0s autopkgtest [14:56:15]: starting date and time: 2025-05-04 14:56:15+0000 0s autopkgtest [14:56:15]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [14:56:15]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._e6jvdjb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:libzstd --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=libzstd/1.5.7+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-6.secgroup --name adt-questing-amd64-ncbi-blast+-20250504-145615-juju-7f2275-prod-proposed-migration-environment-20-c93d6d34-1eb9-4b94-be7b-d89d67866317 --image adt/ubuntu-questing-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 47s autopkgtest [14:57:02]: testbed dpkg architecture: amd64 47s autopkgtest [14:57:02]: testbed apt version: 3.0.0 48s autopkgtest [14:57:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 48s autopkgtest [14:57:03]: testbed release detected to be: None 49s autopkgtest [14:57:04]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 49s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [115 kB] 49s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1153 kB] 50s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.3 kB] 50s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 Packages [167 kB] 50s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main i386 Packages [118 kB] 50s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/universe i386 Packages [450 kB] 50s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe amd64 Packages [1235 kB] 50s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse amd64 Packages [50.7 kB] 50s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/multiverse i386 Packages [26.2 kB] 50s Fetched 3458 kB in 1s (3005 kB/s) 51s Reading package lists... 52s autopkgtest [14:57:07]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 52s Starting 2 pkgProblemResolver with broken count: 0 52s Done 53s Entering ResolveByKeep 53s 53s Calculating upgrade... 53s The following packages will be upgraded: 53s base-passwd ethtool libevdev2 libmm-glib0 libunistring5 libzstd1 patch 53s publicsuffix zstd 53s 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 2417 kB of archives. 53s After this operation, 519 kB disk space will be freed. 53s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 base-passwd amd64 3.6.7 [54.0 kB] 53s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [308 kB] 54s Get:3 http://ftpmaster.internal/ubuntu questing/main amd64 libunistring5 amd64 1.3-2 [607 kB] 54s Get:4 http://ftpmaster.internal/ubuntu questing/main amd64 ethtool amd64 1:6.14-2 [245 kB] 54s Get:5 http://ftpmaster.internal/ubuntu questing/main amd64 libevdev2 amd64 1.13.4+dfsg-1 [37.9 kB] 54s Get:6 http://ftpmaster.internal/ubuntu questing/main amd64 publicsuffix all 20250328.1952-0.1 [135 kB] 54s Get:7 http://ftpmaster.internal/ubuntu questing/main amd64 libmm-glib0 amd64 1.24.0-1 [262 kB] 54s Get:8 http://ftpmaster.internal/ubuntu questing/main amd64 patch amd64 2.8-1 [95.8 kB] 54s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main amd64 zstd amd64 1.5.7+dfsg-1 [672 kB] 54s Preconfiguring packages ... 54s Fetched 2417 kB in 1s (3648 kB/s) 54s (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 ... 80517 files and directories currently installed.) 54s Preparing to unpack .../base-passwd_3.6.7_amd64.deb ... 54s Unpacking base-passwd (3.6.7) over (3.6.6) ... 54s Setting up base-passwd (3.6.7) ... 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 ... 80517 files and directories currently installed.) 55s Preparing to unpack .../libzstd1_1.5.7+dfsg-1_amd64.deb ... 55s Unpacking libzstd1:amd64 (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 55s Setting up libzstd1:amd64 (1.5.7+dfsg-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 ... 80517 files and directories currently installed.) 55s Preparing to unpack .../0-libunistring5_1.3-2_amd64.deb ... 55s Unpacking libunistring5:amd64 (1.3-2) over (1.3-1) ... 55s Preparing to unpack .../1-ethtool_1%3a6.14-2_amd64.deb ... 55s Unpacking ethtool (1:6.14-2) over (1:6.11-1) ... 55s Preparing to unpack .../2-libevdev2_1.13.4+dfsg-1_amd64.deb ... 55s Unpacking libevdev2:amd64 (1.13.4+dfsg-1) over (1.13.3+dfsg-1) ... 55s Preparing to unpack .../3-publicsuffix_20250328.1952-0.1_all.deb ... 55s Unpacking publicsuffix (20250328.1952-0.1) over (20250108.1153-0.1) ... 55s Preparing to unpack .../4-libmm-glib0_1.24.0-1_amd64.deb ... 55s Unpacking libmm-glib0:amd64 (1.24.0-1) over (1.23.4-0ubuntu3) ... 55s Preparing to unpack .../5-patch_2.8-1_amd64.deb ... 55s Unpacking patch (2.8-1) over (2.7.6-7build3) ... 55s Preparing to unpack .../6-zstd_1.5.7+dfsg-1_amd64.deb ... 55s Unpacking zstd (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 55s Setting up libunistring5:amd64 (1.3-2) ... 55s Setting up patch (2.8-1) ... 55s Setting up libmm-glib0:amd64 (1.24.0-1) ... 55s Setting up libevdev2:amd64 (1.13.4+dfsg-1) ... 55s Setting up publicsuffix (20250328.1952-0.1) ... 55s Setting up zstd (1.5.7+dfsg-1) ... 55s Setting up ethtool (1:6.14-2) ... 55s Processing triggers for man-db (2.13.0-1) ... 56s Processing triggers for libc-bin (2.41-6ubuntu1) ... 56s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Starting pkgProblemResolver with broken count: 0 57s Starting 2 pkgProblemResolver with broken count: 0 57s Done 57s Solving dependencies... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s autopkgtest [14:57:15]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 15:05:05 UTC 2025 60s autopkgtest [14:57:15]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 63s Get:1 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B] 63s Get:2 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB] 63s Get:3 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB] 63s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC 63s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 63s gpgv: Can't check signature: No public key 63s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found 64s autopkgtest [14:57:19]: testing package ncbi-blast+ version 2.16.0+ds-6build1 65s autopkgtest [14:57:20]: build not needed 70s autopkgtest [14:57:25]: test run-unit-test: preparing testbed 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 71s Starting pkgProblemResolver with broken count: 0 71s Starting 2 pkgProblemResolver with broken count: 0 71s Done 71s The following NEW packages will be installed: 71s libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+ 71s ncbi-blast+-legacy ncbi-data 71s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 71s Need to get 20.3 MB of archives. 71s After this operation, 89.4 MB of additional disk space will be used. 71s Get:1 http://ftpmaster.internal/ubuntu questing/main amd64 libgomp1 amd64 15-20250404-0ubuntu1 [151 kB] 72s Get:2 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedcrypto16 amd64 3.6.2-3ubuntu1 [276 kB] 72s Get:3 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedx509-7 amd64 3.6.2-3ubuntu1 [37.1 kB] 72s Get:4 http://ftpmaster.internal/ubuntu questing/universe amd64 libmbedtls21 amd64 3.6.2-3ubuntu1 [126 kB] 72s Get:5 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 72s Get:6 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-blast+ amd64 2.16.0+ds-6build1 [15.8 MB] 72s Get:7 http://ftpmaster.internal/ubuntu questing/universe amd64 ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B] 73s Fetched 20.3 MB in 1s (19.2 MB/s) 73s Selecting previously unselected package libgomp1:amd64. 73s (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 ... 80518 files and directories currently installed.) 73s Preparing to unpack .../0-libgomp1_15-20250404-0ubuntu1_amd64.deb ... 73s Unpacking libgomp1:amd64 (15-20250404-0ubuntu1) ... 73s Selecting previously unselected package libmbedcrypto16:amd64. 73s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_amd64.deb ... 73s Unpacking libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 73s Selecting previously unselected package libmbedx509-7:amd64. 73s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_amd64.deb ... 73s Unpacking libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 73s Selecting previously unselected package libmbedtls21:amd64. 73s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_amd64.deb ... 73s Unpacking libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 73s Selecting previously unselected package ncbi-data. 73s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 73s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 73s Selecting previously unselected package ncbi-blast+. 73s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_amd64.deb ... 73s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 73s Selecting previously unselected package ncbi-blast+-legacy. 73s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ... 73s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ... 73s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 73s Setting up libgomp1:amd64 (15-20250404-0ubuntu1) ... 73s Setting up libmbedcrypto16:amd64 (3.6.2-3ubuntu1) ... 73s Setting up libmbedx509-7:amd64 (3.6.2-3ubuntu1) ... 73s Setting up libmbedtls21:amd64 (3.6.2-3ubuntu1) ... 73s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 73s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ... 73s Processing triggers for man-db (2.13.0-1) ... 74s Processing triggers for libc-bin (2.41-6ubuntu1) ... 75s autopkgtest [14:57:30]: test run-unit-test: [----------------------- 75s ---Creating Database-- 75s 75s 75s Building a new DB, current time: 05/04/2025 14:57:30 75s New DB name: /tmp/autopkgtest.3XGrgP/autopkgtest_tmp/testdb 75s New DB title: testdatabase.fa 75s Sequence type: Nucleotide 75s Keep MBits: T 75s Maximum file size: 3000000000B 75s Adding sequences from FASTA; added 3 sequences in 0.12005 seconds. 75s 75s 75s ---Searching Database for Hits--- 75s Warning: [blastn] Examining 5 or more matches is recommended 75s # BLASTN 2.16.0+ 75s # Query: gnl|MYDB|1 this is sequence 1 75s # Database: testdb 75s # Fields: query id, subject id, evalue, bit score 75s # 2 hits found 75s gnl|MYDB|1 gnl2 0.0 1299 75s gnl|MYDB|1 gnl1 0.0 1299 75s # BLAST processed 1 queries 75s ---Search and Fetch An Entry From Database--- 75s >gnl1 75s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 75s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 75s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 75s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 75s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 75s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 75s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 75s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 75s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 75s PASS 75s autopkgtest [14:57:30]: test run-unit-test: -----------------------] 76s run-unit-test PASS 76s autopkgtest [14:57:31]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 76s autopkgtest [14:57:31]: @@@@@@@@@@@@@@@@@@@@ summary 76s run-unit-test PASS 93s nova [W] Skipping flock for amd64 93s Creating nova instance adt-questing-amd64-ncbi-blast+-20250504-145615-juju-7f2275-prod-proposed-migration-environment-20-c93d6d34-1eb9-4b94-be7b-d89d67866317 from image adt/ubuntu-questing-amd64-server-20250504.img (UUID 4cf89fcc-bb54-4e0d-9acf-e03be076f6e4)... 93s nova [W] Timed out waiting for 33b89586-b68a-4df9-a303-4f8d0e816c5d to get deleted.