0s autopkgtest [18:03:56]: starting date and time: 2025-03-15 18:03:56+0000 0s autopkgtest [18:03:56]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [18:03:56]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.esphjcd1/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 tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.76 lxd-armhf-10.145.243.76:autopkgtest/ubuntu/plucky/armhf 21s autopkgtest [18:04:17]: testbed dpkg architecture: armhf 23s autopkgtest [18:04:19]: testbed apt version: 2.9.33 29s autopkgtest [18:04:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 34s autopkgtest [18:04:30]: testbed release detected to be: None 43s autopkgtest [18:04:39]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 46s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 46s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 46s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 47s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [114 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1832 B] 47s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 47s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [312 kB] 47s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [11.1 kB] 47s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 47s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 47s Get:15 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1394 kB] 68s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 68s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 70s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 70s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 70s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 85s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 87s Fetched 41.0 MB in 41s (990 kB/s) 88s Reading package lists... 94s autopkgtest [18:05:30]: upgrading testbed (apt dist-upgrade and autopurge) 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 96s Starting 2 pkgProblemResolver with broken count: 0 96s Done 97s Entering ResolveByKeep 97s 97s Calculating upgrade... 98s The following packages will be upgraded: 98s libc-bin libc6 locales pinentry-curses python3-jinja2 sos strace 98s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 8683 kB of archives. 98s After this operation, 23.6 kB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 107s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 107s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 107s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 109s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 110s Preconfiguring packages ... 110s Fetched 8683 kB in 11s (756 kB/s) 110s (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.) 110s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 110s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc6:armhf (2.41-1ubuntu2) ... 111s (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.) 111s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 111s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 111s Setting up libc-bin (2.41-1ubuntu2) ... 111s (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.) 111s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 111s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 112s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 112s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 112s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 112s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 112s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 112s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 112s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 112s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 112s Setting up sos (4.9.0-5) ... 113s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 113s Setting up locales (2.41-1ubuntu2) ... 114s Generating locales (this might take a while)... 116s en_US.UTF-8... done 116s Generation complete. 116s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 116s Setting up strace (6.13+ds-1ubuntu1) ... 116s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for systemd (257.3-1ubuntu3) ... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 121s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [18:06:00]: rebooting testbed after setup commands that affected boot 164s autopkgtest [18:06:40]: 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 189s autopkgtest [18:07:05]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 199s Get:1 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (dsc) [2131 B] 199s Get:2 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (tar) [52.8 kB] 199s Get:3 http://ftpmaster.internal/ubuntu plucky/universe tm-align 20190822+dfsg-2build1 (diff) [818 kB] 199s gpgv: Signature made Sun Mar 22 16:27:16 2020 UTC 199s gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 199s gpgv: issuer "doko@ubuntu.com" 199s gpgv: Can't check signature: No public key 199s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-2build1.dsc: no acceptable signature found 200s autopkgtest [18:07:16]: testing package tm-align version 20190822+dfsg-2build1 202s autopkgtest [18:07:18]: build not needed 204s autopkgtest [18:07:20]: test run-unit-test: preparing testbed 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s Starting pkgProblemResolver with broken count: 0 207s Starting 2 pkgProblemResolver with broken count: 0 207s Done 207s The following NEW packages will be installed: 207s libgfortran5 tm-align 208s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 208s Need to get 1198 kB of archives. 208s After this operation, 2244 kB of additional disk space will be used. 208s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 208s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf tm-align armhf 20190822+dfsg-2build1 [867 kB] 209s Fetched 1198 kB in 2s (692 kB/s) 209s Selecting previously unselected package libgfortran5:armhf. 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 ... 64655 files and directories currently installed.) 210s Preparing to unpack .../libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 210s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 210s Selecting previously unselected package tm-align. 210s Preparing to unpack .../tm-align_20190822+dfsg-2build1_armhf.deb ... 210s Unpacking tm-align (20190822+dfsg-2build1) ... 210s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 210s Setting up tm-align (20190822+dfsg-2build1) ... 210s Processing triggers for libc-bin (2.41-1ubuntu2) ... 210s Processing triggers for man-db (2.13.0-1) ... 218s autopkgtest [18:07:34]: test run-unit-test: [----------------------- 219s Run TMalign... 220s 220s ************************************************************************** 220s * TM-align (Version 20190822) * 220s * An algorithm for protein structure alignment and comparison * 220s * Based on statistics: * 220s * 0.0 < TM-score < 0.30, random structural similarity * 220s * 0.5 < TM-score < 1.00, in about the same fold * 220s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 220s * Please email your comments and suggestions to: zhng@umich.edu * 220s ************************************************************************** 220s 220s Name of Chain_1: 1ni7.pdb 220s Name of Chain_2: 5eep.pdb 220s Length of Chain_1: 149 residues 220s Length of Chain_2: 140 residues 220s 220s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 220s TM-score= 0.85044 (if normalized by length of Chain_1) 220s TM-score= 0.90009 (if normalized by length of Chain_2) 220s (You should use TM-score normalized by length of the reference protein) 220s 220s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 220s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 220s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 220s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 220s 220s Run TMscore... 220s 220s ***************************************************************************** 220s * TM-SCORE * 220s * A scoring function to assess the similarity of protein structures * 220s * Based on statistics: * 220s * 0.0 < TM-score < 0.17, random structural similarity * 220s * 0.5 < TM-score < 1.00, in about the same fold * 220s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 220s * For comments, please email to: zhng@umich.edu * 220s ***************************************************************************** 220s 220s Structure1: 1ni7.pdb Length= 149 220s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 220s Number of residues in common= 140 220s RMSD of the common residues= 1.616 220s 220s TM-score = 0.8987 (d0= 4.40) 220s MaxSub-score= 0.8459 (d0= 3.50) 220s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 220s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 220s 220s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 220s i t(i) u(i,1) u(i,2) u(i,3) 220s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 220s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 220s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 220s 220s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 220s (":" denotes the residue pairs of distance < 5.0 Angstrom) 220s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 220s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 220s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 220s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 220s 220s autopkgtest [18:07:36]: test run-unit-test: -----------------------] 224s autopkgtest [18:07:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 224s run-unit-test PASS 228s autopkgtest [18:07:44]: @@@@@@@@@@@@@@@@@@@@ summary 228s run-unit-test PASS