0s autopkgtest [04:43:30]: starting date and time: 2025-02-22 04:43:30+0000 0s autopkgtest [04:43:30]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [04:43:30]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.p1x1eywx/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glib2.0 --apt-upgrade exonerate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glib2.0/2.83.4-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-33.secgroup --name adt-plucky-arm64-exonerate-20250222-044330-juju-7f2275-prod-proposed-migration-environment-2-80f5eb4c-9582-414b-938b-60214b47891e --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/ 132s autopkgtest [04:45:42]: testbed dpkg architecture: arm64 133s autopkgtest [04:45:43]: testbed apt version: 2.9.30ubuntu1 133s autopkgtest [04:45:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 133s autopkgtest [04:45:43]: testbed release detected to be: None 134s autopkgtest [04:45:44]: updating testbed package index (apt update) 134s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 135s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 135s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 135s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 135s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [80.1 kB] 135s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 135s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 135s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [508 kB] 135s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [122 kB] 135s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 135s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [451 kB] 135s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [9060 B] 135s Fetched 1305 kB in 1s (1382 kB/s) 136s Reading package lists... 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 138s Calculating upgrade... 138s Calculating upgrade... 138s The following packages will be upgraded: 138s apparmor base-files cloud-init cloud-init-base gcc-14-base libapparmor1 138s libclang-cpp18 libclang1-19 libgnutls30t64 libllvm18 libllvm19 liblsof0 138s libnss3 libperl5.40 lsof motd-news-config perl perl-base perl-modules-5.40 138s ucf vim-common vim-tiny xxd 139s 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 139s Need to get 90.2 MB of archives. 139s After this operation, 11.3 kB of additional disk space will be used. 139s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 motd-news-config all 13.6ubuntu1 [5168 B] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 base-files arm64 13.6ubuntu1 [75.6 kB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 perl-modules-5.40 all 5.40.1-2 [3217 kB] 139s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libperl5.40 arm64 5.40.1-2 [4779 kB] 140s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 perl arm64 5.40.1-2 [262 kB] 140s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 perl-base arm64 5.40.1-2 [1788 kB] 140s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-base arm64 14.2.0-17ubuntu3 [53.6 kB] 140s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libapparmor1 arm64 4.1.0~beta5-0ubuntu5 [53.7 kB] 140s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls30t64 arm64 3.8.9-2ubuntu2 [962 kB] 140s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 ucf all 3.0050 [43.5 kB] 140s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-tiny arm64 2:9.1.0967-1ubuntu2 [807 kB] 140s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-common all 2:9.1.0967-1ubuntu2 [396 kB] 140s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 xxd arm64 2:9.1.0967-1ubuntu2 [67.8 kB] 140s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 apparmor arm64 4.1.0~beta5-0ubuntu5 [660 kB] 140s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-2 [236 kB] 140s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-2 [54.0 kB] 140s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 cloud-init-base all 25.1-0ubuntu1 [616 kB] 140s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libclang-cpp18 arm64 1:18.1.8-16build1 [13.1 MB] 141s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libllvm18 arm64 1:18.1.8-16build1 [26.3 MB] 143s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libllvm19 arm64 1:19.1.7-1ubuntu2 [27.3 MB] 145s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libclang1-19 arm64 1:19.1.7-1ubuntu2 [7986 kB] 146s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libnss3 arm64 2:3.108-1ubuntu1 [1446 kB] 146s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 cloud-init all 25.1-0ubuntu1 [2088 B] 146s Preconfiguring packages ... 146s Fetched 90.2 MB in 7s (12.1 MB/s) 147s (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 ... 116668 files and directories currently installed.) 147s Preparing to unpack .../motd-news-config_13.6ubuntu1_all.deb ... 147s Unpacking motd-news-config (13.6ubuntu1) over (13.5ubuntu3) ... 147s Preparing to unpack .../base-files_13.6ubuntu1_arm64.deb ... 147s Unpacking base-files (13.6ubuntu1) over (13.5ubuntu3) ... 147s Setting up base-files (13.6ubuntu1) ... 147s Updating /root/.profile to current default. 148s motd-news.service is a disabled or a static unit not running, not starting it. 148s (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 ... 116668 files and directories currently installed.) 148s Preparing to unpack .../perl_5.40.1-2_arm64.deb ... 148s Unpacking perl (5.40.1-2) over (5.40.0-8) ... 148s Preparing to unpack .../perl-modules-5.40_5.40.1-2_all.deb ... 148s Unpacking perl-modules-5.40 (5.40.1-2) over (5.40.0-8) ... 148s Preparing to unpack .../libperl5.40_5.40.1-2_arm64.deb ... 148s Unpacking libperl5.40:arm64 (5.40.1-2) over (5.40.0-8) ... 149s Preparing to unpack .../perl-base_5.40.1-2_arm64.deb ... 149s Unpacking perl-base (5.40.1-2) over (5.40.0-8) ... 149s Setting up perl-base (5.40.1-2) ... 149s (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 ... 116668 files and directories currently installed.) 149s Preparing to unpack .../00-gcc-14-base_14.2.0-17ubuntu3_arm64.deb ... 149s Unpacking gcc-14-base:arm64 (14.2.0-17ubuntu3) over (14.2.0-17ubuntu1) ... 149s Preparing to unpack .../01-libapparmor1_4.1.0~beta5-0ubuntu5_arm64.deb ... 149s Unpacking libapparmor1:arm64 (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ... 149s Preparing to unpack .../02-libgnutls30t64_3.8.9-2ubuntu2_arm64.deb ... 149s Unpacking libgnutls30t64:arm64 (3.8.9-2ubuntu2) over (3.8.9-2ubuntu1) ... 149s Preparing to unpack .../03-ucf_3.0050_all.deb ... 149s Unpacking ucf (3.0050) over (3.0049) ... 149s Preparing to unpack .../04-vim-tiny_2%3a9.1.0967-1ubuntu2_arm64.deb ... 149s Unpacking vim-tiny (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 149s Preparing to unpack .../05-vim-common_2%3a9.1.0967-1ubuntu2_all.deb ... 149s Unpacking vim-common (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 150s Preparing to unpack .../06-xxd_2%3a9.1.0967-1ubuntu2_arm64.deb ... 150s Unpacking xxd (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 150s Preparing to unpack .../07-apparmor_4.1.0~beta5-0ubuntu5_arm64.deb ... 150s Unpacking apparmor (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ... 151s Preparing to unpack .../08-lsof_4.99.4+dfsg-2_arm64.deb ... 151s Unpacking lsof (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ... 151s Preparing to unpack .../09-liblsof0_4.99.4+dfsg-2_arm64.deb ... 151s Unpacking liblsof0 (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ... 151s Preparing to unpack .../10-cloud-init-base_25.1-0ubuntu1_all.deb ... 151s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead. 151s for fn in glob1(directory, "%s.*" % fname): 151s Unpacking cloud-init-base (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 152s Preparing to unpack .../11-libclang-cpp18_1%3a18.1.8-16build1_arm64.deb ... 152s Unpacking libclang-cpp18 (1:18.1.8-16build1) over (1:18.1.8-15) ... 152s Preparing to unpack .../12-libllvm18_1%3a18.1.8-16build1_arm64.deb ... 152s Unpacking libllvm18:arm64 (1:18.1.8-16build1) over (1:18.1.8-15) ... 153s Preparing to unpack .../13-libllvm19_1%3a19.1.7-1ubuntu2_arm64.deb ... 153s Unpacking libllvm19:arm64 (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ... 154s Preparing to unpack .../14-libclang1-19_1%3a19.1.7-1ubuntu2_arm64.deb ... 154s Unpacking libclang1-19 (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ... 154s Preparing to unpack .../15-libnss3_2%3a3.108-1ubuntu1_arm64.deb ... 154s Unpacking libnss3:arm64 (2:3.108-1ubuntu1) over (2:3.107-1ubuntu1) ... 154s Preparing to unpack .../16-cloud-init_25.1-0ubuntu1_all.deb ... 154s Unpacking cloud-init (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 154s Setting up libgnutls30t64:arm64 (3.8.9-2ubuntu2) ... 154s Setting up motd-news-config (13.6ubuntu1) ... 154s Setting up libllvm19:arm64 (1:19.1.7-1ubuntu2) ... 154s Setting up libapparmor1:arm64 (4.1.0~beta5-0ubuntu5) ... 154s Setting up libclang1-19 (1:19.1.7-1ubuntu2) ... 154s Setting up gcc-14-base:arm64 (14.2.0-17ubuntu3) ... 154s Setting up liblsof0 (4.99.4+dfsg-2) ... 154s Setting up libnss3:arm64 (2:3.108-1ubuntu1) ... 154s Setting up cloud-init-base (25.1-0ubuntu1) ... 156s Setting up xxd (2:9.1.0967-1ubuntu2) ... 156s Setting up apparmor (4.1.0~beta5-0ubuntu5) ... 156s Installing new version of config file /etc/apparmor.d/fusermount3 ... 157s Reloading AppArmor profiles 159s Setting up vim-common (2:9.1.0967-1ubuntu2) ... 159s Setting up ucf (3.0050) ... 159s Setting up lsof (4.99.4+dfsg-2) ... 159s Setting up perl-modules-5.40 (5.40.1-2) ... 159s Setting up libllvm18:arm64 (1:18.1.8-16build1) ... 159s Setting up cloud-init (25.1-0ubuntu1) ... 159s Setting up vim-tiny (2:9.1.0967-1ubuntu2) ... 159s Setting up libperl5.40:arm64 (5.40.1-2) ... 159s Setting up perl (5.40.1-2) ... 159s Setting up libclang-cpp18 (1:18.1.8-16build1) ... 159s Processing triggers for rsyslog (8.2412.0-2ubuntu1) ... 159s Processing triggers for systemd (257.2-3ubuntu1) ... 159s Processing triggers for man-db (2.13.0-1) ... 161s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) ... 161s Processing triggers for install-info (7.1.1-1) ... 162s Processing triggers for libc-bin (2.40-4ubuntu1) ... 162s Processing triggers for initramfs-tools (0.145ubuntu2) ... 162s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 162s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 182s System running in EFI mode, skipping. 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s Solving dependencies... 184s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 184s autopkgtest [04:46:34]: upgrading testbed (apt dist-upgrade and autopurge) 184s Reading package lists... 184s Building dependency tree... 184s Reading state information... 185s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 185s Starting 2 pkgProblemResolver with broken count: 0 185s Done 186s Entering ResolveByKeep 186s 186s Calculating upgrade... 187s The following packages will be upgraded: 187s gir1.2-glib-2.0 libglib2.0-0t64 libglib2.0-data 187s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 187s Need to get 1808 kB of archives. 187s After this operation, 2048 B of additional disk space will be used. 187s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 gir1.2-glib-2.0 arm64 2.83.4-1 [185 kB] 187s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libglib2.0-0t64 arm64 2.83.4-1 [1570 kB] 188s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libglib2.0-data all 2.83.4-1 [52.9 kB] 188s Fetched 1808 kB in 1s (2488 kB/s) 188s (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 ... 116669 files and directories currently installed.) 188s Preparing to unpack .../gir1.2-glib-2.0_2.83.4-1_arm64.deb ... 188s Unpacking gir1.2-glib-2.0:arm64 (2.83.4-1) over (2.83.3-2) ... 188s Preparing to unpack .../libglib2.0-0t64_2.83.4-1_arm64.deb ... 188s Unpacking libglib2.0-0t64:arm64 (2.83.4-1) over (2.83.3-2) ... 188s Preparing to unpack .../libglib2.0-data_2.83.4-1_all.deb ... 188s Unpacking libglib2.0-data (2.83.4-1) over (2.83.3-2) ... 189s Setting up libglib2.0-0t64:arm64 (2.83.4-1) ... 189s No schema files found: doing nothing. 189s Setting up libglib2.0-data (2.83.4-1) ... 189s Setting up gir1.2-glib-2.0:arm64 (2.83.4-1) ... 189s Processing triggers for libc-bin (2.40-4ubuntu1) ... 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 190s Starting 2 pkgProblemResolver with broken count: 0 190s Done 190s Solving dependencies... 191s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s autopkgtest [04:46:41]: rebooting testbed after setup commands that affected boot 226s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 239s autopkgtest [04:47:29]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 244s autopkgtest [04:47:34]: @@@@@@@@@@@@@@@@@@@@ apt-source exonerate 247s Get:1 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (dsc) [2187 B] 247s Get:2 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (tar) [521 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (diff) [9364 B] 247s gpgv: Signature made Mon Apr 1 05:47:10 2024 UTC 247s gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 247s gpgv: Can't check signature: No public key 247s dpkg-source: warning: cannot verify inline signature for ./exonerate_2.4.0-5build2.dsc: no acceptable signature found 247s autopkgtest [04:47:37]: testing package exonerate version 2.4.0-5build2 247s autopkgtest [04:47:37]: build not needed 248s autopkgtest [04:47:38]: test run-unit-test: preparing testbed 248s Reading package lists... 249s Building dependency tree... 249s Reading state information... 249s Starting pkgProblemResolver with broken count: 0 249s Starting 2 pkgProblemResolver with broken count: 0 249s Done 250s The following NEW packages will be installed: 250s exonerate 250s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 250s Need to get 2003 kB of archives. 250s After this operation, 8249 kB of additional disk space will be used. 250s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 exonerate arm64 2.4.0-5build2 [2003 kB] 251s Fetched 2003 kB in 1s (3175 kB/s) 252s Selecting previously unselected package exonerate. 252s (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 ... 116669 files and directories currently installed.) 252s Preparing to unpack .../exonerate_2.4.0-5build2_arm64.deb ... 252s Unpacking exonerate (2.4.0-5build2) ... 252s Setting up exonerate (2.4.0-5build2) ... 252s Processing triggers for man-db (2.13.0-1) ... 254s autopkgtest [04:47:44]: test run-unit-test: [----------------------- 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaindex.fastafetch.test.sh 254s Made index fastafetch.test.idx 254s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN 254s expect 0 254s >CALM_HUMAN 254s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 254s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 254s EFVQMMTAK 254s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN 254s expect 0 254s >P53_HUMAN 254s MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA 254s PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT 254s CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN 254s TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR 254s DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL 254s KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD 254s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx A_MISSING_FROM_START 254s expect 1 254s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx M_MISSING_FROM_MIDDLE 254s expect 1 254s ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START] (missing -F ?) 254s exiting ... 254s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx z_MISSING_FROM_END 254s expect 1 254s ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE] (missing -F ?) 254s exiting ... 254s ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing -F ?) 254s exiting ... 254s fastaindex fastafetch test OK 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastasort.test.sh 254s Sorted CALM_HUMAN 149 254s Sorted P53_HUMAN 393 254s Sorted TUBE_DROME 462 254s Sorted AF01595 1132 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastanrdb.test.sh 254s Made input file for fastanrdb 254s Successfully ran fastanrdb on: fastanrdb.input.test.fasta 254s Expected number of seqs in output: 4 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastalength.test.sh 254s 149 CALM_HUMAN 254s Calmodulin length OK 254s Calmodulin identifier OK 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaclean.test.sh 254s >CALM_HUMAN:filter(clean) 254s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL 254s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE 254s EFVQMMTAK 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastadiff.test.sh 254s fastadiff: id mismatch: CALM_HUMAN P53_HUMAN 254s Different seqs recognised as different 254s Identity test OK 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaremove.test.sh 254s Have calmodulin in input 254s Calmodulin successfully removed 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastasubseq.test.sh 254s Generated correct subseq 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastavalidcds.test.sh 254s Validiated CDS sequences OK 254s >valid_seq 254s ATGAAACCCGGGTTTTAA 254s Validated correctly a single seq from input 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastarefomat.test.sh 254s Reformatted OK 254s >test 254s ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT 254s Reformatted length consistent 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaoverlap.test.sh 254s ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN] 254s exiting ... 254s 254s ** (process:1386): WARNING **: 04:47:44.893: odd_length length (7) not divisible by 3 254s 254s ** (process:1386): WARNING **: 04:47:44.893: too_short length (4) not divisible by 3 254s 254s ** (process:1386): WARNING **: 04:47:44.893: no_start missing start codon (has:AAA) 254s 254s ** (process:1386): WARNING **: 04:47:44.893: no_end missing stop codon (has:TTT) 254s 254s ** (process:1386): WARNING **: 04:47:44.894: in_frame_stop contains in-frame stop codon (pos:9, codon:TAG) 254s 254s ** (process:1386): WARNING **: 04:47:44.894: non_acgt_base contains non-ACGT base: [pos: 5 base: N] 254s /usr/bin/fastaoverlap working OK 254s Generated 15 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastarevcomp.test.sh 254s Reverse complement created : ./data/cdna/calm.human.dna.fasta 254s Reverse complement created : fastarevcomp.rc.test.fasta 254s RC length is the same 254s RC length is the same 254s 2nd reverse complement same as original 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastacomposition.test.sh 254s Calmodulin cDNA composition correct 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastatranslate.test.sh 254s Extraced CDS for translation 254s Tranlated sequence 254s Tranlsated sequence correct 254s 254s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaclip.test.sh 255s Clipped OK 255s >test:subseq(0,4) 255s ACGT 255s Clipped input correctly 255s 255s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastaexpode.test.sh 255s Made input file for fastaexplode 255s Make output directory for fastaexplode 255s Successfully ran fastaexplode on: fastaexplode.test.fasta 255s Expected number of seqs in output: 4 255s 255s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastasplit.test.sh 255s Split fastasplit.test.fasta OK 255s Split into two files as expected 255s Input len 2136 255s Output len 2136 255s Input and output lengths match 255s 255s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/util/fastasoftmask.fastahardmask.test.sh 255s Softmasked OK 255s >test 255s ACGNAACCGGNNAAACCCGGGNNNAAAACCCCGGGGNNNN 255s Hardmasked OK 255s Hardmasked file is same as original masked file 255s 255s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/exonerate/exonerate.simple.test.sh 255s Exonerate simple test OK 255s Score as expected: 10875 255s 255s /tmp/autopkgtest.nVvlpj/autopkgtest_tmp/ipcress/ipcress.simple.test.sh 255s ** Message: 04:47:45.032: Loaded [1] experiments 255s Ipcress run successfully 255s Found 1 product, as expected 255s PASS 255s autopkgtest [04:47:45]: test run-unit-test: -----------------------] 255s autopkgtest [04:47:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 255s run-unit-test PASS 256s autopkgtest [04:47:46]: @@@@@@@@@@@@@@@@@@@@ summary 256s run-unit-test PASS 273s nova [W] Using flock in prodstack6-arm64 273s flock: timeout while waiting to get lock 273s Creating nova instance adt-plucky-arm64-exonerate-20250222-044330-juju-7f2275-prod-proposed-migration-environment-2-80f5eb4c-9582-414b-938b-60214b47891e from image adt/ubuntu-plucky-arm64-server-20250221.img (UUID 7cc4cd7e-6f5b-4658-9b17-e38e7fa05fb0)... 273s nova [W] Timed out waiting for ff8514e4-2ce8-41c1-8846-d1e334dc03fc to get deleted.