0s autopkgtest [17:31:19]: starting date and time: 2025-03-15 17:31:19+0000 0s autopkgtest [17:31:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:31:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.funuz_ee/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade wise --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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-35.secgroup --name adt-plucky-arm64-wise-20250315-173119-juju-7f2275-prod-proposed-migration-environment-15-968010d7-b625-4e9b-8906-785dfae2c07f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 133s autopkgtest [17:33:32]: testbed dpkg architecture: arm64 133s autopkgtest [17:33:32]: testbed apt version: 2.9.33 133s autopkgtest [17:33:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 133s autopkgtest [17:33:32]: testbed release detected to be: None 134s autopkgtest [17:33:33]: updating testbed package index (apt update) 135s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 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/universe Sources [379 kB] 136s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 136s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 136s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 136s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 136s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 136s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 136s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 136s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 136s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 136s Fetched 1078 kB in 1s (989 kB/s) 137s Reading package lists... 138s + lsb_release --codename --short 138s + RELEASE=plucky 138s + cat 138s + [ plucky != trusty ] 138s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 139s Calculating upgrade... 139s Calculating upgrade... 140s The following packages will be upgraded: 140s pinentry-curses python3-jinja2 strace 140s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s Need to get 647 kB of archives. 140s After this operation, 11.3 kB of additional disk space will be used. 140s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 140s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 140s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 141s Fetched 647 kB in 1s (899 kB/s) 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 ... 117701 files and directories currently installed.) 141s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 141s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 141s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 141s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 142s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 142s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 142s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 142s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 142s Setting up strace (6.13+ds-1ubuntu1) ... 142s Processing triggers for man-db (2.13.0-1) ... 143s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 143s + /usr/lib/apt/apt-helper analyze-pattern ?true 143s + uname -r 143s + sed s/\./\\./g 143s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 143s + apt list ?obsolete 143s + tail -n+2 143s + cut -d/ -f1 143s + grep -v ^linux-.*6\.14\.0-10-generic.* 143s + obsolete_pkgs=linux-headers-6.11.0-8-generic 143s linux-headers-6.11.0-8 143s linux-image-6.11.0-8-generic 143s linux-modules-6.11.0-8-generic 143s linux-tools-6.11.0-8-generic 143s linux-tools-6.11.0-8 143s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Solving dependencies... 145s The following packages will be REMOVED: 145s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 145s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 145s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 145s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 145s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 145s After this operation, 267 MB disk space will be freed. 145s (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 ... 117701 files and directories currently installed.) 145s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 145s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 145s Removing libpython3.12t64:arm64 (3.12.9-1) ... 145s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 145s Removing libnsl2:arm64 (1.3.0-3build3) ... 145s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 146s Removing libunwind8:arm64 (1.6.2-3.1) ... 146s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 146s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 148s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 148s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 148s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 148s /etc/kernel/postrm.d/initramfs-tools: 148s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 148s /etc/kernel/postrm.d/zz-flash-kernel: 148s flash-kernel: Kernel 6.11.0-8-generic has been removed. 149s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 149s /etc/kernel/postrm.d/zz-update-grub: 149s Sourcing file `/etc/default/grub' 149s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 149s Generating grub configuration file ... 149s Found linux image: /boot/vmlinuz-6.14.0-10-generic 149s Found initrd image: /boot/initrd.img-6.14.0-10-generic 150s Warning: os-prober will not be executed to detect other bootable partitions. 150s Systems on them will not be added to the GRUB boot configuration. 150s Check GRUB_DISABLE_OS_PROBER documentation entry. 150s Adding boot menu entry for UEFI Firmware Settings ... 150s done 150s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 150s Processing triggers for libc-bin (2.41-1ubuntu1) ... 150s (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 ... 81650 files and directories currently installed.) 150s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 151s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 151s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 151s + grep -q trusty /etc/lsb-release 151s + [ ! -d /usr/share/doc/unattended-upgrades ] 151s + [ ! -d /usr/share/doc/lxd ] 151s + [ ! -d /usr/share/doc/lxd-client ] 151s + [ ! -d /usr/share/doc/snapd ] 151s + type iptables 151s + cat 151s + chmod 755 /etc/rc.local 151s + . /etc/rc.local 151s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 151s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 151s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 151s + uname -m 151s + [ aarch64 = ppc64le ] 151s + [ -d /run/systemd/system ] 151s + systemd-detect-virt --quiet --vm 151s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 151s + cat 151s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 151s + echo COMPRESS=lz4 151s autopkgtest [17:33:50]: upgrading testbed (apt dist-upgrade and autopurge) 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 152s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 153s Starting 2 pkgProblemResolver with broken count: 0 153s Done 154s Entering ResolveByKeep 154s 154s Calculating upgrade... 155s The following packages will be upgraded: 155s libc-bin libc-dev-bin libc6 libc6-dev locales 155s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Need to get 9530 kB of archives. 155s After this operation, 0 B of additional disk space will be used. 155s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 156s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 156s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 156s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 156s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 157s Preconfiguring packages ... 158s Fetched 9530 kB in 2s (5798 kB/s) 158s (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 ... 81647 files and directories currently installed.) 158s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 158s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 158s Setting up libc6:arm64 (2.41-1ubuntu2) ... 159s (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 ... 81647 files and directories currently installed.) 159s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 159s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up libc-bin (2.41-1ubuntu2) ... 159s (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 ... 81647 files and directories currently installed.) 159s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 159s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up locales (2.41-1ubuntu2) ... 160s Generating locales (this might take a while)... 163s en_US.UTF-8... done 163s Generation complete. 163s Setting up libc-dev-bin (2.41-1ubuntu2) ... 163s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 163s Processing triggers for man-db (2.13.0-1) ... 164s Processing triggers for systemd (257.3-1ubuntu3) ... 165s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Starting pkgProblemResolver with broken count: 0 167s Starting 2 pkgProblemResolver with broken count: 0 167s Done 167s Solving dependencies... 168s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 169s autopkgtest [17:34:08]: rebooting testbed after setup commands that affected boot 191s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 199s autopkgtest [17:34:38]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 202s autopkgtest [17:34:41]: @@@@@@@@@@@@@@@@@@@@ apt-source wise 207s Get:1 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (dsc) [2305 B] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe wise 2.4.1-25 (tar) [3410 kB] 207s 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 [17:34:46]: testing package wise version 2.4.1-25 208s autopkgtest [17:34:47]: build not needed 212s autopkgtest [17:34:51]: test run-unit-test: preparing testbed 213s 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 (1175 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 ... 81647 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) ... 216s Setting up wise-data (2.4.1-25) ... 216s Setting up wise (2.4.1-25) ... 216s Processing triggers for man-db (2.13.0-1) ... 218s autopkgtest [17:34:57]: 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 219s autopkgtest [17:34:58]: test run-unit-test: -----------------------] 219s autopkgtest [17:34:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 219s run-unit-test PASS 220s autopkgtest [17:34:59]: @@@@@@@@@@@@@@@@@@@@ summary 220s run-unit-test PASS 229s nova [W] Using flock in prodstack6-arm64 229s flock: timeout while waiting to get lock 229s Creating nova instance adt-plucky-arm64-wise-20250315-173119-juju-7f2275-prod-proposed-migration-environment-15-968010d7-b625-4e9b-8906-785dfae2c07f from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 229s nova [W] Timed out waiting for 64860bf0-2c17-424c-ba90-1a4b04f4ecc8 to get deleted.