0s autopkgtest [20:24:03]: starting date and time: 2024-11-04 20:24:03+0000 0s autopkgtest [20:24:03]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [20:24:03]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q6sjrzma/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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.9 lxd-armhf-10.145.243.9:autopkgtest/ubuntu/plucky/armhf 51s autopkgtest [20:24:54]: testbed dpkg architecture: armhf 53s autopkgtest [20:24:56]: testbed apt version: 2.9.8 53s autopkgtest [20:24:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 61s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 61s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 61s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [1876 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [22.1 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [178 kB] 62s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [219 kB] 62s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [1379 kB] 62s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [21.4 kB] 62s Fetched 3777 kB in 1s (3052 kB/s) 62s Reading package lists... 79s tee: /proc/self/fd/2: Permission denied 100s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 100s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 100s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 100s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 101s Reading package lists... 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 103s The following packages were automatically installed and are no longer required: 103s libperl5.38t64 perl-modules-5.38 103s Use 'apt autoremove' to remove them. 103s The following NEW packages will be installed: 103s libperl5.40 perl-modules-5.40 103s The following packages will be upgraded: 103s base-files distro-info-data fwupd gcc-14-base info install-info iproute2 103s libatomic1 libblockdev-crypto3 libblockdev-fs3 libblockdev-loop3 103s libblockdev-mdraid3 libblockdev-nvme3 libblockdev-part3 libblockdev-swap3 103s libblockdev-utils3 libblockdev3 libdb5.3t64 libdw1t64 libelf1t64 libevdev2 103s libftdi1-2 libfwupd2 libgcc-s1 libinih1 libkeyutils1 liblocale-gettext-perl 103s libpipeline1 libsgutils2-1.46-2 libstdc++6 libtext-charwidth-perl 103s libtext-iconv-perl libtraceevent1 libtraceevent1-plugin motd-news-config 103s nano perl perl-base python3-configobj python3-json-pointer python3-lazr.uri 103s python3-oauthlib python3-zipp sg3-utils sg3-utils-udev vim-common vim-tiny 103s xxd 103s 48 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 19.8 MB of archives. 103s After this operation, 42.8 MB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf motd-news-config all 13.5ubuntu2 [5274 B] 103s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf base-files armhf 13.5ubuntu2 [68.6 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf perl-modules-5.40 all 5.40.0-6 [3214 kB] 104s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libperl5.40 armhf 5.40.0-6 [4140 kB] 104s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf perl armhf 5.40.0-6 [262 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf perl-base armhf 5.40.0-6 [1674 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblocale-gettext-perl armhf 1.07-7build1 [15.0 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-iconv-perl armhf 1.7-8build4 [12.8 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libtext-charwidth-perl armhf 0.04-11build4 [9128 B] 104s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-9 [655 kB] 104s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libatomic1 armhf 14.2.0-7ubuntu1 [7842 B] 104s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf gcc-14-base armhf 14.2.0-7ubuntu1 [51.2 kB] 104s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libstdc++6 armhf 14.2.0-7ubuntu1 [711 kB] 104s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf libgcc-s1 armhf 14.2.0-7ubuntu1 [40.8 kB] 104s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf install-info armhf 7.1.1-1 [61.4 kB] 104s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf distro-info-data all 0.63 [6588 B] 104s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf libdw1t64 armhf 0.192-4 [243 kB] 104s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf libelf1t64 armhf 0.192-4 [50.2 kB] 104s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf iproute2 armhf 6.10.0-2ubuntu1 [1082 kB] 104s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf libkeyutils1 armhf 1.6.3-4ubuntu2 [8712 B] 104s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf vim-tiny armhf 2:9.1.0777-1ubuntu1 [693 kB] 104s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf vim-common all 2:9.1.0777-1ubuntu1 [394 kB] 104s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf xxd armhf 2:9.1.0777-1ubuntu1 [66.8 kB] 104s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf info armhf 7.1.1-1 [126 kB] 104s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf libevdev2 armhf 1.13.3+dfsg-1 [29.7 kB] 104s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf libpipeline1 armhf 1.5.8-1 [26.9 kB] 104s Get:27 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1-plugin armhf 1:1.8.3-1ubuntu1 [18.1 kB] 104s Get:28 http://ftpmaster.internal/ubuntu plucky/main armhf libtraceevent1 armhf 1:1.8.3-1ubuntu1 [52.1 kB] 104s Get:29 http://ftpmaster.internal/ubuntu plucky/main armhf nano armhf 8.2-1 [276 kB] 104s Get:30 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd2 armhf 1.9.26-2 [125 kB] 104s Get:31 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 1.9.26-2 [4404 kB] 104s Get:32 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-utils3 armhf 3.2.0-2 [17.4 kB] 104s Get:33 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-crypto3 armhf 3.2.0-2 [22.3 kB] 104s Get:34 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-fs3 armhf 3.2.0-2 [34.3 kB] 104s Get:35 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-loop3 armhf 3.2.0-2 [6552 B] 104s Get:36 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-mdraid3 armhf 3.2.0-2 [13.4 kB] 104s Get:37 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-nvme3 armhf 3.2.0-2 [17.6 kB] 104s Get:38 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-part3 armhf 3.2.0-2 [16.5 kB] 104s Get:39 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev-swap3 armhf 3.2.0-2 [8942 B] 104s Get:40 http://ftpmaster.internal/ubuntu plucky/main armhf libblockdev3 armhf 3.2.0-2 [44.2 kB] 104s Get:41 http://ftpmaster.internal/ubuntu plucky/main armhf libftdi1-2 armhf 1.5-7 [25.7 kB] 104s Get:42 http://ftpmaster.internal/ubuntu plucky/main armhf libinih1 armhf 58-1ubuntu1 [6750 B] 104s Get:43 http://ftpmaster.internal/ubuntu plucky/main armhf libsgutils2-1.46-2 armhf 1.46-3ubuntu5 [82.5 kB] 104s Get:44 http://ftpmaster.internal/ubuntu plucky/main armhf python3-configobj all 5.0.9-1 [33.9 kB] 104s Get:45 http://ftpmaster.internal/ubuntu plucky/main armhf python3-json-pointer all 2.4-2 [8396 B] 104s Get:46 http://ftpmaster.internal/ubuntu plucky/main armhf python3-lazr.uri all 1.0.6-4 [13.6 kB] 104s Get:47 http://ftpmaster.internal/ubuntu plucky/main armhf python3-oauthlib all 3.2.2-2 [89.8 kB] 104s Get:48 http://ftpmaster.internal/ubuntu plucky/main armhf python3-zipp all 3.20.2-1 [10.1 kB] 104s Get:49 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils armhf 1.46-3ubuntu5 [816 kB] 104s Get:50 http://ftpmaster.internal/ubuntu plucky/main armhf sg3-utils-udev all 1.46-3ubuntu5 [5916 B] 105s Preconfiguring packages ... 105s Fetched 19.8 MB in 1s (14.3 MB/s) 105s (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 ... 59386 files and directories currently installed.) 105s Preparing to unpack .../motd-news-config_13.5ubuntu2_all.deb ... 105s Unpacking motd-news-config (13.5ubuntu2) over (13.3ubuntu6) ... 105s Preparing to unpack .../base-files_13.5ubuntu2_armhf.deb ... 105s Unpacking base-files (13.5ubuntu2) over (13.3ubuntu6) ... 105s Setting up base-files (13.5ubuntu2) ... 105s Installing new version of config file /etc/issue ... 105s Installing new version of config file /etc/issue.net ... 105s Installing new version of config file /etc/lsb-release ... 106s motd-news.service is a disabled or a static unit not running, not starting it. 106s (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 ... 59386 files and directories currently installed.) 106s Preparing to unpack .../perl_5.40.0-6_armhf.deb ... 106s Unpacking perl (5.40.0-6) over (5.38.2-5) ... 106s Selecting previously unselected package perl-modules-5.40. 106s Preparing to unpack .../perl-modules-5.40_5.40.0-6_all.deb ... 106s Unpacking perl-modules-5.40 (5.40.0-6) ... 106s Selecting previously unselected package libperl5.40:armhf. 106s Preparing to unpack .../libperl5.40_5.40.0-6_armhf.deb ... 106s Unpacking libperl5.40:armhf (5.40.0-6) ... 106s Preparing to unpack .../perl-base_5.40.0-6_armhf.deb ... 106s Unpacking perl-base (5.40.0-6) over (5.38.2-5) ... 106s Setting up perl-base (5.40.0-6) ... 106s (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 ... 61462 files and directories currently installed.) 106s Preparing to unpack .../liblocale-gettext-perl_1.07-7build1_armhf.deb ... 106s Unpacking liblocale-gettext-perl (1.07-7build1) over (1.07-7) ... 106s Preparing to unpack .../libtext-iconv-perl_1.7-8build4_armhf.deb ... 106s Unpacking libtext-iconv-perl:armhf (1.7-8build4) over (1.7-8build3) ... 107s Preparing to unpack .../libtext-charwidth-perl_0.04-11build4_armhf.deb ... 107s Unpacking libtext-charwidth-perl:armhf (0.04-11build4) over (0.04-11build3) ... 107s Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-9_armhf.deb ... 107s Unpacking libdb5.3t64:armhf (5.3.28+dfsg2-9) over (5.3.28+dfsg2-7) ... 107s Setting up libdb5.3t64:armhf (5.3.28+dfsg2-9) ... 107s (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 ... 61462 files and directories currently installed.) 107s Preparing to unpack .../libatomic1_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking libatomic1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Preparing to unpack .../gcc-14-base_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking gcc-14-base:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Setting up gcc-14-base:armhf (14.2.0-7ubuntu1) ... 107s (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 ... 61462 files and directories currently installed.) 107s Preparing to unpack .../libstdc++6_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking libstdc++6:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Setting up libstdc++6:armhf (14.2.0-7ubuntu1) ... 107s (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 ... 61462 files and directories currently installed.) 107s Preparing to unpack .../libgcc-s1_14.2.0-7ubuntu1_armhf.deb ... 107s Unpacking libgcc-s1:armhf (14.2.0-7ubuntu1) over (14.2.0-4ubuntu2) ... 107s Setting up libgcc-s1:armhf (14.2.0-7ubuntu1) ... 107s (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 ... 61462 files and directories currently installed.) 107s Preparing to unpack .../install-info_7.1.1-1_armhf.deb ... 107s Unpacking install-info (7.1.1-1) over (7.1-3build2) ... 107s Setting up install-info (7.1.1-1) ... 107s (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 ... 61462 files and directories currently installed.) 107s Preparing to unpack .../00-distro-info-data_0.63_all.deb ... 107s Unpacking distro-info-data (0.63) over (0.62) ... 107s Preparing to unpack .../01-libdw1t64_0.192-4_armhf.deb ... 107s Unpacking libdw1t64:armhf (0.192-4) over (0.191-2) ... 107s Preparing to unpack .../02-libelf1t64_0.192-4_armhf.deb ... 107s Unpacking libelf1t64:armhf (0.192-4) over (0.191-2) ... 107s Preparing to unpack .../03-iproute2_6.10.0-2ubuntu1_armhf.deb ... 107s Unpacking iproute2 (6.10.0-2ubuntu1) over (6.10.0-2) ... 107s Preparing to unpack .../04-libkeyutils1_1.6.3-4ubuntu2_armhf.deb ... 107s Unpacking libkeyutils1:armhf (1.6.3-4ubuntu2) over (1.6.3-3build1) ... 107s Preparing to unpack .../05-vim-tiny_2%3a9.1.0777-1ubuntu1_armhf.deb ... 107s Unpacking vim-tiny (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../06-vim-common_2%3a9.1.0777-1ubuntu1_all.deb ... 108s Unpacking vim-common (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../07-xxd_2%3a9.1.0777-1ubuntu1_armhf.deb ... 108s Unpacking xxd (2:9.1.0777-1ubuntu1) over (2:9.1.0496-1ubuntu6) ... 108s Preparing to unpack .../08-info_7.1.1-1_armhf.deb ... 108s Unpacking info (7.1.1-1) over (7.1-3build2) ... 108s Preparing to unpack .../09-libevdev2_1.13.3+dfsg-1_armhf.deb ... 108s Unpacking libevdev2:armhf (1.13.3+dfsg-1) over (1.13.2+dfsg-1) ... 108s Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... 108s Unpacking libpipeline1:armhf (1.5.8-1) over (1.5.7-2) ... 108s Preparing to unpack .../11-libtraceevent1-plugin_1%3a1.8.3-1ubuntu1_armhf.deb ... 108s Unpacking libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) over (1:1.8.2-1ubuntu3) ... 108s Preparing to unpack .../12-libtraceevent1_1%3a1.8.3-1ubuntu1_armhf.deb ... 108s Unpacking libtraceevent1:armhf (1:1.8.3-1ubuntu1) over (1:1.8.2-1ubuntu3) ... 108s Preparing to unpack .../13-nano_8.2-1_armhf.deb ... 108s Unpacking nano (8.2-1) over (8.1-1) ... 108s Preparing to unpack .../14-libfwupd2_1.9.26-2_armhf.deb ... 108s Unpacking libfwupd2:armhf (1.9.26-2) over (1.9.24-1) ... 108s Preparing to unpack .../15-fwupd_1.9.26-2_armhf.deb ... 108s Unpacking fwupd (1.9.26-2) over (1.9.24-1) ... 108s Preparing to unpack .../16-libblockdev-utils3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-utils3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../17-libblockdev-crypto3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-crypto3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../18-libblockdev-fs3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-fs3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../19-libblockdev-loop3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-loop3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../20-libblockdev-mdraid3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-mdraid3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../21-libblockdev-nvme3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-nvme3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../22-libblockdev-part3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-part3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../23-libblockdev-swap3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev-swap3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../24-libblockdev3_3.2.0-2_armhf.deb ... 108s Unpacking libblockdev3:armhf (3.2.0-2) over (3.1.1-2) ... 108s Preparing to unpack .../25-libftdi1-2_1.5-7_armhf.deb ... 108s Unpacking libftdi1-2:armhf (1.5-7) over (1.5-6build5) ... 108s Preparing to unpack .../26-libinih1_58-1ubuntu1_armhf.deb ... 108s Unpacking libinih1:armhf (58-1ubuntu1) over (55-1ubuntu2) ... 108s Preparing to unpack .../27-libsgutils2-1.46-2_1.46-3ubuntu5_armhf.deb ... 108s Unpacking libsgutils2-1.46-2:armhf (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 108s Preparing to unpack .../28-python3-configobj_5.0.9-1_all.deb ... 108s Unpacking python3-configobj (5.0.9-1) over (5.0.8-3) ... 109s Preparing to unpack .../29-python3-json-pointer_2.4-2_all.deb ... 109s Unpacking python3-json-pointer (2.4-2) over (2.0-0ubuntu1) ... 109s Preparing to unpack .../30-python3-lazr.uri_1.0.6-4_all.deb ... 109s Unpacking python3-lazr.uri (1.0.6-4) over (1.0.6-3) ... 109s Preparing to unpack .../31-python3-oauthlib_3.2.2-2_all.deb ... 109s Unpacking python3-oauthlib (3.2.2-2) over (3.2.2-1) ... 109s Preparing to unpack .../32-python3-zipp_3.20.2-1_all.deb ... 109s Unpacking python3-zipp (3.20.2-1) over (3.20.0-1) ... 109s Preparing to unpack .../33-sg3-utils_1.46-3ubuntu5_armhf.deb ... 109s Unpacking sg3-utils (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 109s Preparing to unpack .../34-sg3-utils-udev_1.46-3ubuntu5_all.deb ... 109s Unpacking sg3-utils-udev (1.46-3ubuntu5) over (1.46-3ubuntu4) ... 109s Setting up libpipeline1:armhf (1.5.8-1) ... 109s Setting up motd-news-config (13.5ubuntu2) ... 109s Setting up libtext-iconv-perl:armhf (1.7-8build4) ... 109s Setting up libtext-charwidth-perl:armhf (0.04-11build4) ... 109s Setting up libkeyutils1:armhf (1.6.3-4ubuntu2) ... 109s Setting up distro-info-data (0.63) ... 109s Setting up libinih1:armhf (58-1ubuntu1) ... 109s Setting up libfwupd2:armhf (1.9.26-2) ... 109s Setting up libsgutils2-1.46-2:armhf (1.46-3ubuntu5) ... 109s Setting up python3-lazr.uri (1.0.6-4) ... 109s Setting up python3-zipp (3.20.2-1) ... 109s Setting up xxd 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disabled or a static unit not running, not starting it. 110s fwupd.service is a disabled or a static unit not running, not starting it. 110s Setting up info (7.1.1-1) ... 110s Setting up liblocale-gettext-perl (1.07-7build1) ... 110s Setting up sg3-utils (1.46-3ubuntu5) ... 110s Setting up libblockdev-mdraid3:armhf (3.2.0-2) ... 110s Setting up libblockdev-crypto3:armhf (3.2.0-2) ... 110s Setting up libblockdev-swap3:armhf (3.2.0-2) ... 110s Setting up iproute2 (6.10.0-2ubuntu1) ... 110s Setting up libblockdev-loop3:armhf (3.2.0-2) ... 110s Setting up vim-tiny (2:9.1.0777-1ubuntu1) ... 110s Setting up libblockdev3:armhf (3.2.0-2) ... 110s Installing new version of config file /etc/libblockdev/3/conf.d/00-default.cfg ... 110s Setting up libblockdev-part3:armhf (3.2.0-2) ... 110s Setting up sg3-utils-udev (1.46-3ubuntu5) ... 110s update-initramfs: deferring update (trigger activated) 110s Setting up libperl5.40:armhf (5.40.0-6) ... 110s Setting up perl (5.40.0-6) ... 110s Setting up libtraceevent1-plugin:armhf (1:1.8.3-1ubuntu1) ... 110s Processing triggers for initramfs-tools (0.142ubuntu34) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Processing triggers for man-db (2.12.1-3) ... 112s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu10) ... 112s update-initramfs: deferring update (trigger activated) 112s Processing triggers for dbus (1.14.10-4ubuntu5) ... 112s Processing triggers for install-info (7.1.1-1) ... 112s Processing triggers for initramfs-tools (0.142ubuntu34) ... 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s The following packages will be REMOVED: 113s libperl5.38t64* perl-modules-5.38* 114s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 114s After this operation, 41.6 MB disk space will be freed. 114s (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 ... 61462 files and directories currently installed.) 114s Removing libperl5.38t64:armhf (5.38.2-5) ... 114s Removing perl-modules-5.38 (5.38.2-5) ... 114s Processing triggers for man-db (2.12.1-3) ... 114s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s autopkgtest [20:25:59]: rebooting testbed after setup commands that affected boot 184s autopkgtest [20:27:07]: testbed running kernel: Linux 6.8.0-47-generic #47~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Oct 2 16:39:14 UTC 2 209s autopkgtest [20:27:32]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 219s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 219s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 219s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 219s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 219s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 219s gpgv: issuer "tille@debian.org" 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 220s autopkgtest [20:27:43]: testing package tm-align version 20190822+dfsg-3 222s autopkgtest [20:27:45]: build not needed 224s autopkgtest [20:27:47]: test run-unit-test: preparing testbed 233s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s Starting pkgProblemResolver with broken count: 0 234s Starting 2 pkgProblemResolver with broken count: 0 234s Done 235s The following additional packages will be installed: 235s libgfortran5 tm-align 235s Suggested packages: 235s pymol rasmol 235s The following NEW packages will be installed: 235s autopkgtest-satdep libgfortran5 tm-align 235s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 1182 kB/1182 kB of archives. 235s After this operation, 2114 kB of additional disk space will be used. 235s Get:1 /tmp/autopkgtest.VZN07m/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [704 B] 235s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-7ubuntu1 [311 kB] 235s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf tm-align armhf 20190822+dfsg-3 [871 kB] 236s Fetched 1182 kB in 1s (1905 kB/s) 236s Selecting previously unselected package libgfortran5:armhf. 236s (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 ... 59532 files and directories currently installed.) 236s Preparing to unpack .../libgfortran5_14.2.0-7ubuntu1_armhf.deb ... 236s Unpacking libgfortran5:armhf (14.2.0-7ubuntu1) ... 236s Selecting previously unselected package tm-align. 236s Preparing to unpack .../tm-align_20190822+dfsg-3_armhf.deb ... 236s Unpacking tm-align (20190822+dfsg-3) ... 236s Selecting previously unselected package autopkgtest-satdep. 236s Preparing to unpack .../1-autopkgtest-satdep.deb ... 236s Unpacking autopkgtest-satdep (0) ... 236s Setting up libgfortran5:armhf (14.2.0-7ubuntu1) ... 236s Setting up tm-align (20190822+dfsg-3) ... 236s Setting up autopkgtest-satdep (0) ... 236s Processing triggers for man-db (2.12.1-3) ... 236s Processing triggers for libc-bin (2.40-1ubuntu3) ... 248s (Reading database ... 59548 files and directories currently installed.) 248s Removing autopkgtest-satdep (0) ... 254s autopkgtest [20:28:17]: test run-unit-test: [----------------------- 255s Run TMalign... 255s 255s ************************************************************************** 255s * TM-align (Version 20190822) * 255s * An algorithm for protein structure alignment and comparison * 255s * Based on statistics: * 255s * 0.0 < TM-score < 0.30, random structural similarity * 255s * 0.5 < TM-score < 1.00, in about the same fold * 255s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 255s * Please email your comments and suggestions to: zhng@umich.edu * 255s ************************************************************************** 255s 255s Name of Chain_1: 1ni7.pdb 255s Name of Chain_2: 5eep.pdb 255s Length of Chain_1: 149 residues 255s Length of Chain_2: 140 residues 255s 255s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 255s TM-score= 0.85044 (if normalized by length of Chain_1) 255s TM-score= 0.90009 (if normalized by length of Chain_2) 255s (You should use TM-score normalized by length of the reference protein) 255s 255s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 255s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 255s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 255s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 255s 255s Run TMscore... 255s 255s ***************************************************************************** 255s * TM-SCORE * 255s * A scoring function to assess the similarity of protein structures * 255s * Based on statistics: * 255s * 0.0 < TM-score < 0.17, random structural similarity * 255s * 0.5 < TM-score < 1.00, in about the same fold * 255s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 255s * For comments, please email to: zhng@umich.edu * 255s ***************************************************************************** 255s 255s Structure1: 1ni7.pdb Length= 149 255s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 255s Number of residues in common= 140 255s RMSD of the common residues= 1.616 255s 255s TM-score = 0.8987 (d0= 4.40) 255s MaxSub-score= 0.8459 (d0= 3.50) 255s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 255s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 255s 255s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 255s i t(i) u(i,1) u(i,2) u(i,3) 255s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 255s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 255s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 255s 255s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 255s (":" denotes the residue pairs of distance < 5.0 Angstrom) 255s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 255s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 255s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 255s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 255s 256s autopkgtest [20:28:19]: test run-unit-test: -----------------------] 261s run-unit-test PASS 261s autopkgtest [20:28:24]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s autopkgtest [20:28:28]: @@@@@@@@@@@@@@@@@@@@ summary 265s run-unit-test PASS