuntu1) ... 175s Checking for services that may need to be restarted... 175s Checking init scripts... 175s Restarting services possibly affected by the upgrade: 175s cron: restarting...done. 175s 175s Services restarted successfully. 175s (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 ... 116610 files and directories currently installed.) 175s Preparing to unpack .../libc-bin_2.41-1ubuntu1_arm64.deb ... 175s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 175s Setting up libc-bin (2.41-1ubuntu1) ... 176s (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 ... 116610 files and directories currently installed.) 176s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_arm64.deb ... 176s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 176s Setting up iproute2 (6.13.0-1ubuntu1) ... 176s Setting up locales (2.41-1ubuntu1) ... 176s Installing new version of config file /etc/locale.alias ... 177s Generating locales (this might take a while)... 181s en_US.UTF-8... done 181s Generation complete. 181s Setting up libc-dev-bin (2.41-1ubuntu1) ... 181s Setting up libc6-dev:arm64 (2.41-1ubuntu1) ... 181s Processing triggers for man-db (2.13.0-1) ... 182s Processing triggers for systemd (257.2-3ubuntu1) ... 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 185s Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s autopkgtest [08:12:12]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 190s autopkgtest [08:12:13]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 192s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (dsc) [2258 B] 192s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (tar) [141 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.3+dfsg-1ubuntu1 (diff) [10.2 kB] 192s gpgv: Signature made Tue Apr 16 02:55:48 2024 UTC 192s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 192s gpgv: issuer "steve.langasek@ubuntu.com" 192s gpgv: Can't check signature: No public key 192s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.3+dfsg-1ubuntu1.dsc: no acceptable signature found 192s autopkgtest [08:12:15]: testing package parsnp version 2.0.3+dfsg-1ubuntu1 192s autopkgtest [08:12:15]: build not needed 193s autopkgtest [08:12:16]: test run-unit-test: preparing testbed 193s Reading package lists... 194s Building dependency tree... 194s Reading state information... 194s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 195s The following NEW packages will be installed: 195s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono 195s fonts-urw-base35 harvest-tools libblas3 libcairo2 libcapnp-1.1.0 libdeflate0 195s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 195s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 195s liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 libprotobuf32t64 195s libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 libwebpdemux2 195s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer parsnp phipack 195s python3-biopython python3-cairo python3-freetype python3-numpy python3-pil 195s python3-pyspoa python3-reportlab python3-rlpycairo python3-tqdm raxml 195s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 196s 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 31.9 MB of archives. 196s After this operation, 110 MB of additional disk space will be used. 196s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 196s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 196s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 196s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 196s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 196s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 196s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 196s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-1.1ubuntu2 [37.4 kB] 196s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcapnp-1.1.0 arm64 1.1.0-2 [1371 kB] 196s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libprotobuf32t64 arm64 3.21.12-10build1 [867 kB] 197s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 harvest-tools arm64 1.3-8build6 [121 kB] 197s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 197s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-1.1ubuntu2 [142 kB] 197s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 197s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 197s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 197s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 197s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 197s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 197s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-17ubuntu1 [437 kB] 197s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-17ubuntu1 [145 kB] 197s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 197s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 197s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 197s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 197s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 197s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 197s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 197s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 197s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmuscle1 arm64 3.7+4565-8 [273 kB] 197s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 197s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 197s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 libspoa7.0.0 arm64 4.1.4-2 [60.1 kB] 197s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 197s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 197s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 197s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 197s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 197s Get:40 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 197s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-13 [4148 kB] 197s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.0-2ubuntu3 [182 kB] 197s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5 [491 kB] 197s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build1 [139 kB] 197s Get:45 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 197s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 197s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.0-1 [1137 kB] 197s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 197s Get:49 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 197s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2 [1718 kB] 197s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyspoa arm64 0.2.1-1 [81.1 kB] 197s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 197s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 197s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 phipack arm64 0.0.20160614-5 [49.9 kB] 197s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 raxml arm64 8.2.13+dfsg-1 [999 kB] 197s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 parsnp arm64 2.0.3+dfsg-1ubuntu1 [200 kB] 198s Fetched 31.9 MB in 2s (18.2 MB/s) 198s Selecting previously unselected package sgml-base. 198s (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 ... 116611 files and directories currently installed.) 198s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 198s Unpacking sgml-base (1.31) ... 198s Selecting previously unselected package fonts-dejavu-mono. 198s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 198s Unpacking fonts-dejavu-mono (2.37-8) ... 198s Selecting previously unselected package fonts-dejavu-core. 198s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 198s Unpacking fonts-dejavu-core (2.37-8) ... 198s Selecting previously unselected package libfontenc1:arm64. 198s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 198s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 198s Selecting previously unselected package x11-common. 198s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu3_all.deb ... 198s Unpacking x11-common (1:7.7+23ubuntu3) ... 198s Selecting previously unselected package xfonts-encodings. 198s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 198s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 198s Selecting previously unselected package xfonts-utils. 198s Preparing to unpack .../06-xfonts-utils_1%3a7.7+7_arm64.deb ... 198s Unpacking xfonts-utils (1:7.7+7) ... 198s Selecting previously unselected package fonts-urw-base35. 198s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 199s Unpacking fonts-urw-base35 (20200910-8) ... 199s Selecting previously unselected package fontconfig-config. 199s Preparing to unpack .../08-fontconfig-config_2.15.0-1.1ubuntu2_arm64.deb ... 199s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ... 199s Selecting previously unselected package libcapnp-1.1.0:arm64. 199s Preparing to unpack .../09-libcapnp-1.1.0_1.1.0-2_arm64.deb ... 199s Unpacking libcapnp-1.1.0:arm64 (1.1.0-2) ... 199s Selecting previously unselected package libprotobuf32t64:arm64. 199s Preparing to unpack .../10-libprotobuf32t64_3.21.12-10build1_arm64.deb ... 199s Unpacking libprotobuf32t64:arm64 (3.21.12-10build1) ... 199s Selecting previously unselected package harvest-tools. 199s Preparing to unpack .../11-harvest-tools_1.3-8build6_arm64.deb ... 199s Unpacking harvest-tools (1.3-8build6) ... 199s Selecting previously unselected package libblas3:arm64. 199s Preparing to unpack .../12-libblas3_3.12.1-2_arm64.deb ... 199s Unpacking libblas3:arm64 (3.12.1-2) ... 199s Selecting previously unselected package libfontconfig1:arm64. 199s Preparing to unpack .../13-libfontconfig1_2.15.0-1.1ubuntu2_arm64.deb ... 199s Unpacking libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 199s Selecting previously unselected package libpixman-1-0:arm64. 199s Preparing to unpack .../14-libpixman-1-0_0.44.0-3_arm64.deb ... 199s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 199s Selecting previously unselected package libxcb-render0:arm64. 200s Preparing to unpack .../15-libxcb-render0_1.17.0-2_arm64.deb ... 200s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 200s Selecting previously unselected package libxcb-shm0:arm64. 200s Preparing to unpack .../16-libxcb-shm0_1.17.0-2_arm64.deb ... 200s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 200s Selecting previously unselected package libxrender1:arm64. 200s Preparing to unpack .../17-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 200s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 200s Selecting previously unselected package libcairo2:arm64. 200s Preparing to unpack .../18-libcairo2_1.18.2-2_arm64.deb ... 200s Unpacking libcairo2:arm64 (1.18.2-2) ... 200s Selecting previously unselected package libdeflate0:arm64. 200s Preparing to unpack .../19-libdeflate0_1.23-1_arm64.deb ... 200s Unpacking libdeflate0:arm64 (1.23-1) ... 200s Selecting previously unselected package libgfortran5:arm64. 200s Preparing to unpack .../20-libgfortran5_14.2.0-17ubuntu1_arm64.deb ... 200s Unpacking libgfortran5:arm64 (14.2.0-17ubuntu1) ... 200s Selecting previously unselected package libgomp1:arm64. 200s Preparing to unpack .../21-libgomp1_14.2.0-17ubuntu1_arm64.deb ... 200s Unpacking libgomp1:arm64 (14.2.0-17ubuntu1) ... 200s Selecting previously unselected package libgraphite2-3:arm64. 200s Preparing to unpack .../22-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 200s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 200s Selecting previously unselected package libharfbuzz0b:arm64. 200s Preparing to unpack .../23-libharfbuzz0b_10.2.0-1_arm64.deb ... 200s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 200s Selecting previously unselected package libimagequant0:arm64. 200s Preparing to unpack .../24-libimagequant0_2.18.0-1build1_arm64.deb ... 200s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 200s Selecting previously unselected package libjpeg-turbo8:arm64. 200s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 200s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 200s Selecting previously unselected package libjpeg8:arm64. 200s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 200s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 200s Selecting previously unselected package liblapack3:arm64. 200s Preparing to unpack .../27-liblapack3_3.12.1-2_arm64.deb ... 200s Unpacking liblapack3:arm64 (3.12.1-2) ... 200s Selecting previously unselected package liblcms2-2:arm64. 200s Preparing to unpack .../28-liblcms2-2_2.16-2_arm64.deb ... 200s Unpacking liblcms2-2:arm64 (2.16-2) ... 200s Selecting previously unselected package liblerc4:arm64. 200s Preparing to unpack .../29-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 200s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 201s Selecting previously unselected package libmuscle1. 201s Preparing to unpack .../30-libmuscle1_3.7+4565-8_arm64.deb ... 201s Unpacking libmuscle1 (3.7+4565-8) ... 201s Selecting previously unselected package libraqm0:arm64. 201s Preparing to unpack .../31-libraqm0_0.10.2-1_arm64.deb ... 201s Unpacking libraqm0:arm64 (0.10.2-1) ... 201s Selecting previously unselected package libsharpyuv0:arm64. 201s Preparing to unpack .../32-libsharpyuv0_1.5.0-0.1_arm64.deb ... 201s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 201s Selecting previously unselected package libspoa7.0.0:arm64. 201s Preparing to unpack .../33-libspoa7.0.0_4.1.4-2_arm64.deb ... 201s Unpacking libspoa7.0.0:arm64 (4.1.4-2) ... 201s Selecting previously unselected package libjbig0:arm64. 201s Preparing to unpack .../34-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 201s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 201s Selecting previously unselected package libwebp7:arm64. 201s Preparing to unpack .../35-libwebp7_1.5.0-0.1_arm64.deb ... 201s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 201s Selecting previously unselected package libtiff6:arm64. 201s Preparing to unpack .../36-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 201s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 201s Selecting previously unselected package libwebpdemux2:arm64. 201s Preparing to unpack .../37-libwebpdemux2_1.5.0-0.1_arm64.deb ... 201s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 201s Selecting previously unselected package libwebpmux3:arm64. 201s Preparing to unpack .../38-libwebpmux3_1.5.0-0.1_arm64.deb ... 201s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 201s Selecting previously unselected package mummer. 201s Preparing to unpack .../39-mummer_3.23+dfsg-8_arm64.deb ... 201s Unpacking mummer (3.23+dfsg-8) ... 201s Selecting previously unselected package python3-numpy. 201s Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-13_arm64.deb ... 201s Unpacking python3-numpy (1:1.26.4+ds-13) ... 202s Selecting previously unselected package libopenjp2-7:arm64. 202s Preparing to unpack .../41-libopenjp2-7_2.5.0-2ubuntu3_arm64.deb ... 202s Unpacking libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 202s Selecting previously unselected package python3-pil:arm64. 202s Preparing to unpack .../42-python3-pil_11.1.0-5_arm64.deb ... 202s Unpacking python3-pil:arm64 (11.1.0-5) ... 202s Selecting previously unselected package python3-cairo. 202s Preparing to unpack .../43-python3-cairo_1.26.1-2build1_arm64.deb ... 202s Unpacking python3-cairo (1.26.1-2build1) ... 202s Selecting previously unselected package python3-freetype. 202s Preparing to unpack .../44-python3-freetype_2.5.1-1_all.deb ... 202s Unpacking python3-freetype (2.5.1-1) ... 202s Selecting previously unselected package python3-rlpycairo. 202s Preparing to unpack .../45-python3-rlpycairo_0.3.0-3_all.deb ... 202s Unpacking python3-rlpycairo (0.3.0-3) ... 202s Selecting previously unselected package python3-reportlab. 202s Preparing to unpack .../46-python3-reportlab_4.3.0-1_all.deb ... 202s Unpacking python3-reportlab (4.3.0-1) ... 202s Selecting previously unselected package xml-core. 202s Preparing to unpack .../47-xml-core_0.19_all.deb ... 202s Unpacking xml-core (0.19) ... 202s Selecting previously unselected package w3c-sgml-lib. 202s Preparing to unpack .../48-w3c-sgml-lib_1.3-3_all.deb ... 202s Unpacking w3c-sgml-lib (1.3-3) ... 202s Selecting previously unselected package python3-biopython. 202s Preparing to unpack .../49-python3-biopython_1.85+dfsg-2_arm64.deb ... 202s Unpacking python3-biopython (1.85+dfsg-2) ... 202s Selecting previously unselected package python3-pyspoa. 202s Preparing to unpack .../50-python3-pyspoa_0.2.1-1_arm64.deb ... 202s Unpacking python3-pyspoa (0.2.1-1) ... 202s Selecting previously unselected package python3-tqdm. 202s Preparing to unpack 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(3.21.12-10build1) ... 203s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 203s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 203s Setting up libxcb-render0:arm64 (1.17.0-2) ... 203s Setting up python3-tqdm (4.67.1-2) ... 203s Setting up x11-common (1:7.7+23ubuntu3) ... 204s Setting up libdeflate0:arm64 (1.23-1) ... 204s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 204s Setting up libgomp1:arm64 (14.2.0-17ubuntu1) ... 204s Setting up python3-freetype (2.5.1-1) ... 204s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 204s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 204s Setting up libblas3:arm64 (3.12.1-2) ... 204s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 204s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 204s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 204s Setting up fonts-dejavu-mono (2.37-8) ... 204s Setting up libspoa7.0.0:arm64 (4.1.4-2) ... 204s Setting up fonts-dejavu-core (2.37-8) ... 204s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 204s Setting up libgfortran5:arm64 (14.2.0-17ubuntu1) ... 204s Setting up libwebp7:arm64 (1.5.0-0.1) ... 204s Setting up mummer (3.23+dfsg-8) ... 204s Setting up libopenjp2-7:arm64 (2.5.0-2ubuntu3) ... 204s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 204s Setting up phipack (0.0.20160614-5) ... 204s Setting up fasttree (2.1.11-2) ... 204s Setting up sgml-base (1.31) ... 204s Setting up libcapnp-1.1.0:arm64 (1.1.0-2) ... 204s Setting up harvest-tools (1.3-8build6) ... 204s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 204s Setting up raxml (8.2.13+dfsg-1) ... 204s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 204s Setting up python3-pyspoa (0.2.1-1) ... 204s Setting up liblapack3:arm64 (3.12.1-2) ... 204s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 204s Setting up libmuscle1 (3.7+4565-8) ... 204s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... 205s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 205s Setting up xfonts-utils (1:7.7+7) ... 205s Setting up libraqm0:arm64 (0.10.2-1) ... 205s Setting up python3-numpy (1:1.26.4+ds-13) ... 207s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 207s Setting up xml-core (0.19) ... 207s Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... 207s Setting up fonts-urw-base35 (20200910-8) ... 207s Setting up libcairo2:arm64 (1.18.2-2) ... 207s Setting up python3-pil:arm64 (11.1.0-5) ... 208s Setting up python3-cairo (1.26.1-2build1) ... 208s Setting up python3-rlpycairo (0.3.0-3) ... 208s Setting up python3-reportlab (4.3.0-1) ... 209s Processing triggers for libc-bin (2.41-1ubuntu1) ... 209s Processing triggers for man-db (2.13.0-1) ... 210s Processing triggers for sgml-base (1.31) ... 210s Setting up w3c-sgml-lib (1.3-3) ... 247s Setting up python3-biopython (1.85+dfsg-2) ... 249s Setting up parsnp (2.0.3+dfsg-1ubuntu1) ... 250s autopkgtest [08:13:13]: test run-unit-test: [----------------------- 250s Test 1: With GenBank Annotations 251s 08:13:14 - INFO - |--Parsnp 2.0.3--| 251s 251s 08:13:14 - INFO - 251s ********************************************************************************** 251s SETTINGS: 251s |-refgenome: mers_virus/ref/England1.gbk 251s |-genomes: 251s mers_virus/genomes/Qatar4.fna 251s mers_virus/genomes/KFU-HKU_19Dam.fna 251s ...42 more file(s)... 251s mers_virus/genomes/Hafr-Al-Batin_2_2013.fna 251s mers_virus/genomes/Al-Hasa_12_2013.fna 251s |-aligner: muscle 251s |-outdir: /tmp/autopkgtest.mRNTqf/autopkgtest_tmp/P_2025_02_16_081314079057 251s |-OS: Linux 251s |-threads: 1 251s ********************************************************************************** 251s 251s 08:13:14 - INFO - <> 251s 08:13:14 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 252s 08:13:14 - INFO - Reconstructing core genome phylogeny... 257s 08:13:20 - INFO - Aligned 46 genomes in 6.13 seconds 257s 08:13:20 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.mRNTqf/autopkgtest_tmp/P_2025_02_16_081314079057 257s Passed 257s 257s Test 2: Without GenBank Annotations 257s 08:13:20 - INFO - |--Parsnp 2.0.3--| 257s 257s 08:13:20 - INFO - 257s ********************************************************************************** 257s SETTINGS: 257s |-refgenome: mers_virus/ref/England1.fna 257s |-genomes: 257s mers_virus/genomes/Qatar4.fna 257s mers_virus/genomes/KFU-HKU_19Dam.fna 257s ...42 more file(s)... 257s mers_virus/genomes/Hafr-Al-Batin_2_2013.fna 257s mers_virus/genomes/Al-Hasa_12_2013.fna 257s |-aligner: muscle 257s |-outdir: /tmp/autopkgtest.mRNTqf/autopkgtest_tmp/P_2025_02_16_081320692885 257s |-OS: Linux 257s |-threads: 1 257s ********************************************************************************** 257s 257s 08:13:20 - INFO - <> 257s 08:13:20 - INFO - No genbank file provided for reference annotations, skipping.. 257s 08:13:20 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 258s 08:13:21 - INFO - Reconstructing core genome phylogeny... 263s 08:13:26 - INFO - Aligned 46 genomes in 6.05 seconds 263s 08:13:26 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.mRNTqf/autopkgtest_tmp/P_2025_02_16_081320692885 263s Passed 263s 264s autopkgtest [08:13:27]: test run-unit-test: -----------------------] 264s run-unit-test PASS 264s autopkgtest [08:13:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s autopkgtest [08:13:28]: @@@@@@@@@@@@@@@@@@@@ summary 265s run-unit-test PASS 270s nova [W] Using flock in prodstack6-arm64 270s Creating nova instance adt-plucky-arm64-parsnp-20250216-080903-juju-7f2275-prod-proposed-migration-environment-2-3c2e07f3-1357-41f3-b3b9-41ebd04e76ea from image adt/ubuntu-plucky-arm64-server-20250216.img (UUID a098a761-c895-418e-827f-00d410a1ece9)... 270s nova [W] Timed out waiting for bda9ac19-fa6e-449b-8246-11ab4366d976 to get deleted.