0s autopkgtest [02:02:48]: starting date: 2024-03-18 0s autopkgtest [02:02:48]: git checkout: 399018f5 lib/adt_testbed.py: Fix supression of warning messages from apt 0s autopkgtest [02:02:48]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yiv5_5yo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-20.secgroup --name adt-noble-arm64-ncbi-blast+-20240318-020248-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 174s autopkgtest [02:05:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 175s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 175s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 175s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 176s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 176s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 176s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 176s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 176s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 176s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 176s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 176s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 176s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 176s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 179s Fetched 9189 kB in 2s (4179 kB/s) 179s Reading package lists... 182s Reading package lists... 182s Building dependency tree... 182s Reading state information... 183s Calculating upgrade... 183s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 183s Reading package lists... 184s Building dependency tree... 184s Reading state information... 184s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 185s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 185s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 185s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 185s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 187s Reading package lists... 187s Reading package lists... 187s Building dependency tree... 187s Reading state information... 188s Calculating upgrade... 188s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 189s Reading package lists... 189s Building dependency tree... 189s Reading state information... 189s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 190s autopkgtest [02:05:58]: testbed dpkg architecture: arm64 191s autopkgtest [02:05:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 192s autopkgtest [02:06:00]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 194s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe ncbi-blast+ 2.12.0+ds-4build1 (dsc) [2451 B] 194s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe ncbi-blast+ 2.12.0+ds-4build1 (tar) [47.5 MB] 194s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe ncbi-blast+ 2.12.0+ds-4build1 (diff) [33.6 kB] 195s gpgv: Signature made Sun Mar 17 18:10:08 2024 UTC 195s gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D 195s gpgv: issuer "steve.langasek@ubuntu.com" 195s gpgv: Can't check signature: No public key 195s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.12.0+ds-4build1.dsc: no acceptable signature found 200s autopkgtest [02:06:08]: testing package ncbi-blast+ version 2.12.0+ds-4build1 200s autopkgtest [02:06:08]: build not needed 207s autopkgtest [02:06:15]: test run-unit-test: preparing testbed 210s Reading package lists... 210s Building dependency tree... 210s Reading state information... 211s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 211s Done 211s Starting pkgProblemResolver with broken count: 0 211s Starting 2 pkgProblemResolver with broken count: 0 211s Done 212s The following additional packages will be installed: 212s libgomp1 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ 212s ncbi-blast+-legacy ncbi-data 212s The following NEW packages will be installed: 212s libgomp1 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 ncbi-blast+ 212s ncbi-blast+-legacy ncbi-data 212s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 212s 1 not fully installed or removed. 212s Need to get 17.0 MB of archives. 212s After this operation, 77.0 MB of additional disk space will be used. 212s Get:1 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 213s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 213s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedcrypto7t64 arm64 2.28.7-1.1ubuntu1 [207 kB] 213s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedx509-1t64 arm64 2.28.7-1.1ubuntu1 [47.2 kB] 213s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libmbedtls14t64 arm64 2.28.7-1.1ubuntu1 [82.2 kB] 213s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4build1 [12.1 MB] 213s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 ncbi-blast+-legacy all 2.12.0+ds-4build1 [4990 B] 214s Fetched 17.0 MB in 1s (14.2 MB/s) 214s Selecting previously unselected package ncbi-data. 214s (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 ... 74758 files and directories currently installed.) 214s Preparing to unpack .../0-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 214s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 215s Selecting previously unselected package libgomp1:arm64. 215s Preparing to unpack .../1-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 215s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 215s Selecting previously unselected package libmbedcrypto7t64:arm64. 215s Preparing to unpack .../2-libmbedcrypto7t64_2.28.7-1.1ubuntu1_arm64.deb ... 215s Unpacking libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Selecting previously unselected package libmbedx509-1t64:arm64. 215s Preparing to unpack .../3-libmbedx509-1t64_2.28.7-1.1ubuntu1_arm64.deb ... 215s Unpacking libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Selecting previously unselected package libmbedtls14t64:arm64. 215s Preparing to unpack .../4-libmbedtls14t64_2.28.7-1.1ubuntu1_arm64.deb ... 215s Unpacking libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Selecting previously unselected package ncbi-blast+. 215s Preparing to unpack .../5-ncbi-blast+_2.12.0+ds-4build1_arm64.deb ... 215s Unpacking ncbi-blast+ (2.12.0+ds-4build1) ... 215s Selecting previously unselected package ncbi-blast+-legacy. 215s Preparing to unpack .../6-ncbi-blast+-legacy_2.12.0+ds-4build1_all.deb ... 215s Unpacking ncbi-blast+-legacy (2.12.0+ds-4build1) ... 215s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 215s Setting up libmbedcrypto7t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 215s Setting up libmbedx509-1t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Setting up libmbedtls14t64:arm64 (2.28.7-1.1ubuntu1) ... 215s Setting up ncbi-blast+ (2.12.0+ds-4build1) ... 215s Setting up ncbi-blast+-legacy (2.12.0+ds-4build1) ... 215s Setting up autopkgtest-satdep (0) ... 215s Processing triggers for man-db (2.12.0-3) ... 216s Processing triggers for libc-bin (2.39-0ubuntu2) ... 219s (Reading database ... 75029 files and directories currently installed.) 219s Removing autopkgtest-satdep (0) ... 220s autopkgtest [02:06:28]: test run-unit-test: [----------------------- 221s ---Creating Database-- 221s 221s 221s Building a new DB, current time: 03/18/2024 02:06:29 221s New DB name: /tmp/autopkgtest.vAWzjN/autopkgtest_tmp/testdb 221s New DB title: testdatabase.fa 221s Sequence type: Nucleotide 221s Keep MBits: T 221s Maximum file size: 1000000000B 221s Adding sequences from FASTA; added 3 sequences in 0.0953879 seconds. 221s 221s 221s ---Searching Database for Hits--- 221s Warning: [blastn] Examining 5 or more matches is recommended 221s # BLASTN 2.12.0+ 221s # Query: gnl|MYDB|1 this is sequence 1 221s # Database: testdb 221s # Fields: query id, subject id, evalue, bit score 221s # 2 hits found 221s gnl|MYDB|1 gnl2 0.0 1299 221s gnl|MYDB|1 gnl1 0.0 1299 221s # BLAST processed 1 queries 221s ---Search and Fetch An Entry From Database--- 221s >gnl1 221s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 221s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 221s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 221s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 221s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 221s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 221s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 221s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 221s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 221s PASS 222s autopkgtest [02:06:30]: test run-unit-test: -----------------------] 222s autopkgtest [02:06:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 222s run-unit-test PASS 222s autopkgtest [02:06:30]: @@@@@@@@@@@@@@@@@@@@ summary 222s run-unit-test PASS 234s Creating nova instance adt-noble-arm64-ncbi-blast+-20240318-020248-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...