0s autopkgtest [17:36:48]: starting date and time: 2025-03-15 17:36:48+0000 0s autopkgtest [17:36:48]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:36:48]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mbzyuyao/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.202 lxd-armhf-10.145.243.202:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [17:37:08]: testbed dpkg architecture: armhf 22s autopkgtest [17:37:10]: testbed apt version: 2.9.33 26s autopkgtest [17:37:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [17:37:16]: testbed release detected to be: None 39s autopkgtest [17:37:27]: updating testbed package index (apt update) 41s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 41s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 42s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 42s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 42s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 43s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 43s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 43s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 43s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 43s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 43s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 43s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 45s Get:16 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 45s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 65s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 67s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 67s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 67s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 82s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 84s Fetched 41.0 MB in 43s (953 kB/s) 85s Reading package lists... 91s autopkgtest [17:38:19]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 94s Starting 2 pkgProblemResolver with broken count: 0 94s Done 95s Entering ResolveByKeep 95s 95s Calculating upgrade... 96s The following packages will be upgraded: 96s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 96s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 8683 kB of archives. 96s After this operation, 23.6 kB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 99s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 104s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 104s Preconfiguring packages ... 105s Fetched 8683 kB in 8s (1054 kB/s) 105s (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 ... 64655 files and directories currently installed.) 105s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 105s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 105s Setting up libc6:armhf (2.41-1ubuntu2) ... 105s (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 ... 64655 files and directories currently installed.) 105s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 105s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 105s Setting up libc-bin (2.41-1ubuntu2) ... 106s (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 ... 64655 files and directories currently installed.) 106s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 106s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 106s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 106s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 106s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 106s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 106s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 106s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 106s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 107s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 107s Setting up sos (4.9.0-5) ... 107s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 107s Setting up locales (2.41-1ubuntu2) ... 108s Generating locales (this might take a while)... 110s en_US.UTF-8... done 110s Generation complete. 110s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 110s Setting up strace (6.13+ds-1ubuntu1) ... 110s Processing triggers for man-db (2.13.0-1) ... 112s Processing triggers for systemd (257.3-1ubuntu3) ... 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s Starting pkgProblemResolver with broken count: 0 115s Starting 2 pkgProblemResolver with broken count: 0 115s Done 116s Solving dependencies... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [17:38:46]: rebooting testbed after setup commands that affected boot 157s autopkgtest [17:39:25]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 181s autopkgtest [17:39:49]: @@@@@@@@@@@@@@@@@@@@ apt-source sibelia 199s Get:1 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (dsc) [2132 B] 199s Get:2 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (tar) [4833 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky/universe sibelia 3.0.7+dfsg-3 (diff) [10.2 kB] 199s gpgv: Signature made Tue Apr 14 08:37:29 2020 UTC 199s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 199s gpgv: issuer "tillea@rki.de" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found 199s autopkgtest [17:40:07]: testing package sibelia version 3.0.7+dfsg-3 201s autopkgtest [17:40:09]: build not needed 204s autopkgtest [17:40:12]: test run-unit-test: preparing testbed 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 207s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 208s The following NEW packages will be installed: 208s lagan libdivsufsort3 sibelia sibelia-examples 208s 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 7578 kB of archives. 208s After this operation, 11.1 MB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf lagan armhf 2.0-10 [180 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libdivsufsort3 armhf 2.0.1-6 [45.4 kB] 208s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf sibelia armhf 3.0.7+dfsg-3 [298 kB] 209s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf sibelia-examples all 3.0.7+dfsg-3 [7055 kB] 214s Fetched 7578 kB in 6s (1236 kB/s) 214s Selecting previously unselected package lagan. 215s (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 ... 64655 files and directories currently installed.) 215s Preparing to unpack .../lagan_2.0-10_armhf.deb ... 215s Unpacking lagan (2.0-10) ... 215s Selecting previously unselected package libdivsufsort3:armhf. 215s Preparing to unpack .../libdivsufsort3_2.0.1-6_armhf.deb ... 215s Unpacking libdivsufsort3:armhf (2.0.1-6) ... 215s Selecting previously unselected package sibelia. 215s Preparing to unpack .../sibelia_3.0.7+dfsg-3_armhf.deb ... 215s Unpacking sibelia (3.0.7+dfsg-3) ... 215s Selecting previously unselected package sibelia-examples. 215s Preparing to unpack .../sibelia-examples_3.0.7+dfsg-3_all.deb ... 215s Unpacking sibelia-examples (3.0.7+dfsg-3) ... 215s Setting up lagan (2.0-10) ... 215s Setting up sibelia-examples (3.0.7+dfsg-3) ... 215s Setting up libdivsufsort3:armhf (2.0.1-6) ... 215s Setting up sibelia (3.0.7+dfsg-3) ... 215s Processing triggers for man-db (2.13.0-1) ... 215s Processing triggers for libc-bin (2.41-1ubuntu2) ... 225s autopkgtest [17:40:33]: test run-unit-test: [----------------------- 227s + cd C-Sibelia/Staphylococcus_aureus 227s + C-Sibelia.py NCTC8325.fasta RN4220.fasta 227s Calculating synteny blocks... 235s Simplification stage 1 of 3 235s Enumerating vertices of the graph, then performing bulge removal... 240s [..................................................] 248s Simplification stage 2 of 3 248s Enumerating vertices of the graph, then performing bulge removal... 253s [..................................................] 261s Simplification stage 3 of 3 261s Enumerating vertices of the graph, then performing bulge removal... 265s [..................................................] 265s Finding synteny blocks and generating the output... 274s Calling variants... 277s An error occured: b"mlagan: multial.c:459: readSubstMatrix: Assertion `file' failed.\n" 277s + cd /tmp/autopkgtest.En96I7/autopkgtest_tmp/Sibelia/Helicobacter_pylori 277s + Sibelia -s loose Helicobacter_pylori.fasta 277s Simplification stage 1 of 4 277s Enumerating vertices of the graph, then performing bulge removal... 284s [..................................................] 284s Simplification stage 2 of 4 284s Enumerating vertices of the graph, then performing bulge removal... 289s [..................................................] 289s Simplification stage 3 of 4 289s Enumerating vertices of the graph, then performing bulge removal... 293s [..................................................] 293s Simplification stage 4 of 4 293s Enumerating vertices of the graph, then performing bulge removal... 296s [..................................................] 296s Finding synteny blocks and generating the output... 303s autopkgtest [17:41:51]: test run-unit-test: -----------------------] 307s autopkgtest [17:41:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 307s run-unit-test PASS 310s autopkgtest [17:41:58]: @@@@@@@@@@@@@@@@@@@@ summary 310s run-unit-test PASS