0s autopkgtest [16:41:52]: starting date and time: 2024-03-23 16:41:52+0000 0s autopkgtest [16:41:52]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [16:41:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.oipdjp7z/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=perl/5.38.2-3.2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-2.secgroup --name adt-noble-s390x-ncbi-blast+-20240323-164152-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 92s autopkgtest [16:43:24]: testbed dpkg architecture: s390x 93s autopkgtest [16:43:25]: testbed apt version: 2.7.12 93s autopkgtest [16:43:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 93s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 94s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 94s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [493 kB] 94s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3969 kB] 94s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [652 kB] 94s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 94s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 94s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 94s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4143 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 96s Fetched 9495 kB in 2s (3945 kB/s) 97s Reading package lists... 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Calculating upgrade... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 99s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s 0 upgraded, 0 newly installed, 0 to remove and 240 not upgraded. 100s Unknown architecture, assuming PC-style ttyS0 100s sh: Attempting to set up Debian/Ubuntu apt sources automatically 100s sh: Distribution appears to be Ubuntu 100s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s eatmydata is already the newest version (131-1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s dbus is already the newest version (1.14.10-4ubuntu1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 101s Building dependency tree... 101s Reading state information... 101s rng-tools-debian is already the newest version (2.4). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s The following packages will be REMOVED: 102s cloud-init* python3-configobj* python3-debconf* 102s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 102s After this operation, 3256 kB disk space will be freed. 102s (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 ... 52170 files and directories currently installed.) 102s Removing cloud-init (24.1.2-0ubuntu1) ... 102s Removing python3-configobj (5.0.8-3) ... 103s Removing python3-debconf (1.5.86) ... 103s Processing triggers for man-db (2.12.0-3) ... 103s (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 ... 51781 files and directories currently installed.) 103s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 103s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 104s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 104s invoke-rc.d: policy-rc.d denied execution of try-restart. 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s linux-generic is already the newest version (6.8.0-11.11+1). 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 104s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 106s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s autopkgtest [16:43:39]: rebooting testbed after setup commands that affected boot 122s autopkgtest [16:43:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 125s autopkgtest [16:43:57]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 129s Get:1 http://ftpmaster.internal/ubuntu noble/universe ncbi-blast+ 2.12.0+ds-4 (dsc) [2311 B] 129s Get:2 http://ftpmaster.internal/ubuntu noble/universe ncbi-blast+ 2.12.0+ds-4 (tar) [47.5 MB] 129s Get:3 http://ftpmaster.internal/ubuntu noble/universe ncbi-blast+ 2.12.0+ds-4 (diff) [33.5 kB] 129s gpgv: Signature made Tue Sep 5 02:41:47 2023 UTC 129s gpgv: using RSA key 7C3AB9CFD230BD30DD009C591E7091B1F14A64A2 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.12.0+ds-4.dsc: no acceptable signature found 135s autopkgtest [16:44:07]: testing package ncbi-blast+ version 2.12.0+ds-4 136s autopkgtest [16:44:08]: build not needed 184s autopkgtest [16:44:56]: test run-unit-test: preparing testbed 188s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s Starting pkgProblemResolver with broken count: 0 189s Starting 2 pkgProblemResolver with broken count: 0 189s Done 189s The following additional packages will be installed: 189s libgomp1 libmbedcrypto7 libmbedtls14 libmbedx509-1 ncbi-blast+ 189s ncbi-blast+-legacy ncbi-data 189s The following NEW packages will be installed: 189s autopkgtest-satdep libgomp1 libmbedcrypto7 libmbedtls14 libmbedx509-1 189s ncbi-blast+ ncbi-blast+-legacy ncbi-data 189s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 189s Need to get 17.5 MB/17.5 MB of archives. 189s After this operation, 73.6 MB of additional disk space will be used. 189s Get:1 /tmp/autopkgtest.oxoZjY/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [716 B] 189s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 189s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedcrypto7 s390x 2.28.7-1ubuntu1 [216 kB] 190s Get:4 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedx509-1 s390x 2.28.7-1ubuntu1 [46.0 kB] 190s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libmbedtls14 s390x 2.28.7-1ubuntu1 [84.5 kB] 190s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 190s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-blast+ s390x 2.12.0+ds-4 [12.6 MB] 190s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x ncbi-blast+-legacy all 2.12.0+ds-4 [4984 B] 191s Fetched 17.5 MB in 1s (13.8 MB/s) 191s Selecting previously unselected package libgomp1:s390x. 191s (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 ... 51726 files and directories currently installed.) 191s Preparing to unpack .../0-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 191s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 191s Selecting previously unselected package libmbedcrypto7:s390x. 191s Preparing to unpack .../1-libmbedcrypto7_2.28.7-1ubuntu1_s390x.deb ... 191s Unpacking libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 191s Selecting previously unselected package libmbedx509-1:s390x. 191s Preparing to unpack .../2-libmbedx509-1_2.28.7-1ubuntu1_s390x.deb ... 191s Unpacking libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 191s Selecting previously unselected package libmbedtls14:s390x. 191s Preparing to unpack .../3-libmbedtls14_2.28.7-1ubuntu1_s390x.deb ... 191s Unpacking libmbedtls14:s390x (2.28.7-1ubuntu1) ... 191s Selecting previously unselected package ncbi-data. 191s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 191s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 191s Selecting previously unselected package ncbi-blast+. 191s Preparing to unpack .../5-ncbi-blast+_2.12.0+ds-4_s390x.deb ... 191s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 191s Selecting previously unselected package ncbi-blast+-legacy. 191s Preparing to unpack .../6-ncbi-blast+-legacy_2.12.0+ds-4_all.deb ... 191s Unpacking ncbi-blast+-legacy (2.12.0+ds-4) ... 191s Selecting previously unselected package autopkgtest-satdep. 191s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 191s Unpacking autopkgtest-satdep (0) ... 191s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 191s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 191s Setting up libmbedcrypto7:s390x (2.28.7-1ubuntu1) ... 191s Setting up libmbedx509-1:s390x (2.28.7-1ubuntu1) ... 191s Setting up libmbedtls14:s390x (2.28.7-1ubuntu1) ... 191s Setting up ncbi-blast+ (2.12.0+ds-4) ... 191s Setting up ncbi-blast+-legacy (2.12.0+ds-4) ... 191s Setting up autopkgtest-satdep (0) ... 191s Processing triggers for man-db (2.12.0-3) ... 192s Processing triggers for libc-bin (2.39-0ubuntu6) ... 194s (Reading database ... 51994 files and directories currently installed.) 194s Removing autopkgtest-satdep (0) ... 194s autopkgtest [16:45:06]: test run-unit-test: [----------------------- 194s ---Creating Database-- 194s 194s 194s Building a new DB, current time: 03/23/2024 16:45:06 194s New DB name: /tmp/autopkgtest.oxoZjY/autopkgtest_tmp/testdb 194s New DB title: testdatabase.fa 194s Sequence type: Nucleotide 194s Keep MBits: T 194s Maximum file size: 1000000000B 195s Adding sequences from FASTA; added 3 sequences in 0.0940259 seconds. 195s 195s 195s ---Searching Database for Hits--- 195s Warning: [blastn] Examining 5 or more matches is recommended 195s # BLASTN 2.12.0+ 195s # Query: gnl|MYDB|1 this is sequence 1 195s # Database: testdb 195s # Fields: query id, subject id, evalue, bit score 195s # 2 hits found 195s gnl|MYDB|1 Unknown 0.0 1299 195s gnl|MYDB|1 gnl1 0.0 1299 195s # BLAST processed 1 queries 195s ---Search and Fetch An Entry From Database--- 195s >gnl1 195s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 195s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 195s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 195s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 195s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 195s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 195s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 195s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 195s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 195s PASS 195s autopkgtest [16:45:07]: test run-unit-test: -----------------------] 195s autopkgtest [16:45:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 195s run-unit-test PASS 196s autopkgtest [16:45:08]: @@@@@@@@@@@@@@@@@@@@ summary 196s run-unit-test PASS 208s Creating nova instance adt-noble-s390x-ncbi-blast+-20240323-164152-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240323.img (UUID 15bd59e1-c29b-45d7-aba1-73ff15182fb5)...