0s autopkgtest [02:43:46]: starting date and time: 2026-02-05 02:43:46+0000 0s autopkgtest [02:43:46]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:43:46]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gmv6cvpd/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:chiark-tcl --apt-upgrade librostlab-blast --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 chiark-tcl/1.3.7build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-arm64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-arm64-3.secgroup --name adt-resolute-arm64-librostlab-blast-20260205-024344-juju-7f2275-prod-proposed-migration-environment-20-b79c83db-c4e8-4274-93e3-9a6af095c922 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-arm64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 16s Creating nova instance adt-resolute-arm64-librostlab-blast-20260205-024344-juju-7f2275-prod-proposed-migration-environment-20-b79c83db-c4e8-4274-93e3-9a6af095c922 from image adt/ubuntu-resolute-arm64-server-20260204.img (UUID f58d981d-b271-4157-b9b1-fd704695563c)... 99s autopkgtest [02:45:25]: testbed dpkg architecture: arm64 99s autopkgtest [02:45:25]: testbed apt version: 3.1.14 100s autopkgtest [02:45:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s autopkgtest [02:45:26]: testbed release detected to be: None 101s autopkgtest [02:45:26]: updating testbed package index (apt update) 102s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 102s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 102s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [227 kB] 102s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5260 B] 102s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1719 kB] 102s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [35.4 kB] 102s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [265 kB] 102s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [7328 B] 102s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [52.9 kB] 102s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [328 B] 102s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [1481 kB] 102s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [40.2 kB] 102s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [26.0 kB] 102s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [776 B] 106s Fetched 3984 kB in 2s (2593 kB/s) 107s Reading package lists... 107s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 108s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 108s Reading package lists... 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s Calculating upgrade... 109s The following packages will be upgraded: 109s libc-bin libc-gconv-modules-extra libc6 locales pollinate python3-linkify-it 109s python3-referencing sed 109s 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 8110 kB of archives. 109s After this operation, 0 B of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 sed arm64 4.9-2build3 [193 kB] 110s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-gconv-modules-extra arm64 2.42-2ubuntu5 [1413 kB] 110s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6 arm64 2.42-2ubuntu5 [1594 kB] 110s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-bin arm64 2.42-2ubuntu5 [599 kB] 110s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 locales all 2.42-2ubuntu5 [4255 kB] 110s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 110s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 pollinate all 4.33-4ubuntu5 [14.0 kB] 110s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 111s dpkg-preconfigure: unable to re-open stdin: No such file or directory 111s Fetched 8110 kB in 1s (8067 kB/s) 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 ... 89360 files and directories currently installed.) 111s Preparing to unpack .../sed_4.9-2build3_arm64.deb ... 111s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 111s Setting up sed (4.9-2build3) ... 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 ... 89360 files and directories currently installed.) 111s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_arm64.deb ... 111s Unpacking libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 111s Setting up libc-gconv-modules-extra:arm64 (2.42-2ubuntu5) ... 112s (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 ... 89360 files and directories currently installed.) 112s Preparing to unpack .../libc6_2.42-2ubuntu5_arm64.deb ... 112s Unpacking libc6:arm64 (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 112s Setting up libc6:arm64 (2.42-2ubuntu5) ... 112s (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 ... 89360 files and directories currently installed.) 112s Preparing to unpack .../libc-bin_2.42-2ubuntu5_arm64.deb ... 112s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 112s Setting up libc-bin (2.42-2ubuntu5) ... 112s (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 ... 89360 files and directories currently installed.) 112s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 112s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 113s Preparing to unpack .../python3-linkify-it_2.0.3-1ubuntu3_all.deb ... 113s Unpacking python3-linkify-it (2.0.3-1ubuntu3) over (2.0.3-1ubuntu2) ... 113s Preparing to unpack .../pollinate_4.33-4ubuntu5_all.deb ... 113s Unpacking pollinate (4.33-4ubuntu5) over (4.33-4ubuntu4) ... 113s Preparing to unpack .../python3-referencing_0.36.2-1ubuntu2_all.deb ... 113s Unpacking python3-referencing (0.36.2-1ubuntu2) over (0.36.2-1ubuntu1) ... 113s Setting up locales (2.42-2ubuntu5) ... 114s Generating locales (this might take a while)... 116s en_US.UTF-8... done 116s Generation complete. 116s Setting up pollinate (4.33-4ubuntu5) ... 127s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 127s Setting up python3-referencing (0.36.2-1ubuntu2) ... 127s Processing triggers for man-db (2.13.1-1) ... 129s Processing triggers for install-info (7.2-5) ... 129s Processing triggers for systemd (259-1ubuntu3) ... 129s autopkgtest [02:45:55]: upgrading testbed (apt dist-upgrade and autopurge) 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 130s Calculating upgrade... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Solving dependencies... 131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [02:45:57]: rebooting testbed after setup commands that affected boot 170s autopkgtest [02:46:36]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 12 16:41:39 UTC 2026 173s autopkgtest [02:46:39]: @@@@@@@@@@@@@@@@@@@@ apt-source librostlab-blast 175s Get:1 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (dsc) [2562 B] 175s Get:2 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (tar) [384 kB] 175s Get:3 http://ftpmaster.internal/ubuntu resolute/universe librostlab-blast 1.0.1-14 (diff) [6716 B] 175s gpgv: Signature made Wed Apr 24 11:20:29 2024 UTC 175s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 175s gpgv: issuer "emollier@debian.org" 175s gpgv: Can't check signature: No public key 175s dpkg-source: warning: cannot verify inline signature for ./librostlab-blast_1.0.1-14.dsc: no acceptable signature found 175s autopkgtest [02:46:41]: testing package librostlab-blast version 1.0.1-14 176s autopkgtest [02:46:42]: build not needed 177s autopkgtest [02:46:43]: test run-unit-test: preparing testbed 177s Reading package lists... 177s Building dependency tree... 177s Reading state information... 177s Solving dependencies... 178s The following NEW packages will be installed: 178s build-essential cpp cpp-15 cpp-15-aarch64-linux-gnu cpp-aarch64-linux-gnu 178s g++ g++-15 g++-15-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-15 178s gcc-15-aarch64-linux-gnu gcc-aarch64-linux-gnu libasan8 libc-dev-bin 178s libc6-dev libcc1-0 libcrypt-dev libgcc-15-dev libgomp1 libhwasan0 libisl23 178s libitm1 libjs-jquery liblsan0 libmpc3 librostlab-blast-doc 178s librostlab-blast0-dev librostlab-blast0v5 librostlab3-dev librostlab3t64 178s libstdc++-15-dev libtsan2 libubsan1 linux-libc-dev rpcsvc-proto 178s 0 upgraded, 36 newly installed, 0 to remove and 0 not upgraded. 178s Need to get 69.3 MB of archives. 178s After this operation, 249 MB of additional disk space will be used. 178s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc-dev-bin arm64 2.42-2ubuntu5 [22.5 kB] 178s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 linux-libc-dev arm64 6.18.0-9.9 [1834 kB] 178s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libcrypt-dev arm64 1:4.5.1-1 [123 kB] 178s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 rpcsvc-proto arm64 1.4.3-1build1 [65.6 kB] 178s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libc6-dev arm64 2.42-2ubuntu5 [1765 kB] 179s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 libisl23 arm64 0.27-1build1 [676 kB] 179s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libmpc3 arm64 1.3.1-2 [55.6 kB] 179s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [11.7 MB] 179s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-15 arm64 15.2.0-12ubuntu1 [1030 B] 179s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [5736 B] 179s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 cpp arm64 4:15.2.0-4ubuntu1 [22.4 kB] 179s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 libcc1-0 arm64 15.2.0-12ubuntu1 [49.0 kB] 179s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 libgomp1 arm64 15.2.0-12ubuntu1 [147 kB] 179s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libitm1 arm64 15.2.0-12ubuntu1 [27.8 kB] 179s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 libasan8 arm64 15.2.0-12ubuntu1 [2920 kB] 179s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 liblsan0 arm64 15.2.0-12ubuntu1 [1316 kB] 179s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 libtsan2 arm64 15.2.0-12ubuntu1 [2688 kB] 179s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 libubsan1 arm64 15.2.0-12ubuntu1 [1175 kB] 179s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libhwasan0 arm64 15.2.0-12ubuntu1 [1638 kB] 180s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libgcc-15-dev arm64 15.2.0-12ubuntu1 [2600 kB] 180s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [23.1 MB] 181s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-15 arm64 15.2.0-12ubuntu1 [519 kB] 181s Get:23 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [1206 B] 181s Get:24 http://ftpmaster.internal/ubuntu resolute/main arm64 gcc arm64 4:15.2.0-4ubuntu1 [5016 B] 181s Get:25 http://ftpmaster.internal/ubuntu resolute/main arm64 libstdc++-15-dev arm64 15.2.0-12ubuntu1 [2549 kB] 181s Get:26 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15-aarch64-linux-gnu arm64 15.2.0-12ubuntu1 [13.2 MB] 181s Get:27 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-15 arm64 15.2.0-12ubuntu1 [25.3 kB] 181s Get:28 http://ftpmaster.internal/ubuntu resolute/main arm64 g++-aarch64-linux-gnu arm64 4:15.2.0-4ubuntu1 [956 B] 181s Get:29 http://ftpmaster.internal/ubuntu resolute/main arm64 g++ arm64 4:15.2.0-4ubuntu1 [1080 B] 181s Get:30 http://ftpmaster.internal/ubuntu resolute/main arm64 build-essential arm64 12.12ubuntu2 [5254 B] 181s Get:31 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 181s Get:32 http://ftpmaster.internal/ubuntu resolute/universe arm64 librostlab-blast-doc all 1.0.1-14 [421 kB] 181s Get:33 http://ftpmaster.internal/ubuntu resolute/universe arm64 librostlab-blast0v5 arm64 1.0.1-14 [85.5 kB] 181s Get:34 http://ftpmaster.internal/ubuntu resolute/universe arm64 librostlab3t64 arm64 1.0.20-14 [5240 B] 181s Get:35 http://ftpmaster.internal/ubuntu resolute/universe arm64 librostlab3-dev arm64 1.0.20-14 [11.4 kB] 181s Get:36 http://ftpmaster.internal/ubuntu resolute/universe arm64 librostlab-blast0-dev arm64 1.0.1-14 [105 kB] 182s Fetched 69.3 MB in 4s (19.7 MB/s) 182s Selecting previously unselected package libc-dev-bin. 182s (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 ... 89360 files and directories currently installed.) 182s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu5_arm64.deb ... 182s Unpacking libc-dev-bin (2.42-2ubuntu5) ... 182s Selecting previously unselected package linux-libc-dev:arm64. 182s Preparing to unpack .../01-linux-libc-dev_6.18.0-9.9_arm64.deb ... 182s Unpacking linux-libc-dev:arm64 (6.18.0-9.9) ... 182s Selecting previously unselected package libcrypt-dev:arm64. 182s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_arm64.deb ... 182s Unpacking libcrypt-dev:arm64 (1:4.5.1-1) ... 182s Selecting previously unselected package rpcsvc-proto. 182s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_arm64.deb ... 182s Unpacking rpcsvc-proto (1.4.3-1build1) ... 182s Selecting previously unselected package libc6-dev:arm64. 182s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu5_arm64.deb ... 182s Unpacking libc6-dev:arm64 (2.42-2ubuntu5) ... 182s Selecting previously unselected package libisl23:arm64. 182s Preparing to unpack .../05-libisl23_0.27-1build1_arm64.deb ... 182s Unpacking libisl23:arm64 (0.27-1build1) ... 182s Selecting previously unselected package libmpc3:arm64. 182s Preparing to unpack .../06-libmpc3_1.3.1-2_arm64.deb ... 182s Unpacking libmpc3:arm64 (1.3.1-2) ... 182s Selecting previously unselected package cpp-15-aarch64-linux-gnu. 182s Preparing to unpack .../07-cpp-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 182s Unpacking cpp-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package cpp-15. 183s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package cpp-aarch64-linux-gnu. 183s Preparing to unpack .../09-cpp-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 183s Unpacking cpp-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Selecting previously unselected package cpp. 183s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_arm64.deb ... 183s Unpacking cpp (4:15.2.0-4ubuntu1) ... 183s Selecting previously unselected package libcc1-0:arm64. 183s Preparing to unpack .../11-libcc1-0_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libcc1-0:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libgomp1:arm64. 183s Preparing to unpack .../12-libgomp1_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libgomp1:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libitm1:arm64. 183s Preparing to unpack .../13-libitm1_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libitm1:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libasan8:arm64. 183s Preparing to unpack .../14-libasan8_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libasan8:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package liblsan0:arm64. 183s Preparing to unpack .../15-liblsan0_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking liblsan0:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libtsan2:arm64. 183s Preparing to unpack .../16-libtsan2_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libtsan2:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libubsan1:arm64. 183s Preparing to unpack .../17-libubsan1_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libubsan1:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libhwasan0:arm64. 183s Preparing to unpack .../18-libhwasan0_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libhwasan0:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package libgcc-15-dev:arm64. 183s Preparing to unpack .../19-libgcc-15-dev_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking libgcc-15-dev:arm64 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package gcc-15-aarch64-linux-gnu. 183s Preparing to unpack .../20-gcc-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 183s Unpacking gcc-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 184s Selecting previously unselected package gcc-15. 184s Preparing to unpack .../21-gcc-15_15.2.0-12ubuntu1_arm64.deb ... 184s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 184s Selecting previously unselected package gcc-aarch64-linux-gnu. 184s Preparing to unpack .../22-gcc-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 184s Unpacking gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 184s Selecting previously unselected package gcc. 184s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_arm64.deb ... 184s Unpacking gcc (4:15.2.0-4ubuntu1) ... 184s Selecting previously unselected package libstdc++-15-dev:arm64. 184s Preparing to unpack .../24-libstdc++-15-dev_15.2.0-12ubuntu1_arm64.deb ... 184s Unpacking libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 184s Selecting previously unselected package g++-15-aarch64-linux-gnu. 184s Preparing to unpack .../25-g++-15-aarch64-linux-gnu_15.2.0-12ubuntu1_arm64.deb ... 184s Unpacking g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 185s Selecting previously unselected package g++-15. 185s Preparing to unpack .../26-g++-15_15.2.0-12ubuntu1_arm64.deb ... 185s Unpacking g++-15 (15.2.0-12ubuntu1) ... 185s Selecting previously unselected package g++-aarch64-linux-gnu. 185s Preparing to unpack .../27-g++-aarch64-linux-gnu_4%3a15.2.0-4ubuntu1_arm64.deb ... 185s Unpacking g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 185s Selecting previously unselected package g++. 185s Preparing to unpack .../28-g++_4%3a15.2.0-4ubuntu1_arm64.deb ... 185s Unpacking g++ (4:15.2.0-4ubuntu1) ... 185s Selecting previously unselected package build-essential. 185s Preparing to unpack .../29-build-essential_12.12ubuntu2_arm64.deb ... 185s Unpacking build-essential (12.12ubuntu2) ... 185s Selecting previously unselected package libjs-jquery. 185s Preparing to unpack .../30-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 185s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 185s Selecting previously unselected package librostlab-blast-doc. 185s Preparing to unpack .../31-librostlab-blast-doc_1.0.1-14_all.deb ... 185s Unpacking librostlab-blast-doc (1.0.1-14) ... 185s Selecting previously unselected package librostlab-blast0v5:arm64. 185s Preparing to unpack .../32-librostlab-blast0v5_1.0.1-14_arm64.deb ... 185s Unpacking librostlab-blast0v5:arm64 (1.0.1-14) ... 185s Selecting previously unselected package librostlab3t64:arm64. 185s Preparing to unpack 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libstdc++-15-dev:arm64 (15.2.0-12ubuntu1) ... 185s Setting up g++-15-aarch64-linux-gnu (15.2.0-12ubuntu1) ... 185s Setting up g++-15 (15.2.0-12ubuntu1) ... 185s Setting up gcc-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 185s Setting up gcc (4:15.2.0-4ubuntu1) ... 185s Setting up g++-aarch64-linux-gnu (4:15.2.0-4ubuntu1) ... 185s Setting up g++ (4:15.2.0-4ubuntu1) ... 185s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 185s Setting up build-essential (12.12ubuntu2) ... 185s Processing triggers for man-db (2.13.1-1) ... 186s Processing triggers for libc-bin (2.42-2ubuntu5) ... 187s autopkgtest [02:46:53]: test run-unit-test: [----------------------- 187s Compile and run... 188s BLASTP 2.2.18 [Mar-02-2008] 188s 188s references: [ Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 188s Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 188s "Gapped BLAST and PSI-BLAST: a new generation of protein database search 188s programs", Nucleic Acids Res. 25:3389-3402., Reference for compositional score matrix adjustment: Altschul, Stephen F., 188s John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, 188s Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches 188s using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109., Reference for composition-based statistics starting in round 2: 188s Schaffer, Alejandro A., L. Aravind, Thomas L. Madden, 188s Sergei Shavirin, John L. Spouge, Yuri I. Wolf, 188s Eugene V. Koonin, and Stephen F. Altschul (2001), 188s "Improving the accuracy of PSI-BLAST protein database searches with 188s composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005. ] 188s 188s rounds: [ ol_idx = 0, ol_cnt = 1, hit_idx = 0, hit_cnt = 1, ol_new_idx = 18446744073709551615, ol_new_cnt = 0, ol_idx = 1, ol_cnt = 1, hit_idx = 1, hit_cnt = 1, ol_new_idx = 2, ol_new_cnt = 0 ] 188s 188s n = query d = (113 letters) 188s 188s Database: big_80 7170017 sequences; 2505616640 total letters 188s 188s 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 ] 188s 188s CONVERGED! 188s 188s 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 ] ] 188s 188s Database: big_80 188s Posted date: Feb 6, 2012 9:39 AM 188s Number of letters in database: 999,999,843 188s Number of sequences in database: 1,100,691 188s 188s Database: /mnt/project/rost_db/data/big/big_80.01 188s Posted date: Feb 6, 2012 9:42 AM 188s Number of letters in database: 999,999,792 188s Number of sequences in database: 2,641,400 188s 188s Database: /mnt/project/rost_db/data/big/big_80.02 188s Posted date: Feb 6, 2012 9:44 AM 188s Number of letters in database: 505,617,005 188s Number of sequences in database: 3,427,926 188s 188s Lambda K H 188s 0.313 0.133 0.375 188s 188s Lambda K H 188s 0.267 0.0413 0.140 188s 188s 188s Matrix: BLOSUM62 188s Gap Penalties: Existence: 11, Extension: 1 188s Number of Hits to DB: 932,412,166 188s Number of Sequences: 7170017 188s Number of extensions: 30007572 188s Number of successful extensions: 53414 188s Number of sequences better than 1.0: 1 188s Number of HSP's better than 1.0 without gapping: 2 188s Number of HSP's successfully gapped in prelim test: 0 188s Number of HSP's that attempted gapping in prelim test: 53412 188s Number of HSP's gapped (non-prelim): 2 188s length of query: 113 188s length of database: 2,505,616,640 188s effective HSP length: 81 188s effective length of query: 32 188s effective length of database: 1,924,845,263 188s effective search space: 61595048416 188s effective search space used: 61595048416 188s T: 11 188s A: 40 188s X1: 16 ( 7.2 bits) 188s X2: 38 (14.6 bits) 188s X3: 64 (24.7 bits) 188s S1: 42 (21.9 bits) 188s S2: 82 (36.2 bits) 189s autopkgtest [02:46:55]: test run-unit-test: -----------------------] 189s run-unit-test PASS 189s autopkgtest [02:46:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 189s autopkgtest [02:46:55]: @@@@@@@@@@@@@@@@@@@@ summary 189s run-unit-test PASS