0s autopkgtest [09:02:16]: starting date and time: 2024-11-13 09:02:16+0000
  0s autopkgtest [09:02:16]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [09:02:16]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tlvgrs2u/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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-7.secgroup --name adt-plucky-amd64-ncbi-blast+-20241113-090216-juju-7f2275-prod-proposed-migration-environment-15-95134fa6-cf82-4160-a66e-f904890cc4bb --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/
 49s autopkgtest [09:03:05]: testbed dpkg architecture: amd64
 49s autopkgtest [09:03:05]: testbed apt version: 2.9.8
 49s autopkgtest [09:03:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
 50s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
 51s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
 51s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB]
 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB]
 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB]
 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB]
 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB]
 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB]
 51s Fetched 2173 kB in 1s (2695 kB/s)
 51s Reading package lists...
 53s Reading package lists...
 53s Building dependency tree...
 53s Reading state information...
 54s Calculating upgrade...
 54s The following NEW packages will be installed:
 54s   python3.13-gdbm
 54s The following packages will be upgraded:
 54s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
 54s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
 54s Need to get 253 kB of archives.
 54s After this operation, 147 kB of additional disk space will be used.
 54s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
 54s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
 54s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
 54s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
 54s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
 54s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB]
 55s Fetched 253 kB in 1s (488 kB/s)
 55s (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 ... 75541 files and directories currently installed.)
 55s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
 55s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
 55s Setting up python3-minimal (3.12.7-1) ...
 55s (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 ... 75541 files and directories currently installed.)
 55s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
 55s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 55s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
 55s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
 55s Selecting previously unselected package python3.13-gdbm.
 55s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
 55s Unpacking python3.13-gdbm (3.13.0-2) ...
 55s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
 55s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
 55s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ...
 55s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
 55s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ...
 55s Setting up python3.13-gdbm (3.13.0-2) ...
 55s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
 55s Setting up python3 (3.12.7-1) ...
 55s Setting up python3-gdbm:amd64 (3.12.7-1) ...
 55s Processing triggers for man-db (2.12.1-3) ...
 56s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 56s Reading package lists...
 56s Building dependency tree...
 56s Reading state information...
 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 57s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
 57s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 57s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 57s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 58s Reading package lists...
 58s Reading package lists...
 58s Building dependency tree...
 58s Reading state information...
 58s Calculating upgrade...
 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 58s Reading package lists...
 58s Building dependency tree...
 58s Reading state information...
 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 61s autopkgtest [09:03:17]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
 62s autopkgtest [09:03:18]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+
 64s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (dsc) [2498 B]
 64s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (tar) [18.4 MB]
 64s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6 (diff) [40.7 kB]
 64s gpgv: Signature made Wed Aug  7 01:47:58 2024 UTC
 64s gpgv:                using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2
 64s gpgv: Can't check signature: No public key
 64s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6.dsc: no acceptable signature found
 66s autopkgtest [09:03:22]: testing package ncbi-blast+ version 2.16.0+ds-6
 66s autopkgtest [09:03:22]: build not needed
 71s autopkgtest [09:03:27]: test run-unit-test: preparing testbed
 74s Reading package lists...
 75s Building dependency tree...
 75s Reading state information...
 75s Starting pkgProblemResolver with broken count: 0
 75s Starting 2 pkgProblemResolver with broken count: 0
 75s Done
 75s The following additional packages will be installed:
 75s   libgomp1 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 ncbi-blast+
 75s   ncbi-blast+-legacy ncbi-data
 75s The following NEW packages will be installed:
 75s   autopkgtest-satdep libgomp1 libmbedcrypto7t64 libmbedtls14t64
 75s   libmbedx509-1t64 ncbi-blast+ ncbi-blast+-legacy ncbi-data
 75s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
 75s Need to get 19.7 MB/19.7 MB of archives.
 75s After this operation, 87.7 MB of additional disk space will be used.
 75s Get:1 /tmp/autopkgtest.O4uxQ1/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B]
 75s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB]
 76s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB]
 76s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB]
 76s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB]
 76s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB]
 77s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6 [15.2 MB]
 79s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 ncbi-blast+-legacy all 2.16.0+ds-6 [4990 B]
 80s Fetched 19.7 MB in 4s (4759 kB/s)
 80s Selecting previously unselected package libgomp1:amd64.
 80s (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 ... 75548 files and directories currently installed.)
 80s Preparing to unpack .../0-libgomp1_14.2.0-8ubuntu1_amd64.deb ...
 80s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ...
 80s Selecting previously unselected package libmbedcrypto7t64:amd64.
 80s Preparing to unpack .../1-libmbedcrypto7t64_2.28.8-1_amd64.deb ...
 80s Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ...
 80s Selecting previously unselected package libmbedx509-1t64:amd64.
 80s Preparing to unpack .../2-libmbedx509-1t64_2.28.8-1_amd64.deb ...
 80s Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ...
 80s Selecting previously unselected package libmbedtls14t64:amd64.
 80s Preparing to unpack .../3-libmbedtls14t64_2.28.8-1_amd64.deb ...
 80s Unpacking libmbedtls14t64:amd64 (2.28.8-1) ...
 80s Selecting previously unselected package ncbi-data.
 80s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ...
 80s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ...
 80s Selecting previously unselected package ncbi-blast+.
 80s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6_amd64.deb ...
 80s Unpacking ncbi-blast+ (2.16.0+ds-6) ...
 80s Selecting previously unselected package ncbi-blast+-legacy.
 80s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6_all.deb ...
 80s Unpacking ncbi-blast+-legacy (2.16.0+ds-6) ...
 80s Selecting previously unselected package autopkgtest-satdep.
 80s Preparing to unpack .../7-1-autopkgtest-satdep.deb ...
 80s Unpacking autopkgtest-satdep (0) ...
 80s Setting up ncbi-data (6.1.20170106+dfsg2-5) ...
 80s Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ...
 80s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ...
 80s Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
 80s Setting up libmbedtls14t64:amd64 (2.28.8-1) ...
 80s Setting up ncbi-blast+ (2.16.0+ds-6) ...
 80s Setting up ncbi-blast+-legacy (2.16.0+ds-6) ...
 80s Setting up autopkgtest-satdep (0) ...
 80s Processing triggers for man-db (2.12.1-3) ...
 80s Processing triggers for libc-bin (2.40-1ubuntu3) ...
 83s (Reading database ... 75822 files and directories currently installed.)
 83s Removing autopkgtest-satdep (0) ...
 84s autopkgtest [09:03:40]: test run-unit-test: [-----------------------
 84s ---Creating Database--
 84s 
 84s 
 84s Building a new DB, current time: 11/13/2024 09:03:40
 84s New DB name:   /tmp/autopkgtest.O4uxQ1/autopkgtest_tmp/testdb
 84s New DB title:  testdatabase.fa
 84s Sequence type: Nucleotide
 84s Keep MBits: T
 84s Maximum file size: 3000000000B
 84s Adding sequences from FASTA; added 3 sequences in 0.111014 seconds.
 84s 
 84s 
 84s ---Searching Database for Hits---
 84s Warning: [blastn] Examining 5 or more matches is recommended
 84s # BLASTN 2.16.0+
 84s # Query: gnl|MYDB|1 this is sequence 1
 84s # Database: testdb
 84s # Fields: query id, subject id, evalue, bit score
 84s # 2 hits found
 84s gnl|MYDB|1	gnl2	0.0	1299
 84s gnl|MYDB|1	gnl1	0.0	1299
 84s # BLAST processed 1 queries
 84s ---Search and Fetch An Entry From Database---
 84s >gnl1 
 84s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
 84s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
 84s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
 84s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
 84s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
 84s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
 84s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
 84s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
 84s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
 84s PASS
 84s autopkgtest [09:03:40]: test run-unit-test: -----------------------]
 85s run-unit-test        PASS
 85s autopkgtest [09:03:41]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
 85s autopkgtest [09:03:41]: @@@@@@@@@@@@@@@@@@@@ summary
 85s run-unit-test        PASS
 98s nova [W] Skipping flock for amd64
 98s Creating nova instance adt-plucky-amd64-ncbi-blast+-20241113-090216-juju-7f2275-prod-proposed-migration-environment-15-95134fa6-cf82-4160-a66e-f904890cc4bb from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...