0s autopkgtest [05:41:21]: starting date and time: 2026-02-05 05:41:21+0000 0s autopkgtest [05:41:21]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [05:41:21]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sw0to6gs/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,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade librostlab-blast --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- lxd -r lxd-armhf-10.145.243.107 lxd-armhf-10.145.243.107:autopkgtest/ubuntu/resolute/armhf 27s autopkgtest [05:41:48]: testbed dpkg architecture: armhf 29s autopkgtest [05:41:50]: testbed apt version: 3.1.14 33s autopkgtest [05:41:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [05:41:56]: testbed release detected to be: None 43s autopkgtest [05:42:04]: updating testbed package index (apt update) 46s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 46s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [124 kB] 46s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 46s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 46s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 49s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 49s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [228 kB] 49s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [253 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [1418 kB] 52s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9664 B] 52s Get:12 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 84s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1400 kB] 85s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1374 kB] 86s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.1 MB] 104s Fetched 43.1 MB in 58s (740 kB/s) 105s Reading package lists... 110s autopkgtest [05:43:11]: upgrading testbed (apt dist-upgrade and autopurge) 112s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 114s The following packages will be upgraded: 114s libc-bin libc-gconv-modules-extra libc6 locales 114s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 7850 kB of archives. 114s After this operation, 0 B of additional disk space will be used. 114s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-gconv-modules-extra armhf 2.42-2ubuntu5 [1417 kB] 116s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6 armhf 2.42-2ubuntu5 [1632 kB] 118s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-bin armhf 2.42-2ubuntu5 [545 kB] 119s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf locales all 2.42-2ubuntu5 [4255 kB] 125s Preconfiguring packages ... 126s Fetched 7850 kB in 11s (705 kB/s) 126s (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 ... 68395 files and directories currently installed.) 126s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_armhf.deb ... 126s Unpacking libc-gconv-modules-extra:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 126s Setting up libc-gconv-modules-extra:armhf (2.42-2ubuntu5) ... 126s (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 ... 68395 files and directories currently installed.) 126s Preparing to unpack .../libc6_2.42-2ubuntu5_armhf.deb ... 126s readlink: /usr/lib/libeatmydata: No such file or directory 126s Unpacking libc6:armhf (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 126s Setting up libc6:armhf (2.42-2ubuntu5) ... 127s (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 ... 68395 files and directories currently installed.) 127s Preparing to unpack .../libc-bin_2.42-2ubuntu5_armhf.deb ... 127s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 127s Setting up libc-bin (2.42-2ubuntu5) ... 127s (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 ... 68395 files and directories currently installed.) 127s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 127s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 127s Setting up locales (2.42-2ubuntu5) ... 128s Generating locales (this might take a while)... 131s en_US.UTF-8... done 131s Generation complete. 131s Processing triggers for systemd (259-1ubuntu3) ... 131s Processing triggers for man-db (2.13.1-1) ... 134s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Solving dependencies... 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s autopkgtest [05:43:38]: rebooting testbed after setup commands that affected boot 179s autopkgtest [05:44:20]: testbed running kernel: Linux 6.8.0-87-generic #88~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Oct 14 14:00:09 UTC 2 204s autopkgtest [05:44:45]: @@@@@@@@@@@@@@@@@@@@ apt-source librostlab-blast 223s Get:1 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (dsc) [2562 B] 223s Get:2 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (tar) [384 kB] 223s Get:3 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (diff) [6716 B] 223s gpgv: Signature made Wed Apr 24 11:20:29 2024 UTC 223s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 223s gpgv: issuer "emollier@debian.org" 223s gpgv: Can't check signature: No public key 223s dpkg-source: warning: cannot verify inline signature for ./librostlab-blast_1.0.1-14.dsc: no acceptable signature found 223s autopkgtest [05:45:04]: testing package librostlab-blast version 1.0.1-14 225s autopkgtest [05:45:06]: build not needed 228s autopkgtest [05:45:09]: test run-unit-test: preparing testbed 230s Reading package lists... 230s Building dependency tree... 230s Reading state information... 230s Solving dependencies... 231s The following NEW packages will be installed: 231s build-essential cpp cpp-15 cpp-15-arm-linux-gnueabihf 231s cpp-arm-linux-gnueabihf g++ g++-15 g++-15-arm-linux-gnueabihf 231s g++-arm-linux-gnueabihf gcc gcc-15 gcc-15-arm-linux-gnueabihf 231s gcc-arm-linux-gnueabihf libasan8 libc-dev-bin libc6-dev libcc1-0 231s libcrypt-dev libgcc-15-dev libgomp1 libisl23 libjs-jquery libmpc3 231s librostlab-blast-doc librostlab-blast0-dev librostlab-blast0v5 231s librostlab3-dev librostlab3t64 libstdc++-15-dev libubsan1 linux-libc-dev 231s rpcsvc-proto 231s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 231s Need to get 54.4 MB of archives. 231s After this operation, 159 MB of additional disk space will be used. 231s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc-dev-bin armhf 2.42-2ubuntu5 [21.8 kB] 231s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf linux-libc-dev armhf 6.18.0-9.9 [1819 kB] 235s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libcrypt-dev armhf 1:4.5.1-1 [128 kB] 235s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf rpcsvc-proto armhf 1.4.3-1build1 [62.6 kB] 235s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libc6-dev armhf 2.42-2ubuntu5 [1416 kB] 237s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libisl23 armhf 0.27-1build1 [553 kB] 238s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf libmpc3 armhf 1.3.1-2 [47.0 kB] 238s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [10.1 MB] 254s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-15 armhf 15.2.0-12ubuntu1 [1032 B] 254s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf cpp-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [5756 B] 254s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf cpp armhf 4:15.2.0-4ubuntu1 [22.4 kB] 254s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libcc1-0 armhf 15.2.0-12ubuntu1 [43.5 kB] 254s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libgomp1 armhf 15.2.0-12ubuntu1 [129 kB] 254s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libasan8 armhf 15.2.0-12ubuntu1 [2949 kB] 258s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libubsan1 armhf 15.2.0-12ubuntu1 [1187 kB] 260s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-15-dev armhf 15.2.0-12ubuntu1 [898 kB] 261s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [19.5 MB] 283s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15 armhf 15.2.0-12ubuntu1 [499 kB] 283s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [1220 B] 283s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf gcc armhf 4:15.2.0-4ubuntu1 [5022 B] 283s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++-15-dev armhf 15.2.0-12ubuntu1 [2638 kB] 286s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15-arm-linux-gnueabihf armhf 15.2.0-12ubuntu1 [11.4 MB] 296s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf g++-15 armhf 15.2.0-12ubuntu1 [25.3 kB] 296s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf g++-arm-linux-gnueabihf armhf 4:15.2.0-4ubuntu1 [968 B] 296s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf g++ armhf 4:15.2.0-4ubuntu1 [1086 B] 296s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf build-essential armhf 12.12ubuntu2 [5256 B] 296s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 296s Get:28 http://ftpmaster.internal/ubuntu resolute/universe armhf librostlab-blast-doc all 1.0.1-14 [421 kB] 296s Get:29 http://ftpmaster.internal/ubuntu resolute/universe armhf librostlab-blast0v5 armhf 1.0.1-14 [86.1 kB] 296s Get:30 http://ftpmaster.internal/ubuntu resolute/universe armhf librostlab3t64 armhf 1.0.20-14 [5100 B] 296s Get:31 http://ftpmaster.internal/ubuntu resolute/universe armhf librostlab3-dev armhf 1.0.20-14 [11.4 kB] 296s Get:32 http://ftpmaster.internal/ubuntu resolute/universe armhf librostlab-blast0-dev armhf 1.0.1-14 [104 kB] 297s Fetched 54.4 MB in 1min 5s (833 kB/s) 297s Selecting previously unselected package libc-dev-bin. 297s (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 ... 68395 files and directories currently installed.) 297s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu5_armhf.deb ... 297s Unpacking libc-dev-bin (2.42-2ubuntu5) ... 297s Selecting previously unselected package linux-libc-dev:armhf. 297s Preparing to unpack .../01-linux-libc-dev_6.18.0-9.9_armhf.deb ... 297s Unpacking linux-libc-dev:armhf (6.18.0-9.9) ... 297s Selecting previously unselected package libcrypt-dev:armhf. 297s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_armhf.deb ... 297s Unpacking libcrypt-dev:armhf (1:4.5.1-1) ... 297s Selecting previously unselected package rpcsvc-proto. 297s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_armhf.deb ... 297s Unpacking rpcsvc-proto (1.4.3-1build1) ... 297s Selecting previously unselected package libc6-dev:armhf. 297s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu5_armhf.deb ... 297s Unpacking libc6-dev:armhf (2.42-2ubuntu5) ... 298s Selecting previously unselected package libisl23:armhf. 298s Preparing to unpack .../05-libisl23_0.27-1build1_armhf.deb ... 298s Unpacking libisl23:armhf (0.27-1build1) ... 298s Selecting previously unselected package libmpc3:armhf. 298s Preparing to unpack .../06-libmpc3_1.3.1-2_armhf.deb ... 298s Unpacking libmpc3:armhf (1.3.1-2) ... 298s Selecting previously unselected package cpp-15-arm-linux-gnueabihf. 298s Preparing to unpack .../07-cpp-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package cpp-15. 298s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package cpp-arm-linux-gnueabihf. 298s Preparing to unpack .../09-cpp-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 298s Unpacking cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 298s Selecting previously unselected package cpp. 298s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_armhf.deb ... 298s Unpacking cpp (4:15.2.0-4ubuntu1) ... 298s Selecting previously unselected package libcc1-0:armhf. 298s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking libcc1-0:armhf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package libgomp1:armhf. 298s Preparing to unpack .../12-libgomp1_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking libgomp1:armhf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package libasan8:armhf. 298s Preparing to unpack .../13-libasan8_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking libasan8:armhf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package libubsan1:armhf. 298s Preparing to unpack .../14-libubsan1_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking libubsan1:armhf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package libgcc-15-dev:armhf. 298s Preparing to unpack .../15-libgcc-15-dev_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 298s Selecting previously unselected package gcc-15-arm-linux-gnueabihf. 298s Preparing to unpack .../16-gcc-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 298s Unpacking gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 299s Selecting previously unselected package gcc-15. 299s Preparing to unpack .../17-gcc-15_15.2.0-12ubuntu1_armhf.deb ... 299s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 299s Selecting previously unselected package gcc-arm-linux-gnueabihf. 299s Preparing to unpack .../18-gcc-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 299s Unpacking gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 299s Selecting previously unselected package gcc. 299s Preparing to unpack .../19-gcc_4%3a15.2.0-4ubuntu1_armhf.deb ... 299s Unpacking gcc (4:15.2.0-4ubuntu1) ... 299s Selecting previously unselected package libstdc++-15-dev:armhf. 299s Preparing to unpack .../20-libstdc++-15-dev_15.2.0-12ubuntu1_armhf.deb ... 299s Unpacking libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 299s Selecting previously unselected package g++-15-arm-linux-gnueabihf. 299s Preparing to unpack .../21-g++-15-arm-linux-gnueabihf_15.2.0-12ubuntu1_armhf.deb ... 299s Unpacking g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 300s Selecting previously unselected package g++-15. 300s Preparing to unpack .../22-g++-15_15.2.0-12ubuntu1_armhf.deb ... 300s Unpacking g++-15 (15.2.0-12ubuntu1) ... 300s Selecting previously unselected package g++-arm-linux-gnueabihf. 300s Preparing to unpack .../23-g++-arm-linux-gnueabihf_4%3a15.2.0-4ubuntu1_armhf.deb ... 300s Unpacking g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 300s Selecting previously unselected package g++. 300s Preparing to unpack .../24-g++_4%3a15.2.0-4ubuntu1_armhf.deb ... 300s Unpacking g++ (4:15.2.0-4ubuntu1) ... 300s Selecting previously unselected package build-essential. 300s Preparing to unpack .../25-build-essential_12.12ubuntu2_armhf.deb ... 300s Unpacking build-essential (12.12ubuntu2) ... 300s Selecting previously unselected package libjs-jquery. 300s Preparing to unpack .../26-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 300s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 300s Selecting previously unselected package librostlab-blast-doc. 300s Preparing to unpack .../27-librostlab-blast-doc_1.0.1-14_all.deb ... 300s Unpacking librostlab-blast-doc (1.0.1-14) ... 300s Selecting previously unselected package librostlab-blast0v5:armhf. 300s Preparing to unpack .../28-librostlab-blast0v5_1.0.1-14_armhf.deb ... 300s Unpacking librostlab-blast0v5:armhf (1.0.1-14) ... 300s Selecting previously unselected package librostlab3t64:armhf. 300s Preparing to unpack .../29-librostlab3t64_1.0.20-14_armhf.deb ... 300s Unpacking librostlab3t64:armhf (1.0.20-14) ... 300s Selecting previously unselected package librostlab3-dev. 300s Preparing to unpack .../30-librostlab3-dev_1.0.20-14_armhf.deb ... 300s Unpacking librostlab3-dev (1.0.20-14) ... 300s Selecting previously unselected package librostlab-blast0-dev. 300s Preparing to unpack .../31-librostlab-blast0-dev_1.0.1-14_armhf.deb ... 300s Unpacking librostlab-blast0-dev (1.0.1-14) ... 300s Setting up librostlab3t64:armhf (1.0.20-14) ... 300s Setting up linux-libc-dev:armhf (6.18.0-9.9) ... 300s Setting up libgomp1:armhf (15.2.0-12ubuntu1) ... 300s Setting up librostlab3-dev (1.0.20-14) ... 300s Setting up rpcsvc-proto (1.4.3-1build1) ... 300s Setting up libmpc3:armhf (1.3.1-2) ... 300s Setting up libubsan1:armhf (15.2.0-12ubuntu1) ... 300s Setting up libcrypt-dev:armhf (1:4.5.1-1) ... 300s Setting up libasan8:armhf (15.2.0-12ubuntu1) ... 300s Setting up librostlab-blast0v5:armhf (1.0.1-14) ... 300s Setting up librostlab-blast0-dev (1.0.1-14) ... 300s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 300s Setting up libisl23:armhf (0.27-1build1) ... 300s Setting up libc-dev-bin (2.42-2ubuntu5) ... 300s Setting up cpp-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 300s Setting up libcc1-0:armhf (15.2.0-12ubuntu1) ... 300s Setting up cpp-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 300s Setting up libgcc-15-dev:armhf (15.2.0-12ubuntu1) ... 300s Setting up gcc-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 300s Setting up librostlab-blast-doc (1.0.1-14) ... 300s Setting up cpp-15 (15.2.0-12ubuntu1) ... 300s Setting up cpp (4:15.2.0-4ubuntu1) ... 300s Setting up libc6-dev:armhf (2.42-2ubuntu5) ... 300s Setting up gcc-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 300s Setting up gcc-15 (15.2.0-12ubuntu1) ... 300s Setting up libstdc++-15-dev:armhf (15.2.0-12ubuntu1) ... 300s Setting up g++-15-arm-linux-gnueabihf (15.2.0-12ubuntu1) ... 300s Setting up gcc (4:15.2.0-4ubuntu1) ... 300s Setting up g++-15 (15.2.0-12ubuntu1) ... 300s Setting up g++-arm-linux-gnueabihf (4:15.2.0-4ubuntu1) ... 300s Setting up g++ (4:15.2.0-4ubuntu1) ... 300s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 300s Setting up build-essential (12.12ubuntu2) ... 300s Processing triggers for man-db (2.13.1-1) ... 301s Processing triggers for libc-bin (2.42-2ubuntu5) ... 313s autopkgtest [05:46:34]: test run-unit-test: [----------------------- 315s Compile and run... 316s BLASTP 2.2.18 [Mar-02-2008] 316s 316s references: [ Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 316s Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 316s "Gapped BLAST and PSI-BLAST: a new generation of protein database search 316s programs", Nucleic Acids Res. 25:3389-3402., Reference for compositional score matrix adjustment: Altschul, Stephen F., 316s John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, 316s Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches 316s using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109., Reference for composition-based statistics starting in round 2: 316s Schaffer, Alejandro A., L. Aravind, Thomas L. Madden, 316s Sergei Shavirin, John L. Spouge, Yuri I. Wolf, 316s Eugene V. Koonin, and Stephen F. Altschul (2001), 316s "Improving the accuracy of PSI-BLAST protein database searches with 316s composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. ] 316s 316s rounds: [ ol_idx = 0, ol_cnt = 1, hit_idx = 0, hit_cnt = 1, ol_new_idx = 4294967295, ol_new_cnt = 0, ol_idx = 1, ol_cnt = 1, hit_idx = 1, hit_cnt = 1, ol_new_idx = 2, ol_new_cnt = 0 ] 316s 316s n = query d = (113 letters) 316s 316s Database: big_80 7170017 sequences; 2147483647 total letters 316s 316s one-line desc: [ n = pdb|pdb|2vh3_B d = : 212 bits, 8e-54 E, n = pdb|pdb|2vh3_B d = : 226 bits, 5e-58 E ] 316s 316s CONVERGED! 316s 316s hits: [ n = pdb|pdb|2vh3_B d = Length = 117 [ bits = 212, raw = 539, E = 8e-54, method = Compositional matrix adjust, ident = 109, pos = 109, gaps = 0, q_strand = , s_strand = , q_frame = 32, s_frame = 32, q_start = 1, q_ali = AXAXSFPPXEIPGSKECLAEALQKHQGFKKKSYALIXAYLNYKEDAENYERAAEDFDSAVKXTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLXTLFQKLYAIPHN, q_end = 113, match_line = A A SFPP EIPGSKECLAEALQKHQGFKKKSYALI AYLNYKEDAENYERAAEDFDSAVK TG KEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSL TLFQKLYAIPHN, s_start = 1, s_ali = AXACSFPPXEIPGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYERAAEDFDSAVKCTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLCTLFQKLYAIPHN, s_end = 113 ], n = pdb|pdb|2vh3_B d = Length = 117 [ bits = 226, raw = 575, E = 5e-58, method = Composition-based stats, ident = 109, pos = 109, gaps = 0, q_strand = , s_strand = , q_frame = 32, s_frame = 32, q_start = 1, q_ali = AXAXSFPPXEIPGSKECLAEALQKHQGFKKKSYALIXAYLNYKEDAENYERAAEDFDSAVKXTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLXTLFQKLYAIPHN, q_end = 113, match_line = A A SFPP EIPGSKECLAEALQKHQGFKKKSYALI AYLNYKEDAENYERAAEDFDSAVK TG KEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSL TLFQKLYAIPHN, s_start = 1, s_ali = AXACSFPPXEIPGSKECLAEALQKHQGFKKKSYALICAYLNYKEDAENYERAAEDFDSAVKCTGXKEGVDLHEGNPELIEEGFEKFLASLKIDRKALGSLCTLFQKLYAIPHN, s_end = 113 ] ] 316s 316s Database: big_80 316s Posted date: Feb 6, 2012 9:39 AM 316s Number of letters in database: 999,999,843 316s Number of sequences in database: 1,100,691 316s 316s Database: /mnt/project/rost_db/data/big/big_80.01 316s Posted date: Feb 6, 2012 9:42 AM 316s Number of letters in database: 999,999,792 316s Number of sequences in database: 2,641,400 316s 316s Database: /mnt/project/rost_db/data/big/big_80.02 316s Posted date: Feb 6, 2012 9:44 AM 316s Number of letters in database: 505,617,005 316s Number of sequences in database: 3,427,926 316s 316s Lambda K H 316s 0.313 0.133 0.375 316s 316s Lambda K H 316s 0.267 0.0413 0.140 316s 316s 316s Matrix: BLOSUM62 316s Gap Penalties: Existence: 11, Extension: 1 316s Number of Hits to DB: 932,412,166 316s Number of Sequences: 7170017 316s Number of extensions: 30007572 316s Number of successful extensions: 53414 316s Number of sequences better than 1.0: 1 316s Number of HSP's better than 1.0 without gapping: 2 316s Number of HSP's successfully gapped in prelim test: 0 316s Number of HSP's that attempted gapping in prelim test: 53412 316s Number of HSP's gapped (non-prelim): 2 316s length of query: 113 316s length of database: 2,505,616,640 316s effective HSP length: 81 316s effective length of query: 32 316s effective length of database: 1,924,845,263 316s effective search space: 61595048416 316s effective search space used: 61595048416 316s T: 11 316s A: 40 316s X1: 16 ( 7.2 bits) 316s X2: 38 (14.6 bits) 316s X3: 64 (24.7 bits) 316s S1: 42 (21.9 bits) 316s S2: 82 (36.2 bits) 316s autopkgtest [05:46:37]: test run-unit-test: -----------------------] 320s autopkgtest [05:46:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 320s run-unit-test PASS 324s autopkgtest [05:46:45]: @@@@@@@@@@@@@@@@@@@@ summary 324s run-unit-test PASS