0s autopkgtest [05:19:34]: starting date and time: 2025-02-22 05:19:34+0000 0s autopkgtest [05:19:34]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [05:19:34]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cyepgswc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glib2.0 --apt-upgrade wise --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-arm64-37.secgroup --name adt-plucky-arm64-wise-20250222-051934-juju-7f2275-prod-proposed-migration-environment-2-bf61940b-40ca-43be-84c2-a856f96ad4f1 --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/ 124s autopkgtest [05:21:38]: testbed dpkg architecture: arm64 124s autopkgtest [05:21:38]: testbed apt version: 2.9.30ubuntu1 124s autopkgtest [05:21:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 125s autopkgtest [05:21:39]: testbed release detected to be: None 126s autopkgtest [05:21:40]: updating testbed package index (apt update) 126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 126s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 126s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 126s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [508 kB] 126s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 126s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [80.1 kB] 126s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 126s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [122 kB] 126s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [7960 B] 126s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [451 kB] 127s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [9060 B] 127s Fetched 1305 kB in 1s (1490 kB/s) 128s Reading package lists... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 130s Calculating upgrade... 130s The following packages will be upgraded: 130s apparmor base-files cloud-init cloud-init-base gcc-14-base libapparmor1 130s libclang-cpp18 libclang1-19 libgnutls30t64 libllvm18 libllvm19 liblsof0 130s libnss3 libperl5.40 lsof motd-news-config perl perl-base perl-modules-5.40 130s ucf vim-common vim-tiny xxd 130s 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Need to get 90.2 MB of archives. 130s After this operation, 11.3 kB of additional disk space will be used. 130s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 motd-news-config all 13.6ubuntu1 [5168 B] 130s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 base-files arm64 13.6ubuntu1 [75.6 kB] 130s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 perl-modules-5.40 all 5.40.1-2 [3217 kB] 131s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libperl5.40 arm64 5.40.1-2 [4779 kB] 131s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 perl arm64 5.40.1-2 [262 kB] 131s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 perl-base arm64 5.40.1-2 [1788 kB] 131s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-base arm64 14.2.0-17ubuntu3 [53.6 kB] 131s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libapparmor1 arm64 4.1.0~beta5-0ubuntu5 [53.7 kB] 131s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgnutls30t64 arm64 3.8.9-2ubuntu2 [962 kB] 131s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 ucf all 3.0050 [43.5 kB] 131s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-tiny arm64 2:9.1.0967-1ubuntu2 [807 kB] 131s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-common all 2:9.1.0967-1ubuntu2 [396 kB] 131s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 xxd arm64 2:9.1.0967-1ubuntu2 [67.8 kB] 131s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 apparmor arm64 4.1.0~beta5-0ubuntu5 [660 kB] 131s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 lsof arm64 4.99.4+dfsg-2 [236 kB] 131s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsof0 arm64 4.99.4+dfsg-2 [54.0 kB] 131s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 cloud-init-base all 25.1-0ubuntu1 [616 kB] 131s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 libclang-cpp18 arm64 1:18.1.8-16build1 [13.1 MB] 132s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 libllvm18 arm64 1:18.1.8-16build1 [26.3 MB] 132s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 libllvm19 arm64 1:19.1.7-1ubuntu2 [27.3 MB] 133s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libclang1-19 arm64 1:19.1.7-1ubuntu2 [7986 kB] 133s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libnss3 arm64 2:3.108-1ubuntu1 [1446 kB] 134s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 cloud-init all 25.1-0ubuntu1 [2088 B] 134s Preconfiguring packages ... 134s Fetched 90.2 MB in 3s (25.9 MB/s) 134s (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.) 134s Preparing to unpack .../motd-news-config_13.6ubuntu1_all.deb ... 134s Unpacking motd-news-config (13.6ubuntu1) over (13.5ubuntu3) ... 134s Preparing to unpack .../base-files_13.6ubuntu1_arm64.deb ... 135s Unpacking base-files (13.6ubuntu1) over (13.5ubuntu3) ... 135s Setting up base-files (13.6ubuntu1) ... 135s Updating /root/.profile to current default. 135s motd-news.service is a disabled or a static unit not running, not starting it. 136s (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.) 136s Preparing to unpack .../perl_5.40.1-2_arm64.deb ... 136s Unpacking perl (5.40.1-2) over (5.40.0-8) ... 136s Preparing to unpack .../perl-modules-5.40_5.40.1-2_all.deb ... 136s Unpacking perl-modules-5.40 (5.40.1-2) over (5.40.0-8) ... 136s Preparing to unpack .../libperl5.40_5.40.1-2_arm64.deb ... 136s Unpacking libperl5.40:arm64 (5.40.1-2) over (5.40.0-8) ... 136s Preparing to unpack .../perl-base_5.40.1-2_arm64.deb ... 136s Unpacking perl-base (5.40.1-2) over (5.40.0-8) ... 137s Setting up perl-base (5.40.1-2) ... 137s (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.) 137s Preparing to unpack .../00-gcc-14-base_14.2.0-17ubuntu3_arm64.deb ... 137s Unpacking gcc-14-base:arm64 (14.2.0-17ubuntu3) over (14.2.0-17ubuntu1) ... 137s Preparing to unpack .../01-libapparmor1_4.1.0~beta5-0ubuntu5_arm64.deb ... 137s Unpacking libapparmor1:arm64 (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ... 137s Preparing to unpack .../02-libgnutls30t64_3.8.9-2ubuntu2_arm64.deb ... 137s Unpacking libgnutls30t64:arm64 (3.8.9-2ubuntu2) over (3.8.9-2ubuntu1) ... 137s Preparing to unpack .../03-ucf_3.0050_all.deb ... 137s Unpacking ucf (3.0050) over (3.0049) ... 137s Preparing to unpack .../04-vim-tiny_2%3a9.1.0967-1ubuntu2_arm64.deb ... 137s Unpacking vim-tiny (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 137s Preparing to unpack .../05-vim-common_2%3a9.1.0967-1ubuntu2_all.deb ... 137s Unpacking vim-common (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 137s Preparing to unpack .../06-xxd_2%3a9.1.0967-1ubuntu2_arm64.deb ... 137s Unpacking xxd (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ... 137s Preparing to unpack .../07-apparmor_4.1.0~beta5-0ubuntu5_arm64.deb ... 138s Unpacking apparmor (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ... 138s Preparing to unpack .../08-lsof_4.99.4+dfsg-2_arm64.deb ... 138s Unpacking lsof (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ... 138s Preparing to unpack .../09-liblsof0_4.99.4+dfsg-2_arm64.deb ... 138s Unpacking liblsof0 (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ... 139s Preparing to unpack .../10-cloud-init-base_25.1-0ubuntu1_all.deb ... 139s /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. 139s for fn in glob1(directory, "%s.*" % fname): 139s Unpacking cloud-init-base (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 139s Preparing to unpack .../11-libclang-cpp18_1%3a18.1.8-16build1_arm64.deb ... 139s Unpacking libclang-cpp18 (1:18.1.8-16build1) over (1:18.1.8-15) ... 139s Preparing to unpack .../12-libllvm18_1%3a18.1.8-16build1_arm64.deb ... 139s Unpacking libllvm18:arm64 (1:18.1.8-16build1) over (1:18.1.8-15) ... 140s Preparing to unpack .../13-libllvm19_1%3a19.1.7-1ubuntu2_arm64.deb ... 140s Unpacking libllvm19:arm64 (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ... 141s Preparing to unpack .../14-libclang1-19_1%3a19.1.7-1ubuntu2_arm64.deb ... 141s Unpacking libclang1-19 (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ... 141s Preparing to unpack .../15-libnss3_2%3a3.108-1ubuntu1_arm64.deb ... 141s Unpacking libnss3:arm64 (2:3.108-1ubuntu1) over (2:3.107-1ubuntu1) ... 142s Preparing to unpack .../16-cloud-init_25.1-0ubuntu1_all.deb ... 142s Unpacking cloud-init (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ... 142s Setting up libgnutls30t64:arm64 (3.8.9-2ubuntu2) ... 142s Setting up motd-news-config (13.6ubuntu1) ... 142s Setting up libllvm19:arm64 (1:19.1.7-1ubuntu2) ... 142s Setting up libapparmor1:arm64 (4.1.0~beta5-0ubuntu5) ... 142s Setting up libclang1-19 (1:19.1.7-1ubuntu2) ... 142s Setting up gcc-14-base:arm64 (14.2.0-17ubuntu3) ... 142s Setting up liblsof0 (4.99.4+dfsg-2) ... 142s Setting up libnss3:arm64 (2:3.108-1ubuntu1) ... 142s Setting up cloud-init-base (25.1-0ubuntu1) ... 143s Setting up xxd (2:9.1.0967-1ubuntu2) ... 143s Setting up apparmor (4.1.0~beta5-0ubuntu5) ... 143s Installing new version of config file /etc/apparmor.d/fusermount3 ... 145s Reloading AppArmor profiles 146s Setting up vim-common (2:9.1.0967-1ubuntu2) ... 146s Setting up ucf (3.0050) ... 146s Setting up lsof (4.99.4+dfsg-2) ... 146s Setting up perl-modules-5.40 (5.40.1-2) ... 146s Setting up libllvm18:arm64 (1:18.1.8-16build1) ... 146s Setting up cloud-init (25.1-0ubuntu1) ... 146s Setting up vim-tiny (2:9.1.0967-1ubuntu2) ... 146s Setting up libperl5.40:arm64 (5.40.1-2) ... 146s Setting up perl (5.40.1-2) ... 146s Setting up libclang-cpp18 (1:18.1.8-16build1) ... 146s Processing triggers for rsyslog (8.2412.0-2ubuntu1) ... 146s Processing triggers for systemd (257.2-3ubuntu1) ... 147s Processing triggers for man-db (2.13.0-1) ... 148s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) ... 148s Processing triggers for install-info (7.1.1-1) ... 148s Processing triggers for libc-bin (2.40-4ubuntu1) ... 148s Processing triggers for initramfs-tools (0.145ubuntu2) ... 149s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic 149s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 168s System running in EFI mode, skipping. 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 168s Solving dependencies... 169s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 169s autopkgtest [05:22:23]: upgrading testbed (apt dist-upgrade and autopurge) 169s Reading package lists... 169s Building dependency tree... 169s Reading state information... 170s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 170s Starting 2 pkgProblemResolver with broken count: 0 170s Done 171s Entering ResolveByKeep 171s 171s Calculating upgrade... 172s The following packages will be upgraded: 172s gir1.2-glib-2.0 libglib2.0-0t64 libglib2.0-data 172s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 1808 kB of archives. 172s After this operation, 2048 B of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 gir1.2-glib-2.0 arm64 2.83.4-1 [185 kB] 172s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libglib2.0-0t64 arm64 2.83.4-1 [1570 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libglib2.0-data all 2.83.4-1 [52.9 kB] 173s Fetched 1808 kB in 1s (2860 kB/s) 173s (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.) 173s Preparing to unpack .../gir1.2-glib-2.0_2.83.4-1_arm64.deb ... 173s Unpacking gir1.2-glib-2.0:arm64 (2.83.4-1) over (2.83.3-2) ... 173s Preparing to unpack .../libglib2.0-0t64_2.83.4-1_arm64.deb ... 173s Unpacking libglib2.0-0t64:arm64 (2.83.4-1) over (2.83.3-2) ... 173s Preparing to unpack .../libglib2.0-data_2.83.4-1_all.deb ... 173s Unpacking libglib2.0-data (2.83.4-1) over (2.83.3-2) ... 173s Setting up libglib2.0-0t64:arm64 (2.83.4-1) ... 173s No schema files found: doing nothing. 173s Setting up libglib2.0-data (2.83.4-1) ... 173s Setting up gir1.2-glib-2.0:arm64 (2.83.4-1) ... 173s Processing triggers for libc-bin (2.40-4ubuntu1) ... 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 175s Solving dependencies... 176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 176s autopkgtest [05:22:30]: rebooting testbed after setup commands that affected boot 200s autopkgtest [05:22:54]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 15:49:33 UTC 2025 203s autopkgtest [05:22:57]: @@@@@@@@@@@@@@@@@@@@ apt-source wise 206s Get:1 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (dsc) [2305 B] 206s Get:2 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (tar) [3410 kB] 206s Get:3 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (diff) [39.9 kB] 207s gpgv: Signature made Thu Aug 15 10:43:37 2024 UTC 207s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 207s gpgv: issuer "emollier@debian.org" 207s gpgv: Can't check signature: No public key 207s dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-25.dsc: no acceptable signature found 207s autopkgtest [05:23:01]: testing package wise version 2.4.1-25 208s autopkgtest [05:23:02]: build not needed 212s autopkgtest [05:23:06]: test run-unit-test: preparing testbed 212s Reading package lists... 213s Building dependency tree... 213s Reading state information... 213s Starting pkgProblemResolver with broken count: 0 213s Starting 2 pkgProblemResolver with broken count: 0 213s Done 214s The following NEW packages will be installed: 214s wise wise-data 214s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 214s Need to get 885 kB of archives. 214s After this operation, 3934 kB of additional disk space will be used. 214s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise-data all 2.4.1-25 [83.0 kB] 214s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 wise arm64 2.4.1-25 [802 kB] 215s Fetched 885 kB in 1s (1585 kB/s) 215s Selecting previously unselected package wise-data. 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 ... 116669 files and directories currently installed.) 215s Preparing to unpack .../wise-data_2.4.1-25_all.deb ... 215s Unpacking wise-data (2.4.1-25) ... 215s Selecting previously unselected package wise. 215s Preparing to unpack .../wise_2.4.1-25_arm64.deb ... 215s Unpacking wise (2.4.1-25) ... 215s Setting up wise-data (2.4.1-25) ... 215s Setting up wise (2.4.1-25) ... 215s Processing triggers for man-db (2.13.0-1) ... 218s autopkgtest [05:23:12]: test run-unit-test: [----------------------- 218s >>> Doing promoterwise promoterwise standard test 218s >>> Calling [promoterwise -silent pw.human pw.mouse > TEMP-PW] 218s >>> promoterwise ... Failed 218s >>> Doing basic-cdna cdna test case (protein v cdna), all outputs 218s >>> Calling [estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP] 218s >>> basic-cdna ... Failed 218s >>> Doing basic-genomic genomic test case (protein v genomic), all outputs 218s >>> Calling [genewise short.pep short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s Warning Error 218s Strangely truncated line in fasta file 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:0 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:1 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:2 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:3 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:4 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:5 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:6 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:7 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:8 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:9 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:10 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:11 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:12 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:13 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:14 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:15 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:16 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:17 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:18 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:19 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:20 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:21 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:22 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:23 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:24 (they must 218s be bound between 0:26, returning 0 here 218s Warning Error 218s Attempting to access CompMat with aminoacid numbers 190:25 (they must 218s be bound between 0:26, returning 0 here 218s >>> basic-genomic ... Failed 218s >>> Doing hmm-binary-cdna cdna test case (protein v cdna), all outputs 218s >>> Calling [estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s FATAL: No support for non-protein, non-nucleic acid alphabets. 218s >>> Bad exit status - 256 (system - ) 218s >>> hmm-binary-cdna ... Failed 218s >>> Doing hmm-wrong-dna HMMs vs DNA sequence when there is no match 218s >>> Calling [genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s Information 218s In making HSHNCPA1 a genomic sequence, converted 3 bases (0.7%) to 218s N's from non ATGCN 218s GeneWise6 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 218s >>> hmm-wrong-dna ... Passed 218s >>> Doing hmm-wrong-dna-est HMMs vs DNA sequence when there is no match 218s >>> Calling [estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s Information 218s In making HSHNCPA1 a cdna sequence, converted 3 bases (0.7%) to N's 218s from non ATGCN 218s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 218s EstWise3 Matrix calculation: [ 0] Cells 0%[ 1000] Cells 3%[ 2000] Cells 6%[ 3000] Cells 9%[ 4000] Cells 12%[ 5000] Cells 15%[ 6000] Cells 18%[ 7000] Cells 21%[ 8000] Cells 24%[ 9000] Cells 27%[ 10000] Cells 30%[ 11000] Cells 33%[ 12000] Cells 36%[ 13000] Cells 39%[ 14000] Cells 42%[ 15000] Cells 45%[ 16000] Cells 48%[ 17000] Cells 51%[ 18000] Cells 54%[ 19000] Cells 57%[ 20000] Cells 60%[ 21000] Cells 63%[ 22000] Cells 66%[ 23000] Cells 69%[ 24000] Cells 73%[ 25000] Cells 76%[ 26000] Cells 79%[ 27000] Cells 82%[ 28000] Cells 85%[ 29000] Cells 88%[ 30000] Cells 91%[ 31000] Cells 94%[ 32000] Cells 97% 218s >>> hmm-wrong-dna-est ... Failed 218s >>> Doing hmm-ascii-genomic cdna test case (protein v cdna), all outputs 218s >>> Calling [genewise -init local HMM.ascii -hmmer short.dna -pretty -para -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s FATAL: No support for non-protein, non-nucleic acid alphabets. 218s >>> Bad exit status - 256 (system - ) 218s >>> hmm-ascii-genomic ... Failed 218s >>> Doing genewise-db genewisedb hmm vs DNA sequences. Could take a while 218s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP] 218s Warning Error 218s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 218s Strangely truncated line in fasta file 218s Warning Error 218s Strangely truncated line in fasta file 218s >>> genewise-db ... Passed 218s >>> Doing genewise-db-lite genewisedb hmm vs DNA sequences, using GWLITE. Could take a while 218s >>> Calling [genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP] 218s Warning Error 218s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 218s Strangely truncated line in fasta file 218s Warning Error 218s Strangely truncated line in fasta file 218s >>> genewise-db-lite ... Passed 218s >>> Doing estwise-db estwisedb hmm vs DNA sequences. Could take a while 218s >>> Calling [estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP] 218s Warning Error 218s DB searching: just finished [Query Pos: 0] [Target Pos: 5] 218s Strangely truncated line in fasta file 218s Warning Error 218s Strangely truncated line in fasta file 218s >>> estwise-db ... Passed 218s >>> Doing pswdb Protein smith waterman db search 218s >>> Calling [pswdb road.pep pep.fa -quiet > TEMP ] 218s Warning Error 218s Strangely truncated line in fasta file 218s Warning Error 218s Before any actual search in db searching 218s Out of memory, trying to realloc 1499031348 bytes 218s 218s Fatal Error 218s Before any actual search in db searching 218s Cannot realloc histogram... going to die... sorry! 218s >>> Bad exit status - 512 (system - ) 218s >>> pswdb ... Failed 218s >>> Doing genewisedb-pfam-mode genewisedb designed for Pfam searching 218s >>> Calling [genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP] 218s Warning Error 218s Strangely truncated line in fasta file 218s >>> genewisedb-pfam-mode ... Failed 218s Tests failed 218s PLEASE: email ewan birney (birney@sanger.ac.uk) with the test.results file 218s 218s autopkgtest [05:23:12]: test run-unit-test: -----------------------] 219s autopkgtest [05:23:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 219s run-unit-test PASS 219s autopkgtest [05:23:13]: @@@@@@@@@@@@@@@@@@@@ summary 219s run-unit-test PASS 226s nova [W] Using flock in prodstack6-arm64 226s flock: timeout while waiting to get lock 226s Creating nova instance adt-plucky-arm64-wise-20250222-051934-juju-7f2275-prod-proposed-migration-environment-2-bf61940b-40ca-43be-84c2-a856f96ad4f1 from image adt/ubuntu-plucky-arm64-server-20250221.img (UUID 7cc4cd7e-6f5b-4658-9b17-e38e7fa05fb0)... 226s nova [W] Timed out waiting for aff4f2b5-3ff2-49d7-8762-d674c22fc54b to get deleted.