0s autopkgtest [14:10:43]: starting date and time: 2025-03-15 14:10:43+0000 0s autopkgtest [14:10:43]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:10:43]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6nysf_yj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade parsnp --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-32.secgroup --name adt-plucky-arm64-parsnp-20250315-141043-juju-7f2275-prod-proposed-migration-environment-20-0e1872f1-1db8-4052-97e3-8fbca14864b5 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 118s autopkgtest [14:12:41]: testbed dpkg architecture: arm64 118s autopkgtest [14:12:41]: testbed apt version: 2.9.33 119s autopkgtest [14:12:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 119s autopkgtest [14:12:42]: testbed release detected to be: None 120s autopkgtest [14:12:43]: updating testbed package index (apt update) 120s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 120s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 120s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 121s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 121s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 121s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 121s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 121s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 121s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 121s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 121s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 121s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 121s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 122s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 122s Fetched 1094 kB in 2s (681 kB/s) 123s Reading package lists... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 125s Calculating upgrade... 125s Calculating upgrade... 126s The following packages will be upgraded: 126s python3-jinja2 strace 126s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Need to get 608 kB of archives. 126s After this operation, 11.3 kB of additional disk space will be used. 126s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 127s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 127s Fetched 608 kB in 1s (770 kB/s) 128s (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 ... 117701 files and directories currently installed.) 128s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 128s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 128s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 128s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 128s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 128s Setting up strace (6.13+ds-1ubuntu1) ... 128s Processing triggers for man-db (2.13.0-1) ... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Solving dependencies... 130s The following packages will be REMOVED: 130s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 130s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 130s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 130s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 130s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 130s After this operation, 267 MB disk space will be freed. 130s (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 ... 117701 files and directories currently installed.) 130s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 130s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 130s Removing libpython3.12t64:arm64 (3.12.9-1) ... 131s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 131s Removing libnsl2:arm64 (1.3.0-3build3) ... 131s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 131s Removing libunwind8:arm64 (1.6.2-3.1) ... 131s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 131s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 133s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 133s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 133s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 133s /etc/kernel/postrm.d/initramfs-tools: 133s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 133s /etc/kernel/postrm.d/zz-flash-kernel: 133s flash-kernel: Kernel 6.11.0-8-generic has been removed. 133s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 134s /etc/kernel/postrm.d/zz-update-grub: 134s Sourcing file `/etc/default/grub' 134s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 134s Generating grub configuration file ... 134s Found linux image: /boot/vmlinuz-6.14.0-10-generic 134s Found initrd image: /boot/initrd.img-6.14.0-10-generic 134s Warning: os-prober will not be executed to detect other bootable partitions. 134s Systems on them will not be added to the GRUB boot configuration. 134s Check GRUB_DISABLE_OS_PROBER documentation entry. 134s Adding boot menu entry for UEFI Firmware Settings ... 134s done 134s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 135s Processing triggers for libc-bin (2.41-1ubuntu1) ... 135s (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 ... 81650 files and directories currently installed.) 135s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 135s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 135s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 135s autopkgtest [14:12:58]: upgrading testbed (apt dist-upgrade and autopurge) 135s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 138s Entering ResolveByKeep 138s 139s Calculating upgrade... 139s The following packages will be upgraded: 139s libc-bin libc-dev-bin libc6 libc6-dev locales 139s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 9530 kB of archives. 139s After this operation, 0 B of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 141s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 141s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 143s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 143s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 147s Preconfiguring packages ... 147s Fetched 9530 kB in 7s (1363 kB/s) 147s (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 ... 81647 files and directories currently installed.) 147s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 147s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 147s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 147s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 147s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 148s Setting up libc6:arm64 (2.41-1ubuntu2) ... 148s (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 ... 81647 files and directories currently installed.) 148s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 148s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 148s Setting up libc-bin (2.41-1ubuntu2) ... 148s (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 ... 81647 files and directories currently installed.) 148s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 148s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 148s Setting up locales (2.41-1ubuntu2) ... 149s Generating locales (this might take a while)... 151s en_US.UTF-8... done 151s Generation complete. 151s Setting up libc-dev-bin (2.41-1ubuntu2) ... 151s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 151s Processing triggers for man-db (2.13.0-1) ... 152s Processing triggers for systemd (257.3-1ubuntu3) ... 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 155s Solving dependencies... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s autopkgtest [14:13:20]: rebooting testbed after setup commands that affected boot 181s autopkgtest [14:13:44]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 184s autopkgtest [14:13:47]: @@@@@@@@@@@@@@@@@@@@ apt-source parsnp 186s Get:1 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (dsc) [2221 B] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (tar) [142 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/universe parsnp 2.0.6+dfsg-1ubuntu1 (diff) [10.5 kB] 186s gpgv: Signature made Thu Feb 20 04:03:51 2025 UTC 186s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 186s gpgv: Can't check signature: No public key 186s dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.6+dfsg-1ubuntu1.dsc: no acceptable signature found 186s autopkgtest [14:13:49]: testing package parsnp version 2.0.6+dfsg-1ubuntu1 187s autopkgtest [14:13:50]: build not needed 187s autopkgtest [14:13:50]: test run-unit-test: preparing testbed 187s Reading package lists... 188s Building dependency tree... 188s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 191s The following NEW packages will be installed: 191s fasttree fontconfig-config fonts-dejavu-core fonts-dejavu-mono 191s fonts-urw-base35 harvest-tools libblas3 libcairo2 libcapnp-1.1.0 libdeflate0 191s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 191s libharfbuzz0b libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 191s liblcms2-2 liblerc4 libmuscle1 libopenjp2-7 libpixman-1-0 libprotobuf32t64 191s libraqm0 libsharpyuv0 libspoa7.0.0 libtiff6 libwebp7 libwebpdemux2 191s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 mummer parsnp phipack 191s python3-biopython python3-cairo python3-freetype python3-numpy 191s python3-numpy-dev python3-pil python3-pyspoa python3-reportlab 191s python3-rlpycairo python3-tqdm raxml sgml-base w3c-sgml-lib x11-common 191s xfonts-encodings xfonts-utils xml-core 191s 0 upgraded, 57 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 31.8 MB of archives. 191s After this operation, 102 MB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy-dev arm64 1:2.2.3+ds-5 [146 kB] 191s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.1-2 [161 kB] 191s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 15-20250222-0ubuntu1 [444 kB] 191s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.1-2 [2307 kB] 193s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:2.2.3+ds-5 [3981 kB] 195s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 sgml-base all 1.31 [11.4 kB] 195s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 196s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 196s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontenc1 arm64 1:1.1.8-1build1 [13.9 kB] 196s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 196s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 196s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 xfonts-utils arm64 1:7.7+7 [95.6 kB] 196s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 204s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 fontconfig-config arm64 2.15.0-2ubuntu1 [37.5 kB] 204s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libcapnp-1.1.0 arm64 1.1.0-2 [1371 kB] 205s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libprotobuf32t64 arm64 3.21.12-10build2 [868 kB] 206s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 harvest-tools arm64 1.3-8build6 [121 kB] 206s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libfontconfig1 arm64 2.15.0-2ubuntu1 [144 kB] 206s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libpixman-1-0 arm64 0.44.0-3 [197 kB] 206s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-render0 arm64 1.17.0-2 [16.6 kB] 206s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libxcb-shm0 arm64 1.17.0-2 [5884 B] 206s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 206s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libcairo2 arm64 1.18.2-2 [560 kB] 206s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 libdeflate0 arm64 1.23-1 [46.2 kB] 206s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 15-20250222-0ubuntu1 [146 kB] 206s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 libgraphite2-3 arm64 1.3.14-2ubuntu1 [70.6 kB] 206s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 libharfbuzz0b arm64 10.2.0-1 [490 kB] 207s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 207s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg-turbo8 arm64 2.1.5-3ubuntu2 [165 kB] 207s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 207s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 liblcms2-2 arm64 2.16-2 [170 kB] 207s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 liblerc4 arm64 4.0.0+ds-5ubuntu1 [167 kB] 207s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmuscle1 arm64 3.7+4565-8 [273 kB] 207s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libraqm0 arm64 0.10.2-1 [14.9 kB] 207s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [16.9 kB] 207s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 libspoa7.0.0 arm64 4.1.4-2 [60.1 kB] 207s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] 207s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebp7 arm64 1.5.0-0.1 [194 kB] 207s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu4 [193 kB] 207s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpdemux2 arm64 1.5.0-0.1 [12.5 kB] 207s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libwebpmux3 arm64 1.5.0-0.1 [25.4 kB] 207s Get:42 http://ftpmaster.internal/ubuntu plucky/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] 207s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libopenjp2-7 arm64 2.5.3-2 [183 kB] 207s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-pil arm64 11.1.0-5build1 [463 kB] 208s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-cairo arm64 1.26.1-2build2 [122 kB] 208s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-freetype all 2.5.1-1 [92.3 kB] 208s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 208s Get:48 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-reportlab all 4.3.1-1 [1137 kB] 208s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 xml-core all 0.19 [20.3 kB] 208s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 208s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biopython arm64 1.85+dfsg-2build1 [1711 kB] 209s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pyspoa arm64 0.2.1-2build1 [61.6 kB] 209s Get:53 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-tqdm all 4.67.1-2 [92.5 kB] 209s Get:54 http://ftpmaster.internal/ubuntu plucky/universe arm64 fasttree arm64 2.1.11-2 [164 kB] 209s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 phipack arm64 0.0.20160614-5 [49.9 kB] 209s Get:56 http://ftpmaster.internal/ubuntu plucky/universe arm64 raxml arm64 8.2.13+dfsg-2 [1009 kB] 210s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 parsnp arm64 2.0.6+dfsg-1ubuntu1 [204 kB] 210s Fetched 31.8 MB in 19s (1673 kB/s) 210s Selecting previously unselected package python3-numpy-dev:arm64. 211s (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 ... 81647 files and directories currently installed.) 211s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_arm64.deb ... 211s Unpacking python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 211s Selecting previously unselected package libblas3:arm64. 211s Preparing to unpack .../01-libblas3_3.12.1-2_arm64.deb ... 211s Unpacking libblas3:arm64 (3.12.1-2) ... 211s Selecting previously unselected package libgfortran5:arm64. 211s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_arm64.deb ... 211s Unpacking libgfortran5:arm64 (15-20250222-0ubuntu1) ... 211s Selecting previously unselected package liblapack3:arm64. 211s Preparing to unpack .../03-liblapack3_3.12.1-2_arm64.deb ... 211s Unpacking liblapack3:arm64 (3.12.1-2) ... 211s Selecting previously unselected package python3-numpy. 211s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_arm64.deb ... 211s Unpacking python3-numpy (1:2.2.3+ds-5) ... 211s Selecting previously unselected package sgml-base. 211s Preparing to unpack .../05-sgml-base_1.31_all.deb ... 211s Unpacking sgml-base (1.31) ... 211s Selecting previously unselected package fonts-dejavu-mono. 211s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 211s Unpacking fonts-dejavu-mono (2.37-8) ... 212s Selecting previously unselected package fonts-dejavu-core. 212s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 212s Unpacking fonts-dejavu-core (2.37-8) ... 212s Selecting previously unselected package libfontenc1:arm64. 212s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1build1_arm64.deb ... 212s Unpacking libfontenc1:arm64 (1:1.1.8-1build1) ... 212s Selecting previously unselected package x11-common. 212s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu3_all.deb ... 212s Unpacking x11-common (1:7.7+23ubuntu3) ... 212s Selecting previously unselected package xfonts-encodings. 212s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 212s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 212s Selecting previously unselected package xfonts-utils. 212s Preparing to unpack .../11-xfonts-utils_1%3a7.7+7_arm64.deb ... 212s Unpacking xfonts-utils (1:7.7+7) ... 212s Selecting previously unselected package fonts-urw-base35. 212s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 212s Unpacking fonts-urw-base35 (20200910-8) ... 212s Selecting previously unselected package fontconfig-config. 212s Preparing to unpack .../13-fontconfig-config_2.15.0-2ubuntu1_arm64.deb ... 213s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 213s Selecting previously unselected package libcapnp-1.1.0:arm64. 213s Preparing to unpack .../14-libcapnp-1.1.0_1.1.0-2_arm64.deb ... 213s Unpacking libcapnp-1.1.0:arm64 (1.1.0-2) ... 213s Selecting previously unselected package libprotobuf32t64:arm64. 213s Preparing to unpack .../15-libprotobuf32t64_3.21.12-10build2_arm64.deb ... 213s Unpacking libprotobuf32t64:arm64 (3.21.12-10build2) ... 213s Selecting previously unselected package harvest-tools. 213s Preparing to unpack .../16-harvest-tools_1.3-8build6_arm64.deb ... 213s Unpacking harvest-tools (1.3-8build6) ... 213s Selecting previously unselected package libfontconfig1:arm64. 213s Preparing to unpack .../17-libfontconfig1_2.15.0-2ubuntu1_arm64.deb ... 213s Unpacking libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 213s Selecting previously unselected package libpixman-1-0:arm64. 213s Preparing to unpack .../18-libpixman-1-0_0.44.0-3_arm64.deb ... 213s Unpacking libpixman-1-0:arm64 (0.44.0-3) ... 213s Selecting previously unselected package libxcb-render0:arm64. 213s Preparing to unpack .../19-libxcb-render0_1.17.0-2_arm64.deb ... 213s Unpacking libxcb-render0:arm64 (1.17.0-2) ... 213s Selecting previously unselected package libxcb-shm0:arm64. 213s Preparing to unpack .../20-libxcb-shm0_1.17.0-2_arm64.deb ... 213s Unpacking libxcb-shm0:arm64 (1.17.0-2) ... 213s Selecting previously unselected package libxrender1:arm64. 213s Preparing to unpack .../21-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 213s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 213s Selecting previously unselected package libcairo2:arm64. 213s Preparing to unpack .../22-libcairo2_1.18.2-2_arm64.deb ... 213s Unpacking libcairo2:arm64 (1.18.2-2) ... 213s Selecting previously unselected package libdeflate0:arm64. 213s Preparing to unpack .../23-libdeflate0_1.23-1_arm64.deb ... 213s Unpacking libdeflate0:arm64 (1.23-1) ... 213s Selecting previously unselected package libgomp1:arm64. 213s Preparing to unpack .../24-libgomp1_15-20250222-0ubuntu1_arm64.deb ... 213s Unpacking libgomp1:arm64 (15-20250222-0ubuntu1) ... 213s Selecting previously unselected package libgraphite2-3:arm64. 213s Preparing to unpack .../25-libgraphite2-3_1.3.14-2ubuntu1_arm64.deb ... 213s Unpacking libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 213s Selecting previously unselected package libharfbuzz0b:arm64. 213s Preparing to unpack .../26-libharfbuzz0b_10.2.0-1_arm64.deb ... 213s Unpacking libharfbuzz0b:arm64 (10.2.0-1) ... 214s Selecting previously unselected package libimagequant0:arm64. 214s Preparing to unpack .../27-libimagequant0_2.18.0-1build1_arm64.deb ... 214s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 214s Selecting previously unselected package libjpeg-turbo8:arm64. 214s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-3ubuntu2_arm64.deb ... 214s Unpacking libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 214s Selecting previously unselected package libjpeg8:arm64. 214s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_arm64.deb ... 214s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 214s Selecting previously unselected package liblcms2-2:arm64. 214s Preparing to unpack .../30-liblcms2-2_2.16-2_arm64.deb ... 214s Unpacking liblcms2-2:arm64 (2.16-2) ... 214s Selecting previously unselected package liblerc4:arm64. 214s Preparing to unpack .../31-liblerc4_4.0.0+ds-5ubuntu1_arm64.deb ... 214s Unpacking liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 214s Selecting previously unselected package libmuscle1. 214s Preparing to unpack .../32-libmuscle1_3.7+4565-8_arm64.deb ... 214s Unpacking libmuscle1 (3.7+4565-8) ... 214s Selecting previously unselected package libraqm0:arm64. 214s Preparing to unpack .../33-libraqm0_0.10.2-1_arm64.deb ... 214s Unpacking libraqm0:arm64 (0.10.2-1) ... 214s Selecting previously unselected package libsharpyuv0:arm64. 214s Preparing to unpack .../34-libsharpyuv0_1.5.0-0.1_arm64.deb ... 214s Unpacking libsharpyuv0:arm64 (1.5.0-0.1) ... 214s Selecting previously unselected package libspoa7.0.0:arm64. 214s Preparing to unpack .../35-libspoa7.0.0_4.1.4-2_arm64.deb ... 214s Unpacking libspoa7.0.0:arm64 (4.1.4-2) ... 214s Selecting previously unselected package libjbig0:arm64. 214s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu2_arm64.deb ... 214s Unpacking libjbig0:arm64 (2.1-6.1ubuntu2) ... 214s Selecting previously unselected package libwebp7:arm64. 214s Preparing to unpack .../37-libwebp7_1.5.0-0.1_arm64.deb ... 214s Unpacking libwebp7:arm64 (1.5.0-0.1) ... 214s Selecting previously unselected package libtiff6:arm64. 214s Preparing to unpack .../38-libtiff6_4.5.1+git230720-4ubuntu4_arm64.deb ... 214s Unpacking libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 214s Selecting previously unselected package libwebpdemux2:arm64. 214s Preparing to unpack .../39-libwebpdemux2_1.5.0-0.1_arm64.deb ... 214s Unpacking libwebpdemux2:arm64 (1.5.0-0.1) ... 214s Selecting previously unselected package libwebpmux3:arm64. 214s Preparing to unpack .../40-libwebpmux3_1.5.0-0.1_arm64.deb ... 214s Unpacking libwebpmux3:arm64 (1.5.0-0.1) ... 214s Selecting previously unselected package mummer. 214s Preparing to unpack .../41-mummer_3.23+dfsg-8_arm64.deb ... 214s Unpacking mummer (3.23+dfsg-8) ... 214s Selecting previously unselected package libopenjp2-7:arm64. 214s Preparing to unpack .../42-libopenjp2-7_2.5.3-2_arm64.deb ... 214s Unpacking libopenjp2-7:arm64 (2.5.3-2) ... 214s Selecting previously unselected package python3-pil:arm64. 214s Preparing to unpack .../43-python3-pil_11.1.0-5build1_arm64.deb ... 214s Unpacking python3-pil:arm64 (11.1.0-5build1) ... 214s Selecting previously unselected package python3-cairo. 214s Preparing to unpack .../44-python3-cairo_1.26.1-2build2_arm64.deb ... 214s Unpacking python3-cairo (1.26.1-2build2) ... 214s Selecting previously unselected package python3-freetype. 214s Preparing to unpack .../45-python3-freetype_2.5.1-1_all.deb ... 214s Unpacking python3-freetype (2.5.1-1) ... 215s Selecting previously unselected package python3-rlpycairo. 215s Preparing to unpack .../46-python3-rlpycairo_0.3.0-3_all.deb ... 215s Unpacking python3-rlpycairo (0.3.0-3) ... 215s Selecting previously unselected package python3-reportlab. 215s Preparing to unpack .../47-python3-reportlab_4.3.1-1_all.deb ... 215s Unpacking python3-reportlab (4.3.1-1) ... 215s Selecting previously unselected package xml-core. 215s Preparing to unpack .../48-xml-core_0.19_all.deb ... 215s Unpacking xml-core (0.19) ... 215s Selecting previously unselected package w3c-sgml-lib. 215s Preparing to unpack .../49-w3c-sgml-lib_1.3-3_all.deb ... 215s Unpacking w3c-sgml-lib (1.3-3) ... 215s Selecting previously unselected package python3-biopython. 215s Preparing to unpack .../50-python3-biopython_1.85+dfsg-2build1_arm64.deb ... 215s Unpacking python3-biopython (1.85+dfsg-2build1) ... 215s Selecting previously unselected package python3-pyspoa. 215s Preparing to unpack .../51-python3-pyspoa_0.2.1-2build1_arm64.deb ... 215s Unpacking python3-pyspoa (0.2.1-2build1) ... 215s Selecting previously unselected package python3-tqdm. 215s Preparing to unpack .../52-python3-tqdm_4.67.1-2_all.deb ... 215s Unpacking python3-tqdm (4.67.1-2) ... 215s Selecting previously unselected package fasttree. 215s Preparing to unpack .../53-fasttree_2.1.11-2_arm64.deb ... 215s Unpacking fasttree (2.1.11-2) ... 215s Selecting previously unselected package phipack. 215s Preparing to unpack .../54-phipack_0.0.20160614-5_arm64.deb ... 215s Unpacking phipack (0.0.20160614-5) ... 215s Selecting previously unselected package raxml. 215s Preparing to unpack .../55-raxml_8.2.13+dfsg-2_arm64.deb ... 215s Unpacking raxml (8.2.13+dfsg-2) ... 215s Selecting previously unselected package parsnp. 215s Preparing to unpack .../56-parsnp_2.0.6+dfsg-1ubuntu1_arm64.deb ... 215s Unpacking parsnp (2.0.6+dfsg-1ubuntu1) ... 215s Setting up libgraphite2-3:arm64 (1.3.14-2ubuntu1) ... 215s Setting up liblcms2-2:arm64 (2.16-2) ... 215s Setting up libpixman-1-0:arm64 (0.44.0-3) ... 215s Setting up libsharpyuv0:arm64 (1.5.0-0.1) ... 215s Setting up libprotobuf32t64:arm64 (3.21.12-10build2) ... 215s Setting up liblerc4:arm64 (4.0.0+ds-5ubuntu1) ... 215s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 215s Setting up libxcb-render0:arm64 (1.17.0-2) ... 215s Setting up python3-tqdm (4.67.1-2) ... 216s Setting up x11-common (1:7.7+23ubuntu3) ... 216s Setting up libdeflate0:arm64 (1.23-1) ... 216s Setting up libxcb-shm0:arm64 (1.17.0-2) ... 216s Setting up libgomp1:arm64 (15-20250222-0ubuntu1) ... 216s Setting up python3-freetype (2.5.1-1) ... 217s Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... 217s Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... 217s Setting up libblas3:arm64 (3.12.1-2) ... 217s 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 217s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 217s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 217s Setting up fonts-dejavu-mono (2.37-8) ... 217s Setting up libspoa7.0.0:arm64 (4.1.4-2) ... 217s Setting up python3-numpy-dev:arm64 (1:2.2.3+ds-5) ... 217s Setting up fonts-dejavu-core (2.37-8) ... 217s Setting up libjpeg-turbo8:arm64 (2.1.5-3ubuntu2) ... 217s Setting up libgfortran5:arm64 (15-20250222-0ubuntu1) ... 217s Setting up libwebp7:arm64 (1.5.0-0.1) ... 217s Setting up mummer (3.23+dfsg-8) ... 217s Setting up libopenjp2-7:arm64 (2.5.3-2) ... 217s Setting up libharfbuzz0b:arm64 (10.2.0-1) ... 217s Setting up phipack (0.0.20160614-5) ... 217s Setting up fasttree (2.1.11-2) ... 217s Setting up sgml-base (1.31) ... 217s Setting up libcapnp-1.1.0:arm64 (1.1.0-2) ... 217s Setting up harvest-tools (1.3-8build6) ... 217s Setting up libwebpmux3:arm64 (1.5.0-0.1) ... 217s Setting up raxml (8.2.13+dfsg-2) ... 217s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 217s Setting up python3-pyspoa (0.2.1-2build1) ... 217s Setting up liblapack3:arm64 (3.12.1-2) ... 217s 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 217s Setting up libmuscle1 (3.7+4565-8) ... 217s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 217s Setting up libwebpdemux2:arm64 (1.5.0-0.1) ... 217s Setting up xfonts-utils (1:7.7+7) ... 217s Setting up libraqm0:arm64 (0.10.2-1) ... 217s Setting up python3-numpy (1:2.2.3+ds-5) ... 219s Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu4) ... 219s Setting up xml-core (0.19) ... 220s Setting up libfontconfig1:arm64 (2.15.0-2ubuntu1) ... 220s Setting up fonts-urw-base35 (20200910-8) ... 220s Setting up libcairo2:arm64 (1.18.2-2) ... 220s Setting up python3-pil:arm64 (11.1.0-5build1) ... 221s Setting up python3-cairo (1.26.1-2build2) ... 221s Setting up python3-rlpycairo (0.3.0-3) ... 221s Setting up python3-reportlab (4.3.1-1) ... 222s Processing triggers for libc-bin (2.41-1ubuntu2) ... 222s Processing triggers for man-db (2.13.0-1) ... 223s Processing triggers for sgml-base (1.31) ... 223s Setting up w3c-sgml-lib (1.3-3) ... 260s Setting up python3-biopython (1.85+dfsg-2build1) ... 261s Setting up parsnp (2.0.6+dfsg-1ubuntu1) ... 263s autopkgtest [14:15:06]: test run-unit-test: [----------------------- 263s Test 1: With GenBank Annotations 263s 14:15:06 - INFO - |--Parsnp 2.0.6--| 263s 263s 14:15:06 - INFO - 263s ********************************************************************************** 263s SETTINGS: 263s |-refgenome: mers_virus/ref/England1.gbk 263s |-genomes: 263s mers_virus/genomes/Qatar4.fna 263s mers_virus/genomes/KFU-HKU_19Dam.fna 263s ...42 more file(s)... 263s mers_virus/genomes/Hafr-Al-Batin_2_2013.fna 263s mers_virus/genomes/Al-Hasa_12_2013.fna 263s |-aligner: muscle 263s |-outdir: /tmp/autopkgtest.FQAXZV/autopkgtest_tmp/P_2025_03_15_141506568113 263s |-OS: Linux 263s |-threads: 1 263s ********************************************************************************** 263s 263s 14:15:06 - INFO - <> 263s 14:15:06 - INFO - Too few genomes to run partitions of size >50. Running all genomes at once. 263s 14:15:06 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 264s 14:15:07 - INFO - Reconstructing core genome phylogeny... 268s 14:15:11 - INFO - Aligned 47 genomes in 4.86 seconds 268s 14:15:11 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.FQAXZV/autopkgtest_tmp/P_2025_03_15_141506568113 268s Passed 268s 268s Test 2: Without GenBank Annotations 268s 14:15:11 - INFO - |--Parsnp 2.0.6--| 268s 268s 14:15:11 - INFO - 268s ********************************************************************************** 268s SETTINGS: 268s |-refgenome: mers_virus/ref/England1.fna 268s |-genomes: 268s mers_virus/genomes/Qatar4.fna 268s mers_virus/genomes/KFU-HKU_19Dam.fna 268s ...42 more file(s)... 268s mers_virus/genomes/Hafr-Al-Batin_2_2013.fna 268s mers_virus/genomes/Al-Hasa_12_2013.fna 268s |-aligner: muscle 268s |-outdir: /tmp/autopkgtest.FQAXZV/autopkgtest_tmp/P_2025_03_15_141511796000 268s |-OS: Linux 268s |-threads: 1 268s ********************************************************************************** 268s 268s 14:15:11 - INFO - <> 268s 14:15:11 - INFO - No genbank file provided for reference annotations, skipping.. 268s 14:15:11 - INFO - Too few genomes to run partitions of size >50. Running all genomes at once. 268s 14:15:11 - INFO - Running Parsnp multi-MUM search and libMUSCLE aligner... 269s 14:15:12 - INFO - Reconstructing core genome phylogeny... 273s 14:15:16 - INFO - Aligned 47 genomes in 4.88 seconds 273s 14:15:16 - INFO - Parsnp finished! All output available in /tmp/autopkgtest.FQAXZV/autopkgtest_tmp/P_2025_03_15_141511796000 273s Passed 273s 274s autopkgtest [14:15:17]: test run-unit-test: -----------------------] 274s autopkgtest [14:15:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 274s run-unit-test PASS 275s autopkgtest [14:15:18]: @@@@@@@@@@@@@@@@@@@@ summary 275s run-unit-test PASS 292s nova [W] Using flock in prodstack6-arm64 292s Creating nova instance adt-plucky-arm64-parsnp-20250315-141043-juju-7f2275-prod-proposed-migration-environment-20-0e1872f1-1db8-4052-97e3-8fbca14864b5 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 292s nova [W] Timed out waiting for 72e735bc-4834-4a0e-a7e0-d02072b69146 to get deleted.