0s autopkgtest [22:27:40]: starting date and time: 2024-11-01 22:27:40+0000 0s autopkgtest [22:27:40]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [22:27:40]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rjpolf4r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tm-align --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tm-align/20190822+dfsg-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-29.secgroup --name adt-plucky-arm64-tm-align-20241101-222740-juju-7f2275-prod-proposed-migration-environment-15-b7c0c425-f018-4426-8d50-c486d904718f --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 64s autopkgtest [22:28:44]: testbed dpkg architecture: arm64 64s autopkgtest [22:28:44]: testbed apt version: 2.9.8 64s autopkgtest [22:28:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 65s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [176 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [41.0 kB] 66s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 66s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [2639 kB] 66s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [230 kB] 66s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 66s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [1932 kB] 66s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [34.6 kB] 67s Fetched 5184 kB in 1s (4333 kB/s) 67s Reading package lists... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Calculating upgrade... 71s The following packages will be upgraded: 71s libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 libblockdev-mdraid3 71s libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 libblockdev-utils3 71s libblockdev3 libevdev2 libftdi1-2 libinih1 libpipeline1 nano 71s python3-lazr.uri 72s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 594 kB of archives. 72s After this operation, 19.5 kB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libevdev2 arm64 1.13.3+dfsg-1 [36.0 kB] 72s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpipeline1 arm64 1.5.8-1 [30.6 kB] 72s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 nano arm64 8.2-1 [289 kB] 72s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-utils3 arm64 3.2.0-2 [18.8 kB] 72s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-crypto3 arm64 3.2.0-2 [22.6 kB] 72s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-fs3 arm64 3.2.0-2 [35.8 kB] 72s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-loop3 arm64 3.2.0-2 [7276 B] 72s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-mdraid3 arm64 3.2.0-2 [12.8 kB] 72s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-nvme3 arm64 3.2.0-2 [17.2 kB] 72s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-part3 arm64 3.2.0-2 [14.9 kB] 72s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev-swap3 arm64 3.2.0-2 [7832 B] 72s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libblockdev3 arm64 3.2.0-2 [52.4 kB] 72s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libftdi1-2 arm64 1.5-7 [28.4 kB] 72s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libinih1 arm64 58-1ubuntu1 [7412 B] 72s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-lazr.uri all 1.0.6-4 [13.6 kB] 72s Fetched 594 kB in 1s (1049 kB/s) 73s (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 ... 79705 files and directories currently installed.) 73s Preparing to unpack .../00-libevdev2_1.13.3+dfsg-1_arm64.deb ... 73s Unpacking libevdev2:arm64 (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 73s Preparing to unpack .../01-libpipeline1_1.5.8-1_arm64.deb ... 73s Unpacking libpipeline1:arm64 (1.5.8-1) over (1.5.7-2) ... 73s Preparing to unpack .../02-nano_8.2-1_arm64.deb ... 73s Unpacking nano (8.2-1) over (8.1-1) ... 73s Preparing to unpack .../03-libblockdev-utils3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-utils3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../04-libblockdev-crypto3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-crypto3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../05-libblockdev-fs3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-fs3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../06-libblockdev-loop3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-loop3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../07-libblockdev-mdraid3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-mdraid3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../08-libblockdev-nvme3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-nvme3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../09-libblockdev-part3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-part3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../10-libblockdev-swap3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev-swap3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../11-libblockdev3_3.2.0-2_arm64.deb ... 73s Unpacking libblockdev3:arm64 (3.2.0-2) over (3.1.1-2) ... 73s Preparing to unpack .../12-libftdi1-2_1.5-7_arm64.deb ... 73s Unpacking libftdi1-2:arm64 (1.5-7) over (1.5-6build5) ... 73s Preparing to unpack .../13-libinih1_58-1ubuntu1_arm64.deb ... 73s Unpacking libinih1:arm64 (58-1ubuntu1) over (55-1ubuntu2) ... 73s Preparing to unpack .../14-python3-lazr.uri_1.0.6-4_all.deb ... 74s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 74s Setting up libpipeline1:arm64 (1.5.8-1) ... 74s Setting up libinih1:arm64 (58-1ubuntu1) ... 74s Setting up python3-lazr.uri (1.0.6-4) ... 74s Setting up libftdi1-2:arm64 (1.5-7) ... 74s Setting up libblockdev-utils3:arm64 (3.2.0-2) ... 74s Setting up libblockdev-nvme3:arm64 (3.2.0-2) ... 74s Setting up nano (8.2-1) ... 74s Setting up libblockdev-fs3:arm64 (3.2.0-2) ... 74s Setting up libevdev2:arm64 (1.13.3+dfsg-1) ... 74s Setting up libblockdev-mdraid3:arm64 (3.2.0-2) ... 74s Setting up libblockdev-crypto3:arm64 (3.2.0-2) ... 74s Setting up libblockdev-swap3:arm64 (3.2.0-2) ... 74s Setting up libblockdev-loop3:arm64 (3.2.0-2) ... 74s Setting up libblockdev3:arm64 (3.2.0-2) ... 74s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 74s Setting up libblockdev-part3:arm64 (3.2.0-2) ... 74s Processing triggers for libc-bin (2.40-1ubuntu3) ... 74s Processing triggers for man-db (2.12.1-3) ... 75s Processing triggers for install-info (7.1.1-1) ... 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 77s Reading package lists... 77s Reading package lists... 78s Building dependency tree... 78s Reading state information... 78s Calculating upgrade... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 80s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [22:29:04]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 84s autopkgtest [22:29:04]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 85s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 86s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 86s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 86s gpgv: issuer "tille@debian.org" 86s gpgv: Can't check signature: No public key 86s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 86s autopkgtest [22:29:06]: testing package tm-align version 20190822+dfsg-3 86s autopkgtest [22:29:06]: build not needed 87s autopkgtest [22:29:07]: test run-unit-test: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s Starting pkgProblemResolver with broken count: 0 89s Starting 2 pkgProblemResolver with broken count: 0 89s Done 89s The following additional packages will be installed: 89s libgfortran5 tm-align 89s Suggested packages: 89s pymol rasmol 90s The following NEW packages will be installed: 90s autopkgtest-satdep libgfortran5 tm-align 90s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 1305 kB/1306 kB of archives. 90s After this operation, 2775 kB of additional disk space will be used. 90s Get:1 /tmp/autopkgtest.z9kDu1/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 90s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 90s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 tm-align arm64 20190822+dfsg-3 [868 kB] 91s Fetched 1305 kB in 1s (1994 kB/s) 91s Selecting previously unselected package libgfortran5:arm64. 91s (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 ... 79705 files and directories currently installed.) 91s Preparing to unpack .../libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 91s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 91s Selecting previously unselected package tm-align. 91s Preparing to unpack .../tm-align_20190822+dfsg-3_arm64.deb ... 91s Unpacking tm-align (20190822+dfsg-3) ... 91s Selecting previously unselected package autopkgtest-satdep. 91s Preparing to unpack .../1-autopkgtest-satdep.deb ... 91s Unpacking autopkgtest-satdep (0) ... 91s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 91s Setting up tm-align (20190822+dfsg-3) ... 91s Setting up autopkgtest-satdep (0) ... 91s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for libc-bin (2.40-1ubuntu3) ... 94s (Reading database ... 79721 files and directories currently installed.) 94s Removing autopkgtest-satdep (0) ... 95s autopkgtest [22:29:15]: test run-unit-test: [----------------------- 95s Run TMalign... 95s 95s ************************************************************************** 95s * TM-align (Version 20190822) * 95s * An algorithm for protein structure alignment and comparison * 95s * Based on statistics: * 95s * 0.0 < TM-score < 0.30, random structural similarity * 95s * 0.5 < TM-score < 1.00, in about the same fold * 95s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 95s * Please email your comments and suggestions to: zhng@umich.edu * 95s ************************************************************************** 95s 95s Name of Chain_1: 1ni7.pdb 95s Name of Chain_2: 5eep.pdb 95s Length of Chain_1: 149 residues 95s Length of Chain_2: 140 residues 95s 95s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 95s TM-score= 0.85044 (if normalized by length of Chain_1) 95s TM-score= 0.90009 (if normalized by length of Chain_2) 95s (You should use TM-score normalized by length of the reference protein) 95s 95s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 95s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 95s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 95s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 95s 95s Run TMscore... 95s 95s ***************************************************************************** 95s * TM-SCORE * 95s * A scoring function to assess the similarity of protein structures * 95s * Based on statistics: * 95s * 0.0 < TM-score < 0.17, random structural similarity * 95s * 0.5 < TM-score < 1.00, in about the same fold * 95s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 95s * For comments, please email to: zhng@umich.edu * 95s ***************************************************************************** 95s 95s Structure1: 1ni7.pdb Length= 149 95s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 95s Number of residues in common= 140 95s RMSD of the common residues= 1.616 95s 95s TM-score = 0.8987 (d0= 4.40) 95s MaxSub-score= 0.8459 (d0= 3.50) 95s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 95s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 95s 95s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 95s i t(i) u(i,1) u(i,2) u(i,3) 95s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 95s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 95s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 95s 95s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 95s (":" denotes the residue pairs of distance < 5.0 Angstrom) 95s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 95s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 95s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 95s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 95s 95s autopkgtest [22:29:15]: test run-unit-test: -----------------------] 96s autopkgtest [22:29:16]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 96s run-unit-test PASS 96s autopkgtest [22:29:16]: @@@@@@@@@@@@@@@@@@@@ summary 96s run-unit-test PASS 108s nova [W] Skipping flock in bos03-arm64 108s Creating nova instance adt-plucky-arm64-tm-align-20241101-222740-juju-7f2275-prod-proposed-migration-environment-15-b7c0c425-f018-4426-8d50-c486d904718f from image adt/ubuntu-plucky-arm64-server-20241101.img (UUID 520a937f-514a-4e80-b76b-163a8c247e3e)...