0s autopkgtest [09:42:17]: starting date and time: 2024-11-13 09:42:17+0000 0s autopkgtest [09:42:17]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:42:17]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.etv1bidk/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- 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-ncbi-blast+-20241113-094217-juju-7f2275-prod-proposed-migration-environment-15-28214932-8b2d-4b08-be01-314d11968a0a --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/ 100s autopkgtest [09:43:57]: testbed dpkg architecture: arm64 100s autopkgtest [09:43:57]: testbed apt version: 2.9.8 100s autopkgtest [09:43:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 104s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 104s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 104s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 104s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 104s Fetched 1793 kB in 1s (1835 kB/s) 104s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 110s The following NEW packages will be installed: 110s python3.13-gdbm 110s The following packages will be upgraded: 110s libpython3-stdlib python3 python3-gdbm python3-minimal 111s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 101 kB of archives. 111s After this operation, 141 kB of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 111s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 111s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 111s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 112s Fetched 101 kB in 0s (286 kB/s) 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 ... 79924 files and directories currently installed.) 112s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 112s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 112s Setting up python3-minimal (3.12.7-1) ... 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 ... 79924 files and directories currently installed.) 112s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 112s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 112s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 112s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 113s Selecting previously unselected package python3.13-gdbm. 113s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 113s Unpacking python3.13-gdbm (3.13.0-2) ... 113s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 113s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 113s Setting up python3.13-gdbm (3.13.0-2) ... 113s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 113s Setting up python3 (3.12.7-1) ... 113s Setting up python3-gdbm:arm64 (3.12.7-1) ... 113s Processing triggers for man-db (2.12.1-3) ... 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 117s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 117s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 117s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 118s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 118s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 118s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 Packages [1418 kB] 118s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 Packages [15.5 MB] 120s Fetched 18.7 MB in 3s (5809 kB/s) 121s Reading package lists... 121s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Calculating upgrade... 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [09:44:27]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 131s autopkgtest [09:44:28]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 136s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (dsc) [2498 B] 136s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (tar) [18.4 MB] 136s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (diff) [40.7 kB] 136s gpgv: Signature made Wed Aug 7 01:47:58 2024 UTC 136s gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 136s gpgv: Can't check signature: No public key 136s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6.dsc: no acceptable signature found 138s autopkgtest [09:44:35]: testing package ncbi-blast+ version 2.16.0+ds-6 138s autopkgtest [09:44:35]: build not needed 144s autopkgtest [09:44:41]: test run-unit-test: preparing testbed 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Starting pkgProblemResolver with broken count: 0 150s Starting 2 pkgProblemResolver with broken count: 0 150s Done 151s The following additional packages will be installed: 151s libgomp1 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ 151s ncbi-blast+-legacy ncbi-data 151s The following NEW packages will be installed: 151s autopkgtest-satdep libgomp1 libmbedcrypto7t64 libmbedtls14t64 151s libmbedx509-1t64 ncbi-blast+ ncbi-blast+-legacy ncbi-data 151s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 151s Need to get 19.2 MB/19.2 MB of archives. 151s After this operation, 90.3 MB of additional disk space will be used. 151s Get:1 /tmp/autopkgtest.CiDw2V/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 151s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedcrypto7t64 arm64 2.28.8-1 [209 kB] 151s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedx509-1t64 arm64 2.28.8-1 [47.2 kB] 151s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmbedtls14t64 arm64 2.28.8-1 [82.2 kB] 151s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 152s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6 [14.7 MB] 153s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 ncbi-blast+-legacy all 2.16.0+ds-6 [4990 B] 153s Fetched 19.2 MB in 2s (10.8 MB/s) 153s Selecting previously unselected package libgomp1:arm64. 153s (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 ... 79931 files and directories currently installed.) 153s Preparing to unpack .../0-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 153s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 153s Selecting previously unselected package libmbedcrypto7t64:arm64. 153s Preparing to unpack .../1-libmbedcrypto7t64_2.28.8-1_arm64.deb ... 153s Unpacking libmbedcrypto7t64:arm64 (2.28.8-1) ... 153s Selecting previously unselected package libmbedx509-1t64:arm64. 153s Preparing to unpack .../2-libmbedx509-1t64_2.28.8-1_arm64.deb ... 153s Unpacking libmbedx509-1t64:arm64 (2.28.8-1) ... 153s Selecting previously unselected package libmbedtls14t64:arm64. 153s Preparing to unpack .../3-libmbedtls14t64_2.28.8-1_arm64.deb ... 153s Unpacking libmbedtls14t64:arm64 (2.28.8-1) ... 153s Selecting previously unselected package ncbi-data. 153s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 153s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 154s Selecting previously unselected package ncbi-blast+. 154s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6_arm64.deb ... 154s Unpacking ncbi-blast+ (2.16.0+ds-6) ... 154s Selecting previously unselected package ncbi-blast+-legacy. 154s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6_all.deb ... 154s Unpacking ncbi-blast+-legacy (2.16.0+ds-6) ... 154s Selecting previously unselected package autopkgtest-satdep. 154s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 154s Unpacking autopkgtest-satdep (0) ... 154s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 154s Setting up libmbedcrypto7t64:arm64 (2.28.8-1) ... 154s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 154s Setting up libmbedx509-1t64:arm64 (2.28.8-1) ... 154s Setting up libmbedtls14t64:arm64 (2.28.8-1) ... 154s Setting up ncbi-blast+ (2.16.0+ds-6) ... 154s Setting up ncbi-blast+-legacy (2.16.0+ds-6) ... 154s Setting up autopkgtest-satdep (0) ... 154s Processing triggers for man-db (2.12.1-3) ... 155s Processing triggers for libc-bin (2.40-1ubuntu3) ... 159s (Reading database ... 80205 files and directories currently installed.) 159s Removing autopkgtest-satdep (0) ... 160s autopkgtest [09:44:57]: test run-unit-test: [----------------------- 160s ---Creating Database-- 160s 160s 160s Building a new DB, current time: 11/13/2024 09:44:57 160s New DB name: /tmp/autopkgtest.CiDw2V/autopkgtest_tmp/testdb 160s New DB title: testdatabase.fa 160s Sequence type: Nucleotide 160s Keep MBits: T 160s Maximum file size: 3000000000B 160s Adding sequences from FASTA; added 3 sequences in 0.178406 seconds. 160s 160s 160s ---Searching Database for Hits--- 160s Warning: [blastn] Examining 5 or more matches is recommended 160s # BLASTN 2.16.0+ 160s # Query: gnl|MYDB|1 this is sequence 1 160s # Database: testdb 160s # Fields: query id, subject id, evalue, bit score 160s # 2 hits found 160s gnl|MYDB|1 gnl2 0.0 1299 160s gnl|MYDB|1 gnl1 0.0 1299 160s # BLAST processed 1 queries 160s ---Search and Fetch An Entry From Database--- 160s >gnl1 160s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 160s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 160s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 160s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 160s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 160s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 160s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 160s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 160s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 160s PASS 161s autopkgtest [09:44:58]: test run-unit-test: -----------------------] 161s autopkgtest [09:44:58]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 161s run-unit-test PASS 162s autopkgtest [09:44:59]: @@@@@@@@@@@@@@@@@@@@ summary 162s run-unit-test PASS 175s nova [W] Skipping flock in bos03-arm64 175s Creating nova instance adt-plucky-arm64-ncbi-blast+-20241113-094217-juju-7f2275-prod-proposed-migration-environment-15-28214932-8b2d-4b08-be01-314d11968a0a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...