0s autopkgtest [17:14:10]: starting date and time: 2025-03-15 17:14:10+0000 1s autopkgtest [17:14:11]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 1s autopkgtest [17:14:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mo_uoup1/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade unikmer --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-arm64-36.secgroup --name adt-plucky-arm64-unikmer-20250315-171409-juju-7f2275-prod-proposed-migration-environment-15-bf396693-7eb4-44ae-bee6-db3c34ec624c --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/ 177s autopkgtest [17:17:07]: testbed dpkg architecture: arm64 177s autopkgtest [17:17:07]: testbed apt version: 2.9.33 178s autopkgtest [17:17:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 178s autopkgtest [17:17:08]: testbed release detected to be: None 179s autopkgtest [17:17:09]: updating testbed package index (apt update) 180s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 180s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 180s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 180s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 180s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 181s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 181s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 181s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [111 kB] 181s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1856 B] 181s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 181s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [324 kB] 182s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [14.7 kB] 182s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 182s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [268 B] 182s Fetched 1078 kB in 2s (523 kB/s) 183s Reading package lists... 184s + lsb_release --codename --short 184s + RELEASE=plucky 184s + cat 184s + [ plucky != trusty ] 184s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 184s Reading package lists... 184s Building dependency tree... 184s Reading state information... 185s Calculating upgrade... 185s Calculating upgrade... 185s The following packages will be upgraded: 185s pinentry-curses python3-jinja2 strace 186s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 647 kB of archives. 186s After this operation, 11.3 kB of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pinentry-curses arm64 1.3.1-2ubuntu3 [39.2 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 187s Fetched 647 kB in 1s (572 kB/s) 187s (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.) 187s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 187s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 187s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_arm64.deb ... 187s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 187s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 188s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 188s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 188s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 188s Setting up strace (6.13+ds-1ubuntu1) ... 188s Processing triggers for man-db (2.13.0-1) ... 189s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 189s + /usr/lib/apt/apt-helper analyze-pattern ?true 189s + uname -r 189s + sed s/\./\\./g 189s + running_kernel_pattern=^linux-.*6\.14\.0-10-generic.* 189s + apt list ?obsolete 189s + tail -n+2 189s + cut -d/ -f1 189s + grep -v ^linux-.*6\.14\.0-10-generic.* 189s + obsolete_pkgs=linux-headers-6.11.0-8-generic 189s linux-headers-6.11.0-8 189s linux-image-6.11.0-8-generic 189s linux-modules-6.11.0-8-generic 189s linux-tools-6.11.0-8-generic 189s linux-tools-6.11.0-8 189s + 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-genericReading package lists... 189s Building dependency tree... linux-tools-6.11.0-8 189s 189s Reading state information... 189s Solving dependencies... 190s The following packages will be REMOVED: 190s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 190s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 190s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 190s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 190s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 190s After this operation, 267 MB disk space will be freed. 190s (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.) 190s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 190s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 190s Removing libpython3.12t64:arm64 (3.12.9-1) ... 190s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 191s Removing libnsl2:arm64 (1.3.0-3build3) ... 191s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 191s Removing libunwind8:arm64 (1.6.2-3.1) ... 191s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 191s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 193s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 193s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 193s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 193s /etc/kernel/postrm.d/initramfs-tools: 193s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 193s /etc/kernel/postrm.d/zz-flash-kernel: 193s flash-kernel: Kernel 6.11.0-8-generic has been removed. 193s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 194s /etc/kernel/postrm.d/zz-update-grub: 194s Sourcing file `/etc/default/grub' 194s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 194s Generating grub configuration file ... 194s Found linux image: /boot/vmlinuz-6.14.0-10-generic 194s Found initrd image: /boot/initrd.img-6.14.0-10-generic 194s Warning: os-prober will not be executed to detect other bootable partitions. 194s Systems on them will not be added to the GRUB boot configuration. 194s Check GRUB_DISABLE_OS_PROBER documentation entry. 194s Adding boot menu entry for UEFI Firmware Settings ... 194s done 194s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 194s Processing triggers for libc-bin (2.41-1ubuntu1) ... 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 ... 81650 files and directories currently installed.) 195s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 195s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 195s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 195s + grep -q trusty /etc/lsb-release 195s + [ ! -d /usr/share/doc/unattended-upgrades ] 195s + [ ! -d /usr/share/doc/lxd ] 195s + [ ! -d /usr/share/doc/lxd-client ] 195s + [ ! -d /usr/share/doc/snapd ] 195s + type iptables 195s + cat 195s + chmod 755 /etc/rc.local 195s + . /etc/rc.local 195s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 195s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 195s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 195s + uname -m 195s + [ aarch64 = ppc64le ] 195s + [ -d /run/systemd/system ] 195s + systemd-detect-virt --quiet --vm 195s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 195s + cat 195s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 195s + echo COMPRESS=lz4 195s autopkgtest [17:17:25]: upgrading testbed (apt dist-upgrade and autopurge) 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 196s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 196s Starting 2 pkgProblemResolver with broken count: 0 196s Done 197s Entering ResolveByKeep 197s 197s Calculating upgrade... 198s The following packages will be upgraded: 198s libc-bin libc-dev-bin libc6 libc6-dev locales 198s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 9530 kB of archives. 198s After this operation, 0 B of additional disk space will be used. 198s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 200s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 200s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 204s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 205s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 210s Preconfiguring packages ... 210s Fetched 9530 kB in 12s (772 kB/s) 210s (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.) 210s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 210s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 211s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 211s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 211s Preparing to unpack .../libc6_2.41-1ubuntu2_arm64.deb ... 211s Unpacking libc6:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 211s Setting up libc6:arm64 (2.41-1ubuntu2) ... 211s (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.) 211s Preparing to unpack .../libc-bin_2.41-1ubuntu2_arm64.deb ... 211s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 211s Setting up libc-bin (2.41-1ubuntu2) ... 211s (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.) 211s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 211s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 212s Setting up locales (2.41-1ubuntu2) ... 212s Generating locales (this might take a while)... 214s en_US.UTF-8... done 214s Generation complete. 214s Setting up libc-dev-bin (2.41-1ubuntu2) ... 214s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 214s Processing triggers for man-db (2.13.0-1) ... 215s Processing triggers for systemd (257.3-1ubuntu3) ... 216s Reading package lists... 217s Building dependency tree... 217s Reading state information... 217s Starting pkgProblemResolver with broken count: 0 217s Starting 2 pkgProblemResolver with broken count: 0 217s Done 217s Solving dependencies... 218s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 219s autopkgtest [17:17:49]: rebooting testbed after setup commands that affected boot 247s autopkgtest [17:18:17]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 250s autopkgtest [17:18:20]: @@@@@@@@@@@@@@@@@@@@ apt-source unikmer 256s Get:1 http://ftpmaster.internal/ubuntu plucky/universe unikmer 0.20.0-1 (dsc) [2144 B] 256s Get:2 http://ftpmaster.internal/ubuntu plucky/universe unikmer 0.20.0-1 (tar) [4228 kB] 256s Get:3 http://ftpmaster.internal/ubuntu plucky/universe unikmer 0.20.0-1 (diff) [5560 B] 256s gpgv: Signature made Sat Jul 6 09:00:41 2024 UTC 256s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 256s gpgv: Can't check signature: No public key 256s dpkg-source: warning: cannot verify inline signature for ./unikmer_0.20.0-1.dsc: no acceptable signature found 257s autopkgtest [17:18:27]: testing package unikmer version 0.20.0-1 257s autopkgtest [17:18:27]: build not needed 258s autopkgtest [17:18:28]: test run-unit-test: preparing testbed 258s Reading package lists... 258s Building dependency tree... 258s Reading state information... 259s Starting pkgProblemResolver with broken count: 0 259s Starting 2 pkgProblemResolver with broken count: 0 259s Done 259s The following NEW packages will be installed: 259s unikmer 260s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 260s Need to get 2886 kB of archives. 260s After this operation, 8991 kB of additional disk space will be used. 260s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 unikmer arm64 0.20.0-1 [2886 kB] 263s Fetched 2886 kB in 3s (1017 kB/s) 263s Selecting previously unselected package unikmer. 263s (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.) 263s Preparing to unpack .../unikmer_0.20.0-1_arm64.deb ... 263s Unpacking unikmer (0.20.0-1) ... 263s Setting up unikmer (0.20.0-1) ... 263s Processing triggers for man-db (2.13.0-1) ... 265s autopkgtest [17:18:35]: test run-unit-test: [----------------------- 265s Test 1 - counting and assigning taxid 265s 17:18:36.525 [INFO] flag -s/--sort overides -c/--compact 267s 17:18:38.609 [INFO] flag -s/--sort overides -c/--compact 270s 17:18:39.974 [INFO] flag -s/--sort overides -c/--compact 270s ================================= 270s PASS 270s Test 2 - view taxid 270s AAAAAAAAACCATCCAAATCTGG 511145 270s AAAAAAAAACCGCTAGTATATTC 511145 270s AAAAAAAAACCTGAAAAAAACGG 511145 270s ================================== 270s PASS 270s Test 3 - check stats 271s file k canonical hashed scaled include-taxid global-taxid sorted compact gzipped version number description 271s A.muciniphila-ATCC_BAA-835.fasta.gz.sorted.unik 23 ✓ ✕ ✕ ✕ 349741 ✓ ✕ ✓ v5.0 2,630,905 271s Ecoli-IAI39.fasta.gz.k23.sorted.unik 23 ✓ ✕ ✕ ✕ 585057 ✓ ✕ ✓ v5.0 4,902,266 271s Ecoli-MG1655.fasta.gz.k23.sorted.unik 23 ✓ ✕ ✕ ✕ 511145 ✓ ✕ ✓ v5.0 4,546,632 271s ================================== 271s PASS 271s autopkgtest [17:18:41]: test run-unit-test: -----------------------] 271s autopkgtest [17:18:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 271s run-unit-test PASS 272s autopkgtest [17:18:42]: @@@@@@@@@@@@@@@@@@@@ summary 272s run-unit-test PASS 283s nova [W] Using flock in prodstack6-arm64 283s Creating nova instance adt-plucky-arm64-unikmer-20250315-171409-juju-7f2275-prod-proposed-migration-environment-15-bf396693-7eb4-44ae-bee6-db3c34ec624c from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 283s nova [W] Timed out waiting for 5590dd0b-696f-4e58-b30f-404938a021d1 to get deleted.