0s autopkgtest [17:44:43]: starting date and time: 2025-03-15 17:44:43+0000 0s autopkgtest [17:44:43]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:44:43]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.crixmvot/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 snpomatic --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.158 lxd-armhf-10.145.243.158:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [17:45:03]: testbed dpkg architecture: armhf 22s autopkgtest [17:45:05]: testbed apt version: 2.9.33 26s autopkgtest [17:45:09]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [17:45:11]: testbed release detected to be: None 35s autopkgtest [17:45:18]: updating testbed package index (apt update) 37s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 37s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 38s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 38s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 38s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 38s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 38s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 38s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 38s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 39s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 54s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 56s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 57s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 57s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 72s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 74s Fetched 41.0 MB in 36s (1131 kB/s) 75s Reading package lists... 80s autopkgtest [17:46:03]: upgrading testbed (apt dist-upgrade and autopurge) 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 83s Starting 2 pkgProblemResolver with broken count: 0 83s Done 84s Entering ResolveByKeep 84s 84s Calculating upgrade... 85s The following packages will be upgraded: 85s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 85s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Need to get 8683 kB of archives. 85s After this operation, 23.6 kB of additional disk space will be used. 85s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 94s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 95s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 95s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 95s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 96s Preconfiguring packages ... 96s Fetched 8683 kB in 10s (859 kB/s) 96s (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.) 96s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 96s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up libc6:armhf (2.41-1ubuntu2) ... 97s (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.) 97s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 97s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 97s Setting up libc-bin (2.41-1ubuntu2) ... 97s (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.) 97s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 97s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 97s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 97s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 97s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 97s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 97s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 97s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 97s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 98s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 98s Setting up sos (4.9.0-5) ... 98s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 98s Setting up locales (2.41-1ubuntu2) ... 99s Generating locales (this might take a while)... 101s en_US.UTF-8... done 101s Generation complete. 101s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 102s Setting up strace (6.13+ds-1ubuntu1) ... 102s Processing triggers for man-db (2.13.0-1) ... 103s Processing triggers for systemd (257.3-1ubuntu3) ... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 106s Starting pkgProblemResolver with broken count: 0 106s Starting 2 pkgProblemResolver with broken count: 0 106s Done 107s Solving dependencies... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [17:46:35]: rebooting testbed after setup commands that affected boot 159s autopkgtest [17:47:22]: 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 184s autopkgtest [17:47:47]: @@@@@@@@@@@@@@@@@@@@ apt-source snpomatic 194s Get:1 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (dsc) [1990 B] 194s Get:2 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (tar) [66.5 kB] 194s Get:3 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (diff) [9876 B] 194s gpgv: Signature made Sat Dec 23 08:22:17 2023 UTC 194s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 194s gpgv: Can't check signature: No public key 194s dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found 194s autopkgtest [17:47:57]: testing package snpomatic version 1.0-7 196s autopkgtest [17:47:59]: build not needed 198s autopkgtest [17:48:01]: test test-example: preparing testbed 200s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 202s The following NEW packages will be installed: 202s libdeflate0 libhts3t64 libhtscodecs2 samtools snpomatic 202s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 202s Need to get 1206 kB of archives. 202s After this operation, 2916 kB of additional disk space will be used. 202s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libdeflate0 armhf 1.23-1 [38.5 kB] 202s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libhts3t64 armhf 1.21+ds-1 [399 kB] 203s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf samtools armhf 1.21-1 [619 kB] 204s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf snpomatic armhf 1.0-7 [82.9 kB] 204s Fetched 1206 kB in 2s (690 kB/s) 204s Selecting previously unselected package libdeflate0:armhf. 204s (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.) 204s Preparing to unpack .../libdeflate0_1.23-1_armhf.deb ... 204s Unpacking libdeflate0:armhf (1.23-1) ... 204s Selecting previously unselected package libhtscodecs2:armhf. 204s Preparing to unpack .../libhtscodecs2_1.6.1-2_armhf.deb ... 204s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 204s Selecting previously unselected package libhts3t64:armhf. 204s Preparing to unpack .../libhts3t64_1.21+ds-1_armhf.deb ... 204s Unpacking libhts3t64:armhf (1.21+ds-1) ... 204s Selecting previously unselected package samtools. 205s Preparing to unpack .../samtools_1.21-1_armhf.deb ... 205s Unpacking samtools (1.21-1) ... 205s Selecting previously unselected package snpomatic. 205s Preparing to unpack .../snpomatic_1.0-7_armhf.deb ... 205s Unpacking snpomatic (1.0-7) ... 205s Setting up libhtscodecs2:armhf (1.6.1-2) ... 205s Setting up libdeflate0:armhf (1.23-1) ... 205s Setting up snpomatic (1.0-7) ... 205s Setting up libhts3t64:armhf (1.21+ds-1) ... 205s Setting up samtools (1.21-1) ... 205s Processing triggers for man-db (2.13.0-1) ... 205s Processing triggers for libc-bin (2.41-1ubuntu2) ... 213s autopkgtest [17:48:16]: test test-example: [----------------------- 215s [wgsim] seed = 42 215s [wgsim_core] calculating the total length of the reference sequence... 215s [wgsim_core] 1 sequences, total length: 11940 215s ref 134 C Y + 215s ref 137 G C - 215s ref 213 A R + 215s ref 276 - A + 215s ref 320 T W + 215s ref 469 A C - 215s ref 631 G T - 215s ref 678 - TTT - 215s ref 682 G K + 215s ref 796 GA - - 215s ref 974 C G - 215s ref 1056 A R + 215s ref 1156 A G - 215s ref 1170 G S + 215s ref 1298 C M + 215s ref 1326 G K + 215s ref 1343 T A - 215s ref 1422 G - - 215s ref 1639 T Y + 215s ref 1722 T G - 215s ref 2008 C M + 215s ref 2060 T K + 215s ref 2103 - G + 215s ref 2179 C M + 215s ref 2322 A M + 215s ref 2328 A W + 215s ref 2381 A T - 215s ref 2560 C Y + 215s ref 2618 G C - 215s ref 2833 - CG - 215s ref 2944 G K + 215s ref 2978 T C - 215s ref 2984 G R + 215s ref 2988 C M + 215s ref 3017 C S + 215s ref 3038 G C - 215s ref 3358 G S + 215s ref 3443 G A - 215s ref 3558 G R + 215s ref 3559 A R + 215s ref 3765 G R + 215s ref 3863 C M + 215s ref 4101 G T - 215s ref 4271 G S + 215s ref 4475 G K + 215s ref 4690 G S + 215s ref 4730 G C - 215s ref 4735 G K + 215s ref 4917 C G - 215s ref 4983 A G - 215s ref 5178 A R + 215s ref 5307 T G - 215s ref 5365 ACA - - 215s ref 5403 G S + 215s ref 5411 T C - 215s ref 5434 C S + 215s ref 5465 G - - 215s ref 5507 T Y + 215s ref 5544 A R + 215s ref 5588 - T - 215s ref 5702 A M + 215s ref 6146 T K + 215s ref 6158 G A - 215s ref 6181 G A - 215s ref 6207 A W + 215s ref 6216 T A - 215s ref 6286 T K + 215s ref 6346 GC - - 215s ref 6697 G S + 215s ref 6745 C S + 215s ref 6754 T C - 215s ref 6818 G R + 215s ref 6922 C T - 215s ref 7123 C A - 215s ref 7644 C Y + 215s ref 7699 T Y + 215s ref 7793 C T - 215s ref 7861 C T - 215s ref 7877 G C - 215s ref 7970 T G - 215s ref 7973 A G - 215s ref 8068 T W + 215s ref 8157 G C - 215s ref 8164 G R + 215s ref 8442 G K + 215s ref 8483 A R + 215s ref 8498 C Y + 215s ref 8532 A M + 215s ref 8721 C Y + 215s ref 9084 G - - 215s ref 9192 G T - 215s ref 9208 C A - 215s ref 9211 G S + 215s ref 9341 C Y + 215s ref 9372 T K + 215s ref 9393 - C + 215s ref 9597 A C - 215s ref 9621 AC - - 215s ref 9739 C A - 215s ref 9790 CATC - - 215s ref 9881 A C - 215s ref 9902 A G - 215s ref 10134 T G - 215s ref 10212 G C - 215s ref 10214 G K + 215s ref 10556 - TA - 215s ref 10751 T W + 215s ref 10777 C S + 215s ref 10799 C Y + 215s ref 10832 C S + 215s ref 10858 A G - 215s ref 11015 C Y + 215s ref 11038 C Y + 215s ref 11108 C Y + 215s ref 11179 A M + 215s ref 11217 G R + 215s ref 11275 C M + 215s ref 11290 C S + 215s ref 11481 G - - 215s ref 11566 T G - 215s ref 11655 A G - 215s ref 11771 G T - 215s Reading all chromosomes from ref.fasta ... read 1 chromosomes. 215s Indexing 1 chromosomes ... sorting ... done. 215s Setting read length to 70 215s Reading solexa pair data from reads.1.fq ... scanned 10000 solexa reads, 222 (2.22%) matched , 222 total matches, 0 skipped. 215s autopkgtest [17:48:18]: test test-example: -----------------------] 219s autopkgtest [17:48:22]: test test-example: - - - - - - - - - - results - - - - - - - - - - 219s test-example PASS 223s autopkgtest [17:48:26]: @@@@@@@@@@@@@@@@@@@@ summary 223s test-example PASS