0s autopkgtest [15:15:39]: starting date and time: 2025-03-15 15:15:39+0000 0s autopkgtest [15:15:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [15:15:39]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gn6q38o9/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.46 lxd-armhf-10.145.243.46:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [15:15:59]: testbed dpkg architecture: armhf 22s autopkgtest [15:16:01]: testbed apt version: 2.9.33 26s autopkgtest [15:16:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [15:16:07]: testbed release detected to be: None 36s autopkgtest [15:16:15]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 39s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 39s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 53s Get:17 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 54s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 55s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 55s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 55s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 65s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 67s Fetched 41.0 MB in 29s (1407 kB/s) 68s Reading package lists... 74s autopkgtest [15:16:53]: upgrading testbed (apt dist-upgrade and autopurge) 76s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 78s Entering ResolveByKeep 78s 79s Calculating upgrade... 79s The following packages will be upgraded: 79s libc-bin libc6 locales python3-jinja2 sos strace 79s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Need to get 8642 kB of archives. 79s After this operation, 23.6 kB of additional disk space will be used. 79s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 85s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 85s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 85s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 86s Preconfiguring packages ... 86s Fetched 8642 kB in 6s (1392 kB/s) 86s (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 ... 64655 files and directories currently installed.) 86s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 86s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 86s Setting up libc6:armhf (2.41-1ubuntu2) ... 87s (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 ... 64655 files and directories currently installed.) 87s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 87s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 87s Setting up libc-bin (2.41-1ubuntu2) ... 87s (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 ... 64655 files and directories currently installed.) 87s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 87s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 87s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 87s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 87s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 87s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 87s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 88s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 88s Setting up sos (4.9.0-5) ... 88s Setting up locales (2.41-1ubuntu2) ... 89s Generating locales (this might take a while)... 91s en_US.UTF-8... done 91s Generation complete. 91s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 91s Setting up strace (6.13+ds-1ubuntu1) ... 91s Processing triggers for man-db (2.13.0-1) ... 92s Processing triggers for systemd (257.3-1ubuntu3) ... 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 96s Solving dependencies... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [15:17:19]: rebooting testbed after setup commands that affected boot 146s autopkgtest [15:18:05]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 173s autopkgtest [15:18:32]: @@@@@@@@@@@@@@@@@@@@ apt-source phybin 183s Get:1 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (dsc) [1607 B] 183s Get:2 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (tar) [112 kB] 183s Get:3 http://ftpmaster.internal/ubuntu plucky/universe phybin 0.3-6 (diff) [7276 B] 184s gpgv: Signature made Fri Dec 30 05:57:25 2022 UTC 184s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 184s gpgv: Can't check signature: No public key 184s dpkg-source: warning: cannot verify inline signature for ./phybin_0.3-6.dsc: no acceptable signature found 184s autopkgtest [15:18:43]: testing package phybin version 0.3-6 186s autopkgtest [15:18:45]: build not needed 188s autopkgtest [15:18:47]: test run-unit-test: preparing testbed 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 191s The following NEW packages will be installed: 191s phybin 192s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 5372 kB of archives. 192s After this operation, 29.2 MB of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf phybin armhf 0.3-6 [5372 kB] 193s Fetched 5372 kB in 1s (4985 kB/s) 193s Selecting previously unselected package phybin. 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 ... 64655 files and directories currently installed.) 193s Preparing to unpack .../phybin_0.3-6_armhf.deb ... 193s Unpacking phybin (0.3-6) ... 193s Setting up phybin (0.3-6) ... 193s Processing triggers for man-db (2.13.0-1) ... 202s autopkgtest [15:19:01]: test run-unit-test: [----------------------- 204s Test 1 - Testing phybin on 112.tr 204s Tree "112" 204s ((6_134_D-alanine--D-alanine_ligase_wRi_WRi_001550, 204s 7_88_D-alanine--D-alanine_ligase_wMel_WD0095), 204s ((1_177_D-alanine--D-alanine_ligase_family_protein_wUni-gwu_gwu_177, 204s 2_1056_D-alanine--D-alanine_ligase_family_protein_wVitA-gwv_gwv_1056), 204s ((3_584_D-alanine--D-alanine_ligase_wBm_Wbm0570, 204s 14_97_D-alanine--D-alanine_ligase_wOo_wOo_01490), 204s (13_1000_D-alanine--D-alanine_ligase_wAlbB_WALBB_840007, 204s (19_986_D-alanine--D-alanine_ligase_wNo_wNo_10410, 204s 5_356_D-alanine--D-alanine_ligase_wPip-Pel_WPa_0403)))), 204s 18_124_D-alanine--D-alanine_ligase_wHa_wHa_01330); 204s ================================= 204s PASS 204s Test 2 - Testing phybin on t30_mismatched 204s Input is a directory, reading all regular files contained (1 regular Cleaning away previous phybin outputs... 204s Parsing 1 Newick tree files. 204s 204s Total unique taxa (10): 204s 1_ 7_ 6_ 18 13 5_ 19 3_ 14 2_ 204s Note: defaulting to expecting ALL 10 to be present.. 204s 204s Number of input tree files: 1 204s Number of bad/unreadable input tree files: 1 204s Number of VALID trees (correct # of leaves/taxa): 2 204s Total tree nodes contained in valid trees: 20 204s Average branch len over valid trees: 0.0 204s Max/Min branch lengths: (0.0,0.0) 204s Creating equivalence classes (bins)... 204s Outcome: 2 clusters found, 0 non-singleton, top bin sizes: [1,1] 204s Up to first 30 bin sizes, excluding singletons: 204s [finished] Wrote contents of each bin to cluster_.txt 204s Wrote representative trees to cluster__avg.tr 204s Waiting for 1 asynchronous tasks to finish... 204s Phybin completed. 204s ================================== 204s PASS 204s files found): "t30_mismatched" 205s autopkgtest [15:19:04]: test run-unit-test: -----------------------] 209s autopkgtest [15:19:08]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 209s run-unit-test PASS 213s autopkgtest [15:19:12]: @@@@@@@@@@@@@@@@@@@@ summary 213s run-unit-test PASS