0s autopkgtest [14:16:55]: starting date and time: 2025-03-15 14:16:55+0000 0s autopkgtest [14:16:55]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:16:55]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nccixe1r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade pscan-tfbs --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-20@bos03-arm64-40.secgroup --name adt-plucky-arm64-pscan-tfbs-20250315-140522-juju-7f2275-prod-proposed-migration-environment-20-1e5cf49d-5b00-4c63-908d-db423571e2b7 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 166s autopkgtest [14:19:41]: testbed dpkg architecture: arm64 166s autopkgtest [14:19:41]: testbed apt version: 2.9.33 166s autopkgtest [14:19:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 167s autopkgtest [14:19:42]: testbed release detected to be: None 167s autopkgtest [14:19:42]: updating testbed package index (apt update) 168s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 168s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 168s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 168s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 168s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 168s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 169s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 169s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 169s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 169s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 169s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 169s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 169s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 169s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 169s Fetched 1094 kB in 2s (667 kB/s) 170s Reading package lists... 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 172s Calculating upgrade... 172s Calculating upgrade... 172s The following packages will be upgraded: 172s python3-jinja2 strace 172s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 608 kB of archives. 172s After this operation, 11.3 kB of additional disk space will be used. 172s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 173s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 174s Fetched 608 kB in 1s (722 kB/s) 174s (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.) 174s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 174s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 174s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 174s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 174s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 174s Setting up strace (6.13+ds-1ubuntu1) ... 174s Processing triggers for man-db (2.13.0-1) ... 175s Reading package lists... 176s Building dependency tree... 176s Reading state information... 176s Solving dependencies... 176s The following packages will be REMOVED: 176s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 176s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 176s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 176s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 177s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 177s After this operation, 267 MB disk space will be freed. 177s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 117701 files and directories currently installed.) 177s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 177s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 177s Removing libpython3.12t64:arm64 (3.12.9-1) ... 177s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 177s Removing libnsl2:arm64 (1.3.0-3build3) ... 177s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 177s Removing libunwind8:arm64 (1.6.2-3.1) ... 177s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 177s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 179s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 179s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 179s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 179s /etc/kernel/postrm.d/initramfs-tools: 179s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 180s /etc/kernel/postrm.d/zz-flash-kernel: 180s flash-kernel: Kernel 6.11.0-8-generic has been removed. 180s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 180s /etc/kernel/postrm.d/zz-update-grub: 180s Sourcing file `/etc/default/grub' 180s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 180s Generating grub configuration file ... 180s Found linux image: /boot/vmlinuz-6.14.0-10-generic 180s Found initrd image: /boot/initrd.img-6.14.0-10-generic 181s Warning: os-prober will not be executed to detect other bootable partitions. 181s Systems on them will not be added to the GRUB boot configuration. 181s Check GRUB_DISABLE_OS_PROBER documentation entry. 181s Adding boot menu entry for UEFI Firmware Settings ... 181s done 181s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 181s Processing triggers for libc-bin (2.41-1ubuntu1) ... 181s (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.) 181s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 181s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 181s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 181s autopkgtest [14:19:56]: upgrading testbed (apt dist-upgrade and autopurge) 181s Reading package lists... 182s Building dependency tree... 182s Reading state information... 182s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 182s Starting 2 pkgProblemResolver with broken count: 0 182s Done 183s Entering ResolveByKeep 183s 184s Calculating upgrade... 184s The following packages will be upgraded: 184s libc-bin libc-dev-bin libc6 libc6-dev locales 184s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 184s Need to get 9530 kB of archives. 184s After this operation, 0 B of additional disk space will be used. 184s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 186s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 189s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 190s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 194s Preconfiguring packages ... 194s Fetched 9530 kB in 9s (1035 kB/s) 194s (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.) 194s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 194s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 194s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 194s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Setting up libc6:arm64 (2.41-1ubuntu2) ... 195s (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.) 195s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 195s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Setting up libc-bin (2.41-1ubuntu2) ... 195s (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.) 195s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 195s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Setting up locales (2.41-1ubuntu2) ... 196s Generating locales (this might take a while)... 198s en_US.UTF-8... done 198s Generation complete. 198s Setting up libc-dev-bin (2.41-1ubuntu2) ... 198s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 198s Processing triggers for man-db (2.13.0-1) ... 199s Processing triggers for systemd (257.3-1ubuntu3) ... 200s Reading package lists... 200s Building dependency tree... 200s Reading state information... 201s Starting pkgProblemResolver with broken count: 0 201s Starting 2 pkgProblemResolver with broken count: 0 201s Done 201s Solving dependencies... 202s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s autopkgtest [14:20:17]: rebooting testbed after setup commands that affected boot 225s autopkgtest [14:20:40]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 228s autopkgtest [14:20:43]: @@@@@@@@@@@@@@@@@@@@ apt-source pscan-tfbs 230s Get:1 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (dsc) [2067 B] 230s Get:2 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (tar) [42.9 kB] 230s Get:3 http://ftpmaster.internal/ubuntu plucky/universe pscan-tfbs 1.2.2-4build2 (diff) [7476 B] 230s gpgv: Signature made Tue Jul 30 06:52:29 2024 UTC 230s gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./pscan-tfbs_1.2.2-4build2.dsc: no acceptable signature found 230s autopkgtest [14:20:45]: testing package pscan-tfbs version 1.2.2-4build2 231s autopkgtest [14:20:46]: build not needed 231s autopkgtest [14:20:46]: test run-unit-test: preparing testbed 231s Reading package lists... 232s Building dependency tree... 232s Reading state information... 232s Starting pkgProblemResolver with broken count: 0 232s Starting 2 pkgProblemResolver with broken count: 0 232s Done 233s The following NEW packages will be installed: 233s libgsl28 libgslcblas0 pscan-tfbs 233s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 233s Need to get 1145 kB of archives. 233s After this operation, 3601 kB of additional disk space will be used. 233s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgslcblas0 arm64 2.8+dfsg-5 [87.3 kB] 233s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgsl28 arm64 2.8+dfsg-5 [983 kB] 234s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 pscan-tfbs arm64 1.2.2-4build2 [75.6 kB] 235s Fetched 1145 kB in 1s (819 kB/s) 235s Selecting previously unselected package libgslcblas0:arm64. 235s (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.) 235s Preparing to unpack .../libgslcblas0_2.8+dfsg-5_arm64.deb ... 235s Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... 235s Selecting previously unselected package libgsl28:arm64. 235s Preparing to unpack .../libgsl28_2.8+dfsg-5_arm64.deb ... 235s Unpacking libgsl28:arm64 (2.8+dfsg-5) ... 235s Selecting previously unselected package pscan-tfbs. 235s Preparing to unpack .../pscan-tfbs_1.2.2-4build2_arm64.deb ... 235s Unpacking pscan-tfbs (1.2.2-4build2) ... 235s Setting up libgslcblas0:arm64 (2.8+dfsg-5) ... 235s Setting up libgsl28:arm64 (2.8+dfsg-5) ... 235s Setting up pscan-tfbs (1.2.2-4build2) ... 235s Processing triggers for man-db (2.13.0-1) ... 236s Processing triggers for libc-bin (2.41-1ubuntu2) ... 237s autopkgtest [14:20:52]: test run-unit-test: [----------------------- 237s Test 1 237s sh: 1: dos2unix: not found 237s 237s Reading matrix file(s)... 2 matrices acquired. 237s 237s Reading background sequence file... 1 background sequences acquired. 237s Processing >NM_000546.3 Homo sapien (1) 237s Writing short matrix output...done 237s 237s [SHORT TFBS MATRIX] 237s NFY 1 0.816888 0.816888 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 237s 1 0.944058 0.944058 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 237s PASS 237s Test 2 237s sh: 1: dos2unix: not found 237s 237s Reading matrix file(s)... 1 matrices acquired. 237s 237s Reading background sequence file... 1 background sequences acquired. 237s Processing >NM_000546.3 Homo sapien (1) 237s Writing short matrix output...done 237s 237s [SHORT TFBS MATRIX] 237s NFY 1 0.816888 0.816888 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 237s PASS 237s autopkgtest [14:20:52]: test run-unit-test: -----------------------] 238s run-unit-test PASS 238s autopkgtest [14:20:53]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 238s autopkgtest [14:20:53]: @@@@@@@@@@@@@@@@@@@@ summary 238s run-unit-test PASS 255s nova [W] Using flock in prodstack6-arm64 255s Creating nova instance adt-plucky-arm64-pscan-tfbs-20250315-140522-juju-7f2275-prod-proposed-migration-environment-20-1e5cf49d-5b00-4c63-908d-db423571e2b7 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 255s nova [W] Timed out waiting for 04b29e3f-cd7c-429f-a04d-bd1b8944934a to get deleted.