0s autopkgtest [16:51:28]: starting date and time: 2025-03-15 16:51:28+0000 0s autopkgtest [16:51:28]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:51:28]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ix2go5dy/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade prodigal --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-prodigal-20250315-165127-juju-7f2275-prod-proposed-migration-environment-20-1239445a-d203-415f-8c3b-64daa3866b98 --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/ 117s autopkgtest [16:53:25]: testbed dpkg architecture: s390x 117s autopkgtest [16:53:25]: testbed apt version: 2.9.33 117s autopkgtest [16:53:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 117s autopkgtest [16:53:25]: testbed release detected to be: None 118s autopkgtest [16:53:26]: updating testbed package index (apt update) 118s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 119s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 119s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 119s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 119s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 119s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 119s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 119s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 120s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 120s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 120s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 120s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 120s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 120s Fetched 1073 kB in 2s (643 kB/s) 121s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s Calculating upgrade... 122s The following packages were automatically installed and are no longer required: 122s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 122s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 122s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 122s linux-tools-6.11.0-8-generic 122s Use 'sudo apt autoremove' to remove them. 122s The following packages will be upgraded: 122s pinentry-curses python3-jinja2 strace 122s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Need to get 652 kB of archives. 122s After this operation, 27.6 kB of additional disk space will be used. 122s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 122s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 122s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 123s Fetched 652 kB in 1s (633 kB/s) 123s (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.) 123s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 123s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 123s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 123s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 123s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 123s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 123s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 123s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 123s Setting up strace (6.13+ds-1ubuntu1) ... 123s Processing triggers for man-db (2.13.0-1) ... 124s Reading package lists... 124s Building dependency tree... 124s Reading state information... 124s Solving dependencies... 124s The following packages will be REMOVED: 124s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 124s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 124s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 124s linux-tools-6.11.0-8-generic* 124s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 124s After this operation, 167 MB disk space will be freed. 124s (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.) 124s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 124s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 124s Removing libpython3.12t64:s390x (3.12.9-1) ... 124s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 124s Removing libnsl2:s390x (1.3.0-3build3) ... 124s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 124s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 125s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 125s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 125s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 56328 files and directories currently installed.) 126s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 126s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 126s autopkgtest [16:53:34]: upgrading testbed (apt dist-upgrade and autopurge) 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 126s Entering ResolveByKeep 126s 127s Calculating upgrade... 127s The following packages will be upgraded: 127s libc-bin libc-dev-bin libc6 libc6-dev locales 127s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 9512 kB of archives. 127s After this operation, 8192 B of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 129s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 129s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 133s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 134s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 140s Preconfiguring packages ... 140s Fetched 9512 kB in 13s (724 kB/s) 140s (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.) 140s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 140s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 140s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 140s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 140s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 140s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 140s Setting up libc6:s390x (2.41-1ubuntu2) ... 140s (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.) 140s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 140s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 141s Setting up libc-bin (2.41-1ubuntu2) ... 141s (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.) 141s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 141s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 141s Setting up locales (2.41-1ubuntu2) ... 141s Generating locales (this might take a while)... 142s en_US.UTF-8... done 142s Generation complete. 142s Setting up libc-dev-bin (2.41-1ubuntu2) ... 142s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 142s Processing triggers for man-db (2.13.0-1) ... 143s Processing triggers for systemd (257.3-1ubuntu3) ... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 144s Solving dependencies... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [16:53:52]: rebooting testbed after setup commands that affected boot 164s autopkgtest [16:54:12]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 167s autopkgtest [16:54:15]: @@@@@@@@@@@@@@@@@@@@ apt-source prodigal 169s Get:1 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (dsc) [1992 B] 169s Get:2 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (tar) [611 kB] 169s Get:3 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (diff) [49.3 kB] 169s gpgv: Signature made Tue Dec 6 13:16:13 2022 UTC 169s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 169s gpgv: issuer "tille@debian.org" 169s gpgv: Can't check signature: No public key 169s dpkg-source: warning: cannot verify inline signature for ./prodigal_2.6.3-6.dsc: no acceptable signature found 169s autopkgtest [16:54:17]: testing package prodigal version 1:2.6.3-6 172s autopkgtest [16:54:20]: build not needed 173s autopkgtest [16:54:21]: test run-unit-test: preparing testbed 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 174s The following NEW packages will be installed: 174s prodigal 175s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 663 kB of archives. 175s After this operation, 12.8 MB of additional disk space will be used. 175s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x prodigal s390x 1:2.6.3-6 [663 kB] 177s Fetched 663 kB in 2s (279 kB/s) 177s Selecting previously unselected package prodigal. 177s (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.) 177s Preparing to unpack .../prodigal_1%3a2.6.3-6_s390x.deb ... 177s Unpacking prodigal (1:2.6.3-6) ... 177s Setting up prodigal (1:2.6.3-6) ... 177s Processing triggers for man-db (2.13.0-1) ... 178s autopkgtest [16:54:26]: test run-unit-test: [----------------------- 178s ------------------------------------- 178s PRODIGAL v2.6.3 [February, 2016] 178s Univ of Tenn / Oak Ridge National Lab 178s Doug Hyatt, Loren Hauser, et al. 178s ------------------------------------- 178s Request: Single Genome, Phase: Training 178s Reading in the sequence(s) to train...174014 bp seq created, 17.63 pct GC 178s Locating all potential starts and stops...2619 nodes 178s Looking for GC bias in different frames...frame bias scores: 1.27 1.60 0.12 179s Building initial set of genes to train from...done! 179s Creating coding model and scoring nodes...done! 179s Examining upstream regions and training starts...done! 179s Writing data to training file testgenome.trn...done! 179s autopkgtest [16:54:27]: test run-unit-test: -----------------------] 179s run-unit-test PASS 179s autopkgtest [16:54:27]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 180s autopkgtest [16:54:28]: @@@@@@@@@@@@@@@@@@@@ summary 180s run-unit-test PASS 198s nova [W] Using flock in prodstack6-s390x 198s Creating nova instance adt-plucky-s390x-prodigal-20250315-165127-juju-7f2275-prod-proposed-migration-environment-20-1239445a-d203-415f-8c3b-64daa3866b98 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 198s nova [W] Timed out waiting for 975feb02-f723-4204-a964-8d904a22d967 to get deleted.