0s autopkgtest [14:20:59]: starting date and time: 2025-03-15 14:20:59+0000 0s autopkgtest [14:20:59]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:20:59]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.25dtn22m/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade phybin --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-arm64-55.secgroup --name adt-plucky-arm64-phybin-20250315-142059-juju-7f2275-prod-proposed-migration-environment-2-7e607abe-8d5d-4d24-ba92-5503a3e35904 --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/ 162s autopkgtest [14:23:41]: testbed dpkg architecture: arm64 162s autopkgtest [14:23:41]: testbed apt version: 2.9.33 162s autopkgtest [14:23:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 163s autopkgtest [14:23:42]: testbed release detected to be: None 164s autopkgtest [14:23:43]: updating testbed package index (apt update) 164s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 164s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 164s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 165s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 165s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 165s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 165s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 165s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [78.2 kB] 165s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 c-n-f Metadata [1976 B] 165s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 c-n-f Metadata [116 B] 165s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [346 kB] 166s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 c-n-f Metadata [15.8 kB] 166s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [4948 B] 166s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 c-n-f Metadata [572 B] 166s Fetched 1094 kB in 2s (598 kB/s) 167s Reading package lists... 168s Reading package lists... 168s Building dependency tree... 168s Reading state information... 169s Calculating upgrade... 169s Calculating upgrade... 169s The following packages will be upgraded: 169s python3-jinja2 strace 170s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 170s Need to get 608 kB of archives. 170s After this operation, 11.3 kB of additional disk space will be used. 170s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 strace arm64 6.13+ds-1ubuntu1 [499 kB] 170s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 171s Fetched 608 kB in 1s (610 kB/s) 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 ... 117701 files and directories currently installed.) 171s Preparing to unpack .../strace_6.13+ds-1ubuntu1_arm64.deb ... 171s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 172s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 172s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 172s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 172s Setting up strace (6.13+ds-1ubuntu1) ... 172s Processing triggers for man-db (2.13.0-1) ... 173s Reading package lists... 173s Building dependency tree... 173s Reading state information... 174s Solving dependencies... 174s The following packages will be REMOVED: 174s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 174s libunwind8* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 174s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 174s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* 174s 0 upgraded, 0 newly installed, 11 to remove and 5 not upgraded. 174s After this operation, 267 MB disk space will be freed. 175s (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.) 175s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 175s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 175s Removing libpython3.12t64:arm64 (3.12.9-1) ... 175s Removing libpython3.12-stdlib:arm64 (3.12.9-1) ... 175s Removing libnsl2:arm64 (1.3.0-3build3) ... 175s Removing libpython3.12-minimal:arm64 (3.12.9-1) ... 175s Removing libunwind8:arm64 (1.6.2-3.1) ... 175s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 175s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 177s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 177s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 177s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 177s /etc/kernel/postrm.d/initramfs-tools: 177s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 177s /etc/kernel/postrm.d/zz-flash-kernel: 177s flash-kernel: Kernel 6.11.0-8-generic has been removed. 177s flash-kernel: A higher version (6.14.0-10-generic) is still installed, no reflashing required. 177s /etc/kernel/postrm.d/zz-update-grub: 177s Sourcing file `/etc/default/grub' 177s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 177s Generating grub configuration file ... 178s Found linux image: /boot/vmlinuz-6.14.0-10-generic 178s Found initrd image: /boot/initrd.img-6.14.0-10-generic 178s Warning: os-prober will not be executed to detect other bootable partitions. 178s Systems on them will not be added to the GRUB boot configuration. 178s Check GRUB_DISABLE_OS_PROBER documentation entry. 178s Adding boot menu entry for UEFI Firmware Settings ... 178s done 178s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 178s Processing triggers for libc-bin (2.41-1ubuntu1) ... 178s (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.) 178s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 179s Purging configuration files for libpython3.12-minimal:arm64 (3.12.9-1) ... 179s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 179s autopkgtest [14:23:58]: upgrading testbed (apt dist-upgrade and autopurge) 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 180s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s Entering ResolveByKeep 181s 181s Calculating upgrade... 182s The following packages will be upgraded: 182s libc-bin libc-dev-bin libc6 libc6-dev locales 182s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 182s Need to get 9530 kB of archives. 182s After this operation, 0 B of additional disk space will be used. 182s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6-dev arm64 2.41-1ubuntu2 [1750 kB] 184s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-dev-bin arm64 2.41-1ubuntu2 [24.0 kB] 184s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc6 arm64 2.41-1ubuntu2 [2910 kB] 187s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libc-bin arm64 2.41-1ubuntu2 [600 kB] 188s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 locales all 2.41-1ubuntu2 [4246 kB] 193s Preconfiguring packages ... 193s Fetched 9530 kB in 11s (856 kB/s) 193s (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.) 193s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_arm64.deb ... 193s Unpacking libc6-dev:arm64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 193s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_arm64.deb ... 193s 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) ... 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 .../libc-bin_2.41-1ubuntu2_arm64.deb ... 194s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Setting up libc-bin (2.41-1ubuntu2) ... 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 .../locales_2.41-1ubuntu2_all.deb ... 194s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Setting up locales (2.41-1ubuntu2) ... 195s Generating locales (this might take a while)... 197s en_US.UTF-8... done 197s Generation complete. 197s Setting up libc-dev-bin (2.41-1ubuntu2) ... 197s Setting up libc6-dev:arm64 (2.41-1ubuntu2) ... 197s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for systemd (257.3-1ubuntu3) ... 199s Reading package lists... 200s Building dependency tree... 200s Reading state information... 200s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s Solving dependencies... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s autopkgtest [14:24:20]: rebooting testbed after setup commands that affected boot 225s autopkgtest [14:24:44]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 15:45:31 UTC 2025 228s autopkgtest [14:24:47]: @@@@@@@@@@@@@@@@@@@@ apt-source phybin 230s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (dsc) [1607 B] 230s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (tar) [112 kB] 230s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (diff) [7276 B] 230s gpgv: Signature made Fri Dec 30 05:57:25 2022 UTC 230s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./phybin_0.3-6.dsc: no acceptable signature found 230s autopkgtest [14:24:49]: testing package phybin version 0.3-6 231s autopkgtest [14:24:50]: build not needed 231s autopkgtest [14:24:50]: test run-unit-test: preparing testbed 232s 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 phybin 233s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 233s Need to get 4869 kB of archives. 233s After this operation, 31.0 MB of additional disk space will be used. 233s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 phybin arm64 0.3-6 [4869 kB] 238s Fetched 4869 kB in 5s (1048 kB/s) 238s Selecting previously unselected package phybin. 239s (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.) 239s Preparing to unpack .../phybin_0.3-6_arm64.deb ... 239s Unpacking phybin (0.3-6) ... 239s Setting up phybin (0.3-6) ... 239s Processing triggers for man-db (2.13.0-1) ... 241s autopkgtest [14:25:00]: test run-unit-test: [----------------------- 241s Test 1 - Testing phybin on 112.tr 241s Tree "112" 241s ((6_134_D-alanine--D-alanine_ligase_wRi_WRi_001550, 241s 7_88_D-alanine--D-alanine_ligase_wMel_WD0095), 241s ((1_177_D-alanine--D-alanine_ligase_family_protein_wUni-gwu_gwu_177, 241s 2_1056_D-alanine--D-alanine_ligase_family_protein_wVitA-gwv_gwv_1056), 241s ((3_584_D-alanine--D-alanine_ligase_wBm_Wbm0570, 241s 14_97_D-alanine--D-alanine_ligase_wOo_wOo_01490), 241s (13_1000_D-alanine--D-alanine_ligase_wAlbB_WALBB_840007, 241s (19_986_D-alanine--D-alanine_ligase_wNo_wNo_10410, 241s 5_356_D-alanine--D-alanine_ligase_wPip-Pel_WPa_0403)))), 241s 18_124_D-alanine--D-alanine_ligase_wHa_wHa_01330); 241s ================================= 241s PASS 241s Test 2 - Testing phybin on t30_mismatched 241s Input is a directory, reading all regular files contained (1 regular files found): "t30_mismatched" 241s Cleaning away previous phybin outputs... 241s Parsing 1 Newick tree files. 241s 241s Total unique taxa (10): 241s 1_ 7_ 6_ 18 13 5_ 19 3_ 14 2_ 241s Note: defaulting to expecting ALL 10 to be present.. 241s 241s Number of input tree files: 1 241s Number of bad/unreadable input tree files: 1 241s Number of VALID trees (correct # of leaves/taxa): 2 241s Total tree nodes contained in valid trees: 20 241s Average branch len over valid trees: 0.0 241s Max/Min branch lengths: (0.0,0.0) 241s Creating equivalence classes (bins)... 241s Outcome: 2 clusters found, 0 non-singleton, top bin sizes: [1,1] 241s Up to first 30 bin sizes, excluding singletons: 241s [finished] Wrote contents of each bin to cluster<N>_<binsize>.txt 241s Wrote representative trees to cluster<N>_<binsize>_avg.tr 241s Waiting for 1 asynchronous tasks to finish... 241s Phybin completed. 241s ================================== 241s PASS 241s autopkgtest [14:25:00]: test run-unit-test: -----------------------] 242s run-unit-test PASS 242s autopkgtest [14:25:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 242s autopkgtest [14:25:01]: @@@@@@@@@@@@@@@@@@@@ summary 242s run-unit-test PASS 248s nova [W] Using flock in prodstack6-arm64 248s Creating nova instance adt-plucky-arm64-phybin-20250315-142059-juju-7f2275-prod-proposed-migration-environment-2-7e607abe-8d5d-4d24-ba92-5503a3e35904 from image adt/ubuntu-plucky-arm64-server-20250315.img (UUID bd6e766c-b51f-4b53-86d6-23aa4d18f524)... 248s nova [W] Timed out waiting for f6f3fe12-6341-47a5-8ac5-96b5a4ed1ff7 to get deleted.