0s autopkgtest [16:48:21]: starting date and time: 2025-03-15 16:48:21+0000 0s autopkgtest [16:48:21]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [16:48:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wgmaxrpj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade snap-aligner --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-arm64-24.secgroup --name adt-plucky-arm64-snap-aligner-20250315-164821-juju-7f2275-prod-proposed-migration-environment-20-2f0f310d-65ce-4d7a-bd53-6770b0ab608c --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/ 165s autopkgtest [16:51:06]: testbed dpkg architecture: arm64 165s autopkgtest [16:51:06]: testbed apt version: 2.9.33 165s autopkgtest [16:51:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 165s autopkgtest [16:51:06]: testbed release detected to be: None 166s autopkgtest [16:51:07]: updating testbed package index (apt update) 166s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 167s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 167s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 167s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 167s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 167s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 167s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 167s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 168s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 168s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 168s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 168s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 168s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 168s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 168s Fetched 1078 kB in 2s (610 kB/s) 169s Reading package lists... 170s Reading package lists... 170s Building dependency tree... 170s Reading state information... 171s Calculating upgrade... 171s Calculating upgrade... 171s The following packages will be upgraded: 171s pinentry-curses python3-jinja2 strace 172s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 172s Need to get 647 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] 172s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 172s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 173s Fetched 647 kB in 1s (550 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 ... 117701 files and directories currently installed.) 173s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 173s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 173s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 173s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 173s 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 pinentry-curses (1.3.1-2ubuntu3) ... 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... 175s Building dependency tree... 175s Reading state information... 175s 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* 176s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 176s After this operation, 267 MB disk space will be freed. 176s (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.) 176s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 176s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 176s Removing libpython3.12t64:arm64 (3.12.9-1) ... 176s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 176s Removing libnsl2:arm64 (1.3.0-3build3) ... 176s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 176s Removing libunwind8:arm64 (1.6.2-3.1) ... 176s 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) ... 178s 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 179s /etc/kernel/postrm.d/zz-flash-kernel: 179s flash-kernel: Kernel 6.11.0-8-generic has been removed. 179s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 179s /etc/kernel/postrm.d/zz-update-grub: 179s Sourcing file `/etc/default/grub' 179s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 179s Generating grub configuration file ... 179s Found linux image: /boot/vmlinuz-6.14.0-10-generic 179s Found initrd image: /boot/initrd.img-6.14.0-10-generic 180s Warning: os-prober will not be executed to detect other bootable partitions. 180s Systems on them will not be added to the GRUB boot configuration. 180s Check GRUB_DISABLE_OS_PROBER documentation entry. 180s Adding boot menu entry for UEFI Firmware Settings ... 180s done 180s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 180s Processing triggers for libc-bin (2.41-1ubuntu1) ... 180s (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.) 180s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 180s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 180s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 180s autopkgtest [16:51:21]: upgrading testbed (apt dist-upgrade and autopurge) 181s Reading package lists... 181s Building dependency tree... 181s Reading state information... 181s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 182s Starting 2 pkgProblemResolver with broken count: 0 182s Done 182s Entering ResolveByKeep 183s 183s Calculating upgrade... 183s The following packages will be upgraded: 183s libc-bin libc-dev-bin libc6 libc6-dev locales 183s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Need to get 9530 kB of archives. 183s After this operation, 0 B of additional disk space will be used. 183s 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] 195s Preconfiguring packages ... 195s Fetched 9530 kB in 12s (820 kB/s) 196s (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.) 196s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 196s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 196s Setting up libc6:arm64 (2.41-1ubuntu2) ... 197s (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.) 197s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 197s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 197s Setting up libc-bin (2.41-1ubuntu2) ... 197s (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.) 197s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 197s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 197s Setting up locales (2.41-1ubuntu2) ... 198s Generating locales (this might take a while)... 200s en_US.UTF-8... done 200s Generation complete. 200s Setting up libc-dev-bin (2.41-1ubuntu2) ... 200s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 200s Processing triggers for man-db (2.13.0-1) ... 201s Processing triggers for systemd (257.3-1ubuntu3) ... 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 203s Starting pkgProblemResolver with broken count: 0 203s Starting 2 pkgProblemResolver with broken count: 0 203s Done 203s Solving dependencies... 204s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s autopkgtest [16:51:45]: rebooting testbed after setup commands that affected boot 228s autopkgtest [16:52:09]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 230s autopkgtest [16:52:11]: @@@@@@@@@@@@@@@@@@@@ apt-source snap-aligner 235s Get:1 http://ftpmaster.internal/ubuntu plucky/universe snap-aligner 2.0.3+dfsg-2 (dsc) [2281 B] 235s Get:2 http://ftpmaster.internal/ubuntu plucky/universe snap-aligner 2.0.3+dfsg-2 (tar) [2023 kB] 235s Get:3 http://ftpmaster.internal/ubuntu plucky/universe snap-aligner 2.0.3+dfsg-2 (diff) [7788 B] 235s gpgv: Signature made Thu Jan 11 20:51:04 2024 UTC 235s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 235s gpgv: issuer "tillea@rki.de" 235s gpgv: Can't check signature: No public key 235s dpkg-source: warning: cannot verify inline signature for ./snap-aligner_2.0.3+dfsg-2.dsc: no acceptable signature found 235s autopkgtest [16:52:16]: testing package snap-aligner version 2.0.3+dfsg-2 235s autopkgtest [16:52:16]: build not needed 236s autopkgtest [16:52:17]: test run-unit-test: preparing testbed 236s Reading package lists... 237s Building dependency tree... 237s Reading state information... 237s Starting pkgProblemResolver with broken count: 0 237s Starting 2 pkgProblemResolver with broken count: 0 237s Done 238s The following NEW packages will be installed: 238s snap-aligner 238s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 238s Need to get 848 kB of archives. 238s After this operation, 1538 kB of additional disk space will be used. 238s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 snap-aligner arm64 2.0.3+dfsg-2 [848 kB] 240s Fetched 848 kB in 1s (669 kB/s) 240s Selecting previously unselected package snap-aligner. 240s (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.) 240s Preparing to unpack .../snap-aligner_2.0.3+dfsg-2_arm64.deb ... 240s Unpacking snap-aligner (2.0.3+dfsg-2) ... 240s Setting up snap-aligner (2.0.3+dfsg-2) ... 240s Processing triggers for man-db (2.13.0-1) ... 242s autopkgtest [16:52:23]: test run-unit-test: [----------------------- 243s Test 1 243s Building index with seed size 24 243s Auto-set key size to 5 243s Auto-set locationSize to 4 243s Hash table slack 0.300000 243s Loading FASTA file 'datatest.fa' into memory...Welcome to SNAP version 2.0.3. 243s 243s 0s 243s Genome has 1 contigs, of which 0 are ALTs 243s Saving genome...0s 243s Computing bias table. 243s Bias computation: 0 / 4202 243s Computed bias table in 0s 243s Allocating memory for hash tables...0s 243s Building hash tables. 243s 0(0%) seeds occur more than once, total of 0(0%) genome locations are not unique, 1,998(47%) bad seeds, 0 both complements used 2,000 no string 243s Hash table build took 0s 243s Building overflow table. 243s Overflow table build and hash table save took 0s 243s Saving overflow table...0s 243s Index build and save took 0s (4,202 bases/s) 243s Passed 243s 243s Test 2 243s Building index with seed size 22 243s Auto-set key size to 5 243s Auto-set locationSize to 4 243s Hash table slack 0.300000 243s Loading FASTA file 'datatest2.fa' into memory...Welcome to SNAP version 2.0.3. 243s 243s 0s 243s Genome has 2 contigs, of which 0 are ALTs 243s Saving genome...0s 243s Computing bias table. 243s Bias computation: 0 / 6404 243s Computed bias table in 0s 243s Allocating memory for hash tables...0s 243s Building hash tables. 243s Welcome to SNAP version 2.0.3. 243s 243s 145(2%) seeds occur more than once, total of 290(4%) genome locations are not unique, 3,997(62%) bad seeds, 0 both complements used 2,022 no string 243s Hash table build took 0s 243s Building overflow table. 243s Overflow table build and hash table save took 0s 243s Saving overflow table...0s 243s Index build and save took 0s (6,404 bases/s) 243s Passed 243s 243s Test 3 243s Loading index from directory... 0s. 4,202 bases, seed size 24. 243s Aligning. 243s Total Reads Aligned, MAPQ >= 10 Aligned, MAPQ < 10 Unaligned Too Short/Too Many Ns Reads/s Time in Aligner (s) 243s 2 2 (100.00%) 0 (0.00%) 0 (0.00%) 0 (0.00%) 133 0 243s Passed 243s 243s autopkgtest [16:52:24]: test run-unit-test: -----------------------] 244s run-unit-test PASS 244s autopkgtest [16:52:25]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s autopkgtest [16:52:25]: @@@@@@@@@@@@@@@@@@@@ summary 244s run-unit-test PASS 263s nova [W] Using flock in prodstack6-arm64 263s Creating nova instance adt-plucky-arm64-snap-aligner-20250315-164821-juju-7f2275-prod-proposed-migration-environment-20-2f0f310d-65ce-4d7a-bd53-6770b0ab608c from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 263s nova [W] Timed out waiting for 44321444-064b-49da-9faf-f90034976199 to get deleted.