0s autopkgtest [16:44:27]: starting date and time: 2025-03-15 16:44:27+0000 0s autopkgtest [16:44:27]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:44:27]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nftlkznu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade sibelia --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-2@bos03-arm64-37.secgroup --name adt-plucky-arm64-sibelia-20250315-164427-juju-7f2275-prod-proposed-migration-environment-2-1aab7bcc-b927-4d0b-9b84-5cd89985166e --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/ 184s autopkgtest [16:47:31]: testbed dpkg architecture: arm64 185s autopkgtest [16:47:32]: testbed apt version: 2.9.33 185s autopkgtest [16:47:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 185s autopkgtest [16:47:32]: testbed release detected to be: None 186s autopkgtest [16:47:33]: updating testbed package index (apt update) 186s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 187s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 187s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 187s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 187s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 187s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 187s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 188s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 188s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 188s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 188s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 188s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 188s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 188s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 188s Fetched 1078 kB in 2s (612 kB/s) 189s Reading package lists... 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s Calculating upgrade... 191s Calculating upgrade... 191s The following packages will be upgraded: 191s pinentry-curses python3-jinja2 strace 191s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 647 kB of archives. 191s After this operation, 11.3 kB of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 192s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 192s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 193s Fetched 647 kB in 1s (639 kB/s) 193s (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.) 193s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 193s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 193s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 193s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 193s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 193s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 193s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 193s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 193s Setting up strace (6.13+ds-1ubuntu1) ... 193s Processing triggers for man-db (2.13.0-1) ... 194s Reading package lists... 194s Building dependency tree... 194s Reading state information... 195s Solving dependencies... 195s The following packages will be REMOVED: 195s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 195s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 195s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 195s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 196s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 196s After this operation, 267 MB disk space will be freed. 196s (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.) 196s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 196s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 196s Removing libpython3.12t64:arm64 (3.12.9-1) ... 196s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 196s Removing libnsl2:arm64 (1.3.0-3build3) ... 196s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 196s Removing libunwind8:arm64 (1.6.2-3.1) ... 196s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 196s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 198s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 198s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 198s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 198s /etc/kernel/postrm.d/initramfs-tools: 198s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 198s /etc/kernel/postrm.d/zz-flash-kernel: 198s flash-kernel: Kernel 6.11.0-8-generic has been removed. 198s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 198s /etc/kernel/postrm.d/zz-update-grub: 198s Sourcing file `/etc/default/grub' 198s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 198s Generating grub configuration file ... 198s Found linux image: /boot/vmlinuz-6.14.0-10-generic 198s Found initrd image: /boot/initrd.img-6.14.0-10-generic 199s Warning: os-prober will not be executed to detect other bootable partitions. 199s Systems on them will not be added to the GRUB boot configuration. 199s Check GRUB_DISABLE_OS_PROBER documentation entry. 199s Adding boot menu entry for UEFI Firmware Settings ... 199s done 199s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 199s Processing triggers for libc-bin (2.41-1ubuntu1) ... 199s (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.) 199s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 199s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 199s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 199s autopkgtest [16:47:46]: upgrading testbed (apt dist-upgrade and autopurge) 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 201s Entering ResolveByKeep 201s 201s Calculating upgrade... 202s The following packages will be upgraded: 202s libc-bin libc-dev-bin libc6 libc6-dev locales 202s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s Need to get 9530 kB of archives. 202s After this operation, 0 B of additional disk space will be used. 202s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 204s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 207s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 208s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 212s Preconfiguring packages ... 212s Fetched 9530 kB in 10s (946 kB/s) 212s (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.) 212s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 212s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Setting up libc6:arm64 (2.41-1ubuntu2) ... 213s (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.) 213s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 213s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 213s Setting up libc-bin (2.41-1ubuntu2) ... 213s (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.) 213s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 213s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 214s Setting up locales (2.41-1ubuntu2) ... 214s Generating locales (this might take a while)... 216s en_US.UTF-8... done 216s Generation complete. 216s Setting up libc-dev-bin (2.41-1ubuntu2) ... 216s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 216s Processing triggers for man-db (2.13.0-1) ... 217s Processing triggers for systemd (257.3-1ubuntu3) ... 218s Reading package lists... 218s Building dependency tree... 218s Reading state information... 218s Starting pkgProblemResolver with broken count: 0 219s Starting 2 pkgProblemResolver with broken count: 0 219s Done 219s Solving dependencies... 219s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 220s autopkgtest [16:48:07]: rebooting testbed after setup commands that affected boot 243s autopkgtest [16:48:30]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 246s autopkgtest [16:48:33]: @@@@@@@@@@@@@@@@@@@@ apt-source sibelia 253s Get:1 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (dsc) [2132 B] 253s Get:2 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (tar) [4833 kB] 253s Get:3 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (diff) [10.2 kB] 253s gpgv: Signature made Tue Apr 14 08:37:29 2020 UTC 253s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 253s gpgv: issuer "tillea@rki.de" 253s gpgv: Can't check signature: No public key 253s dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found 253s autopkgtest [16:48:40]: testing package sibelia version 3.0.7+dfsg-3 254s autopkgtest [16:48:41]: build not needed 255s autopkgtest [16:48:42]: test run-unit-test: preparing testbed 255s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s Starting pkgProblemResolver with broken count: 0 256s Starting 2 pkgProblemResolver with broken count: 0 256s Done 257s The following NEW packages will be installed: 257s lagan libdivsufsort3 sibelia sibelia-examples 257s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 257s Need to get 7577 kB of archives. 257s After this operation, 12.5 MB of additional disk space will be used. 257s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 lagan arm64 2.0-10 [196 kB] 257s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libdivsufsort3 arm64 2.0.1-6 [41.0 kB] 257s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 sibelia arm64 3.0.7+dfsg-3 [286 kB] 257s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 sibelia-examples all 3.0.7+dfsg-3 [7055 kB] 265s Fetched 7577 kB in 8s (971 kB/s) 265s Selecting previously unselected package lagan. 265s (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.) 265s Preparing to unpack .../lagan_2.0-10_arm64.deb ... 265s Unpacking lagan (2.0-10) ... 265s Selecting previously unselected package libdivsufsort3:arm64. 265s Preparing to unpack .../libdivsufsort3_2.0.1-6_arm64.deb ... 265s Unpacking libdivsufsort3:arm64 (2.0.1-6) ... 265s Selecting previously unselected package sibelia. 265s Preparing to unpack .../sibelia_3.0.7+dfsg-3_arm64.deb ... 265s Unpacking sibelia (3.0.7+dfsg-3) ... 265s Selecting previously unselected package sibelia-examples. 265s Preparing to unpack .../sibelia-examples_3.0.7+dfsg-3_all.deb ... 265s Unpacking sibelia-examples (3.0.7+dfsg-3) ... 265s Setting up lagan (2.0-10) ... 265s Setting up sibelia-examples (3.0.7+dfsg-3) ... 265s Setting up libdivsufsort3:arm64 (2.0.1-6) ... 265s Setting up sibelia (3.0.7+dfsg-3) ... 265s Processing triggers for man-db (2.13.0-1) ... 266s Processing triggers for libc-bin (2.41-1ubuntu2) ... 267s autopkgtest [16:48:54]: test run-unit-test: [----------------------- 268s + cd C-Sibelia/Staphylococcus_aureus 268s + C-Sibelia.py NCTC8325.fasta RN4220.fasta 268s Calculating synteny blocks... 274s Simplification stage 1 of 3 274s Enumerating vertices of the graph, then performing bulge removal... 277s [..................................................] 283s Simplification stage 2 of 3 283s Enumerating vertices of the graph, then performing bulge removal... 286s [..................................................] 292s Simplification stage 3 of 3 292s Enumerating vertices of the graph, then performing bulge removal... 295s [..................................................] 295s Finding synteny blocks and generating the output... 302s Calling variants... 304s An error occured: b"mlagan: multial.c:459: readSubstMatrix: Assertion `file' failed.\n" 304s + cd /tmp/autopkgtest.RXT5Sl/autopkgtest_tmp/Sibelia/Helicobacter_pylori 304s + Sibelia -s loose Helicobacter_pylori.fasta 304s Simplification stage 1 of 4 304s Enumerating vertices of the graph, then performing bulge removal... 310s [..................................................] 310s Simplification stage 2 of 4 310s Enumerating vertices of the graph, then performing bulge removal... 314s [..................................................] 314s Simplification stage 3 of 4 314s Enumerating vertices of the graph, then performing bulge removal... 317s [..................................................] 317s Simplification stage 4 of 4 317s Enumerating vertices of the graph, then performing bulge removal... 321s [..................................................] 321s Finding synteny blocks and generating the output... 326s autopkgtest [16:49:53]: test run-unit-test: -----------------------] 327s autopkgtest [16:49:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 327s run-unit-test PASS 327s autopkgtest [16:49:54]: @@@@@@@@@@@@@@@@@@@@ summary 327s run-unit-test PASS 346s nova [W] Using flock in prodstack6-arm64 346s Creating nova instance adt-plucky-arm64-sibelia-20250315-164427-juju-7f2275-prod-proposed-migration-environment-2-1aab7bcc-b927-4d0b-9b84-5cd89985166e from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 346s nova [W] Timed out waiting for afaaca7f-8dd0-4da3-919d-c7923cd791a4 to get deleted.