0s autopkgtest [19:11:14]: starting date and time: 2025-03-15 19:11:14+0000 0s autopkgtest [19:11:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:11:14]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.noswk5t0/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --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 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-28.secgroup --name adt-plucky-s390x-snpomatic-20250315-191114-juju-7f2275-prod-proposed-migration-environment-20-5650bc12-5492-45f3-87f3-982509c2d662 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 85s autopkgtest [19:12:39]: testbed dpkg architecture: s390x 85s autopkgtest [19:12:39]: testbed apt version: 2.9.33 85s autopkgtest [19:12:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s autopkgtest [19:12:39]: testbed release detected to be: None 86s autopkgtest [19:12:40]: updating testbed package index (apt update) 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 87s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 87s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 87s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 89s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB] 89s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 89s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 89s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB] 89s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB] 89s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B] 89s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 89s Fetched 965 kB in 1s (968 kB/s) 89s Reading package lists... 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s Calculating upgrade... 89s The following packages were automatically installed and are no longer required: 89s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 89s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 89s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 89s linux-tools-6.11.0-8-generic 89s Use 'sudo apt autoremove' to remove them. 89s The following packages will be upgraded: 89s pinentry-curses python3-jinja2 strace 89s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 652 kB of archives. 89s After this operation, 27.6 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 90s Fetched 652 kB in 1s (913 kB/s) 90s (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 ... 81428 files and directories currently installed.) 90s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 90s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 90s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 90s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 90s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 90s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 90s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 90s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 90s Setting up strace (6.13+ds-1ubuntu1) ... 90s Processing triggers for man-db (2.13.0-1) ... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 91s Solving dependencies... 91s The following packages will be REMOVED: 91s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 91s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 91s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 91s linux-tools-6.11.0-8-generic* 91s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 91s After this operation, 167 MB disk space will be freed. 91s (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 ... 81428 files and directories currently installed.) 91s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 91s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 91s Removing libpython3.12t64:s390x (3.12.9-1) ... 91s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 92s Removing libnsl2:s390x (1.3.0-3build3) ... 92s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 92s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 92s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 93s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 93s Processing triggers for libc-bin (2.41-1ubuntu1) ... 93s (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 ... 56328 files and directories currently installed.) 93s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 93s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 93s autopkgtest [19:12:47]: upgrading testbed (apt dist-upgrade and autopurge) 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 93s Starting 2 pkgProblemResolver with broken count: 0 93s Done 94s Entering ResolveByKeep 94s 94s Calculating upgrade... 94s The following packages will be upgraded: 94s libc-bin libc-dev-bin libc6 libc6-dev locales 94s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Need to get 9512 kB of archives. 94s After this operation, 8192 B of additional disk space will be used. 94s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 95s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 95s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 96s Preconfiguring packages ... 96s Fetched 9512 kB in 1s (6344 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 ... 56326 files and directories currently installed.) 96s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 96s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 96s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 96s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up libc6:s390x (2.41-1ubuntu2) ... 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 ... 56326 files and directories currently installed.) 96s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 96s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up libc-bin (2.41-1ubuntu2) ... 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 ... 56326 files and directories currently installed.) 96s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 96s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 96s Setting up locales (2.41-1ubuntu2) ... 97s Generating locales (this might take a while)... 98s en_US.UTF-8... done 98s Generation complete. 98s Setting up libc-dev-bin (2.41-1ubuntu2) ... 98s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 98s Processing triggers for man-db (2.13.0-1) ... 98s Processing triggers for systemd (257.3-1ubuntu3) ... 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 99s Solving dependencies... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [19:12:54]: rebooting testbed after setup commands that affected boot 113s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 119s autopkgtest [19:13:13]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 122s autopkgtest [19:13:16]: @@@@@@@@@@@@@@@@@@@@ apt-source snpomatic 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (dsc) [1990 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (tar) [66.5 kB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe snpomatic 1.0-7 (diff) [9876 B] 124s gpgv: Signature made Sat Dec 23 08:22:17 2023 UTC 124s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 124s gpgv: Can't check signature: No public key 124s dpkg-source: warning: cannot verify inline signature for ./snpomatic_1.0-7.dsc: no acceptable signature found 124s autopkgtest [19:13:18]: testing package snpomatic version 1.0-7 124s autopkgtest [19:13:18]: build not needed 124s autopkgtest [19:13:18]: test test-example: preparing testbed 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Starting pkgProblemResolver with broken count: 0 125s Starting 2 pkgProblemResolver with broken count: 0 125s Done 125s The following NEW packages will be installed: 125s libdeflate0 libhts3t64 libhtscodecs2 samtools snpomatic 125s 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. 125s Need to get 1341 kB of archives. 125s After this operation, 3077 kB of additional disk space will be used. 125s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libdeflate0 s390x 1.23-1 [46.1 kB] 126s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 126s Get:3 http://ftpmaster.internal/ubuntu plucky/universe s390x libhts3t64 s390x 1.21+ds-1 [479 kB] 126s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x samtools s390x 1.21-1 [633 kB] 126s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x snpomatic s390x 1.0-7 [92.2 kB] 126s Fetched 1341 kB in 1s (1692 kB/s) 126s Selecting previously unselected package libdeflate0:s390x. 126s (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 ... 56326 files and directories currently installed.) 126s Preparing to unpack .../libdeflate0_1.23-1_s390x.deb ... 126s Unpacking libdeflate0:s390x (1.23-1) ... 126s Selecting previously unselected package libhtscodecs2:s390x. 126s Preparing to unpack .../libhtscodecs2_1.6.1-2_s390x.deb ... 126s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 126s Selecting previously unselected package libhts3t64:s390x. 126s Preparing to unpack .../libhts3t64_1.21+ds-1_s390x.deb ... 126s Unpacking libhts3t64:s390x (1.21+ds-1) ... 126s Selecting previously unselected package samtools. 126s Preparing to unpack .../samtools_1.21-1_s390x.deb ... 126s Unpacking samtools (1.21-1) ... 126s Selecting previously unselected package snpomatic. 126s Preparing to unpack .../snpomatic_1.0-7_s390x.deb ... 126s Unpacking snpomatic (1.0-7) ... 126s Setting up libhtscodecs2:s390x (1.6.1-2) ... 126s Setting up libdeflate0:s390x (1.23-1) ... 126s Setting up snpomatic (1.0-7) ... 126s Setting up libhts3t64:s390x (1.21+ds-1) ... 126s Setting up samtools (1.21-1) ... 126s Processing triggers for man-db (2.13.0-1) ... 127s Processing triggers for libc-bin (2.41-1ubuntu2) ... 128s autopkgtest [19:13:22]: test test-example: [----------------------- 128s [wgsim] seed = 42 128s [wgsim_core] calculating the total length of the reference sequence... 128s [wgsim_core] 1 sequences, total length: 11940 128s ref 134 C Y + 128s ref 137 G C - 128s ref 213 A R + 128s ref 276 - A + 128s ref 320 T W + 128s ref 469 A C - 128s ref 631 G T - 128s ref 678 - TTT - 128s ref 682 G K + 128s ref 796 GA - - 128s ref 974 C G - 128s ref 1056 A R + 128s ref 1156 A G - 128s ref 1170 G S + 128s ref 1298 C M + 128s ref 1326 G K + 128s ref 1343 T A - 128s ref 1422 G - - 128s ref 1639 T Y + 128s ref 1722 T G - 128s ref 2008 C M + 128s ref 2060 T K + 128s ref 2103 - G + 128s ref 2179 C M + 128s ref 2322 A M + 128s ref 2328 A W + 128s ref 2381 A T - 128s ref 2560 C Y + 128s ref 2618 G C - 128s ref 2833 - CG - 128s ref 2944 G K + 128s ref 2978 T C - 128s ref 2984 G R + 128s ref 2988 C M + 128s ref 3017 C S + 128s ref 3038 G C - 128s ref 3358 G S + 128s ref 3443 G A - 128s ref 3558 G R + 128s ref 3559 A R + 128s ref 3765 G R + 128s ref 3863 C M + 128s ref 4101 G T - 128s ref 4271 G S + 128s ref 4475 G K + 128s ref 4690 G S + 128s ref 4730 G C - 128s ref 4735 G K + 128s ref 4917 C G - 128s ref 4983 A G - 128s ref 5178 A R + 128s ref 5307 T G - 128s ref 5365 ACA - - 128s ref 5403 G S + 128s ref 5411 T C - 128s ref 5434 C S + 128s ref 5465 G - - 128s ref 5507 T Y + 128s ref 5544 A R + 128s ref 5588 - T - 128s ref 5702 A M + 128s ref 6146 T K + 128s ref 6158 G A - 128s ref 6181 G A - 128s ref 6207 A W + 128s ref 6216 T A - 128s ref 6286 T K + 128s ref 6346 GC - - 128s ref 6697 G S + 128s ref 6745 C S + 128s ref 6754 T C - 128s ref 6818 G R + 128s ref 6922 C T - 128s ref 7123 C A - 128s ref 7644 C Y + 128s ref 7699 T Y + 128s ref 7793 C T - 128s ref 7861 C T - 128s ref 7877 G C - 128s ref 7970 T G - 128s ref 7973 A G - 128s ref 8068 T W + 128s ref 8157 G C - 128s ref 8164 G R + 128s ref 8442 G K + 128s ref 8483 A R + 128s ref 8498 C Y + 128s ref 8532 A M + 128s ref 8721 C Y + 128s ref 9084 G - - 128s ref 9192 G T - 128s ref 9208 C A - 128s ref 9211 G S + 128s ref 9341 C Y + 128s ref 9372 T K + 128s ref 9393 - C + 128s ref 9597 A C - 128s ref 9621 AC - - 128s ref 9739 C A - 128s ref 9790 CATC - - 128s ref 9881 A C - 128s ref 9902 A G - 128s ref 10134 T G - 128s ref 10212 G C - 128s ref 10214 G K + 128s ref 10556 - TA - 128s ref 10751 T W + 128s ref 10777 C S + 128s ref 10799 C Y + 128s ref 10832 C S + 128s ref 10858 A G - 128s ref 11015 C Y + 128s ref 11038 C Y + 128s ref 11108 C Y + 128s ref 11179 A M + 128s ref 11217 G R + 128s ref 11275 C M + 128s ref 11290 C S + 128s ref 11481 G - - 128s ref 11566 T G - 128s ref 11655 A G - 128s ref 11771 G T - 128s Reading all chromosomes from ref.fasta ... read 1 chromosomes. 128s Indexing 1 chromosomes ... sorting ... done. 128s Setting read length to 70 128s Reading solexa pair data from reads.1.fq ... scanned 10000 solexa reads, 222 (2.22%) matched , 222 total matches, 0 skipped. 128s autopkgtest [19:13:22]: test test-example: -----------------------] 129s autopkgtest [19:13:23]: test test-example: - - - - - - - - - - results - - - - - - - - - - 129s test-example PASS 129s autopkgtest [19:13:23]: @@@@@@@@@@@@@@@@@@@@ summary 129s test-example PASS 146s nova [W] Using flock in prodstack6-s390x 146s Creating nova instance adt-plucky-s390x-snpomatic-20250315-191114-juju-7f2275-prod-proposed-migration-environment-20-5650bc12-5492-45f3-87f3-982509c2d662 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 146s nova [W] Timed out waiting for f0b53b68-4dd9-46fc-99c7-6cc10af7705c to get deleted.