0s autopkgtest [14:31:10]: starting date and time: 2025-03-15 14:31:10+0000 0s autopkgtest [14:31:10]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:31:10]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jmsyjvxi/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-17.secgroup --name adt-plucky-arm64-prodigal-20250315-143110-juju-7f2275-prod-proposed-migration-environment-2-bf00e5b7-593e-41ce-bf7f-1673652262c3 --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/ 141s autopkgtest [14:33:31]: testbed dpkg architecture: arm64 141s autopkgtest [14:33:31]: testbed apt version: 2.9.33 142s autopkgtest [14:33:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 142s autopkgtest [14:33:32]: testbed release detected to be: None 143s autopkgtest [14:33:33]: updating testbed package index (apt update) 143s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 144s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 144s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 144s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 144s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 144s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 144s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 144s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 144s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 144s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 144s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 145s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 145s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 145s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 145s Fetched 1094 kB in 2s (645 kB/s) 146s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 148s Calculating upgrade... 148s Calculating upgrade... 148s The following packages will be upgraded: 148s python3-jinja2 strace 149s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 608 kB of archives. 149s After this operation, 11.3 kB of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 149s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 150s Fetched 608 kB in 1s (692 kB/s) 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 ... 117701 files and directories currently installed.) 150s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 150s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 150s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 150s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 150s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 151s Setting up strace (6.13+ds-1ubuntu1) ... 151s Processing triggers for man-db (2.13.0-1) ... 151s Reading package lists... 152s Building dependency tree... 152s Reading state information... 152s Solving dependencies... 152s The following packages will be REMOVED: 152s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 152s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 152s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 152s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 153s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 153s After this operation, 267 MB disk space will be freed. 153s (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.) 153s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 153s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 153s Removing libpython3.12t64:arm64 (3.12.9-1) ... 153s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 153s Removing libnsl2:arm64 (1.3.0-3build3) ... 153s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 153s Removing libunwind8:arm64 (1.6.2-3.1) ... 153s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 154s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 155s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 156s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 156s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 156s /etc/kernel/postrm.d/initramfs-tools: 156s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 156s /etc/kernel/postrm.d/zz-flash-kernel: 156s flash-kernel: Kernel 6.11.0-8-generic has been removed. 156s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 156s /etc/kernel/postrm.d/zz-update-grub: 156s Sourcing file `/etc/default/grub' 156s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 156s Generating grub configuration file ... 156s Found linux image: /boot/vmlinuz-6.14.0-10-generic 156s Found initrd image: /boot/initrd.img-6.14.0-10-generic 157s Warning: os-prober will not be executed to detect other bootable partitions. 157s Systems on them will not be added to the GRUB boot configuration. 157s Check GRUB_DISABLE_OS_PROBER documentation entry. 157s Adding boot menu entry for UEFI Firmware Settings ... 157s done 157s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 157s Processing triggers for libc-bin (2.41-1ubuntu1) ... 157s (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.) 157s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 157s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 157s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 157s autopkgtest [14:33:47]: upgrading testbed (apt dist-upgrade and autopurge) 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 159s Starting 2 pkgProblemResolver with broken count: 0 159s Done 159s Entering ResolveByKeep 160s 160s Calculating upgrade... 160s The following packages will be upgraded: 160s libc-bin libc-dev-bin libc6 libc6-dev locales 161s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 9530 kB of archives. 161s After this operation, 0 B of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 162s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 162s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 165s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 165s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 169s Preconfiguring packages ... 170s Fetched 9530 kB in 9s (1095 kB/s) 170s (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.) 170s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 170s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 170s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 170s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 170s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 170s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 170s Setting up libc6:arm64 (2.41-1ubuntu2) ... 171s (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.) 171s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 171s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 171s Setting up libc-bin (2.41-1ubuntu2) ... 171s (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.) 171s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 171s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 171s Setting up locales (2.41-1ubuntu2) ... 172s Generating locales (this might take a while)... 174s en_US.UTF-8... done 174s Generation complete. 174s Setting up libc-dev-bin (2.41-1ubuntu2) ... 174s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 174s Processing triggers for man-db (2.13.0-1) ... 175s Processing triggers for systemd (257.3-1ubuntu3) ... 176s Reading package lists... 176s Building dependency tree... 176s Reading state information... 177s Starting pkgProblemResolver with broken count: 0 177s Starting 2 pkgProblemResolver with broken count: 0 177s Done 177s Solving dependencies... 178s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 178s autopkgtest [14:34:08]: rebooting testbed after setup commands that affected boot 201s autopkgtest [14:34:31]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 204s autopkgtest [14:34:34]: @@@@@@@@@@@@@@@@@@@@ apt-source prodigal 207s Get:1 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (dsc) [1992 B] 207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (tar) [611 kB] 207s Get:3 http://ftpmaster.internal/ubuntu plucky/universe prodigal 1:2.6.3-6 (diff) [49.3 kB] 207s gpgv: Signature made Tue Dec 6 13:16:13 2022 UTC 207s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 207s gpgv: issuer "tille@debian.org" 207s gpgv: Can't check signature: No public key 207s dpkg-source: warning: cannot verify inline signature for ./prodigal_2.6.3-6.dsc: no acceptable signature found 207s autopkgtest [14:34:37]: testing package prodigal version 1:2.6.3-6 208s autopkgtest [14:34:38]: build not needed 209s autopkgtest [14:34:39]: test run-unit-test: preparing testbed 209s Reading package lists... 209s Building dependency tree... 209s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 210s The following NEW packages will be installed: 210s prodigal 211s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 822 kB of archives. 211s After this operation, 12.5 MB of additional disk space will be used. 211s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 prodigal arm64 1:2.6.3-6 [822 kB] 212s Fetched 822 kB in 1s (776 kB/s) 212s Selecting previously unselected package prodigal. 212s (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.) 212s Preparing to unpack .../prodigal_1%3a2.6.3-6_arm64.deb ... 212s Unpacking prodigal (1:2.6.3-6) ... 212s Setting up prodigal (1:2.6.3-6) ... 212s Processing triggers for man-db (2.13.0-1) ... 214s autopkgtest [14:34:44]: test run-unit-test: [----------------------- 214s ------------------------------------- 214s PRODIGAL v2.6.3 [February, 2016] 214s Univ of Tenn / Oak Ridge National Lab 214s Doug Hyatt, Loren Hauser, et al. 214s ------------------------------------- 214s Request: Single Genome, Phase: Training 214s Reading in the sequence(s) to train...174014 bp seq created, 17.63 pct GC 214s Locating all potential starts and stops...2619 nodes 214s Looking for GC bias in different frames...frame bias scores: 1.27 1.60 0.12 214s Building initial set of genes to train from...done! 214s Creating coding model and scoring nodes...done! 214s Examining upstream regions and training starts...done! 214s Writing data to training file testgenome.trn...done! 215s autopkgtest [14:34:45]: test run-unit-test: -----------------------] 215s run-unit-test PASS 215s autopkgtest [14:34:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 216s autopkgtest [14:34:46]: @@@@@@@@@@@@@@@@@@@@ summary 216s run-unit-test PASS 234s nova [W] Using flock in prodstack6-arm64 234s Creating nova instance adt-plucky-arm64-prodigal-20250315-143110-juju-7f2275-prod-proposed-migration-environment-2-bf00e5b7-593e-41ce-bf7f-1673652262c3 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 234s nova [W] Timed out waiting for 4c36e00d-bec2-4479-8843-9a483113fbac to get deleted.