0s autopkgtest [14:56:19]: starting date and time: 2025-05-04 14:56:19+0000 0s autopkgtest [14:56:19]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [14:56:19]: host juju-7f2275-prod-proposed-migration-environment-23; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8xdvv2pq/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-23@bos03-arm64-11.secgroup --name adt-questing-arm64-ncbi-blast+-20250504-145619-juju-7f2275-prod-proposed-migration-environment-23-55dc71e2-8c07-47a7-a9ce-f1f4b12247fb --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-23 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 92s autopkgtest [14:57:51]: testbed dpkg architecture: arm64 92s autopkgtest [14:57:51]: testbed apt version: 3.0.0 93s autopkgtest [14:57:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 93s autopkgtest [14:57:52]: testbed release detected to be: None 94s autopkgtest [14:57:53]: updating testbed package index (apt update) 94s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 94s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 94s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 95s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 95s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.3 kB] 95s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1153 kB] 95s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [115 kB] 95s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [151 kB] 95s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1187 kB] 95s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [29.6 kB] 95s Fetched 2779 kB in 1s (2644 kB/s) 96s Reading package lists... 97s autopkgtest [14:57:56]: upgrading testbed (apt dist-upgrade and autopurge) 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 99s Starting 2 pkgProblemResolver with broken count: 0 99s Done 101s Entering ResolveByKeep 102s 102s Calculating upgrade... 102s The following packages will be upgraded: 102s base-passwd ethtool libevdev2 libmm-glib0 libpython3.12-minimal 102s libpython3.12-stdlib libpython3.12t64 libunistring5 libzstd1 patch zstd 103s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 7360 kB of archives. 103s After this operation, 74.8 kB disk space will be freed. 103s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 base-passwd arm64 3.6.7 [54.2 kB] 103s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libzstd1 arm64 1.5.7+dfsg-1 [283 kB] 103s Get:3 http://ftpmaster.internal/ubuntu questing/main arm64 libunistring5 arm64 1.3-2 [601 kB] 103s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 ethtool arm64 1:6.14-2 [242 kB] 103s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 libevdev2 arm64 1.13.4+dfsg-1 [35.8 kB] 103s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libmm-glib0 arm64 1.24.0-1 [262 kB] 103s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12t64 arm64 3.12.10-1 [2314 kB] 103s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-stdlib arm64 3.12.10-1 [2029 kB] 103s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-minimal arm64 3.12.10-1 [836 kB] 103s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 patch arm64 2.8-1 [94.0 kB] 103s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 zstd arm64 1.5.7+dfsg-1 [607 kB] 104s Preconfiguring packages ... 104s Fetched 7360 kB in 1s (9519 kB/s) 104s (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 ... 117820 files and directories currently installed.) 104s Preparing to unpack .../base-passwd_3.6.7_arm64.deb ... 104s Unpacking base-passwd (3.6.7) over (3.6.6) ... 104s Setting up base-passwd (3.6.7) ... 105s (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 ... 117820 files and directories currently installed.) 105s Preparing to unpack .../libzstd1_1.5.7+dfsg-1_arm64.deb ... 105s Unpacking libzstd1:arm64 (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 105s Setting up libzstd1:arm64 (1.5.7+dfsg-1) ... 105s (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 ... 117820 files and directories currently installed.) 105s Preparing to unpack .../0-libunistring5_1.3-2_arm64.deb ... 105s Unpacking libunistring5:arm64 (1.3-2) over (1.3-1) ... 105s Preparing to unpack .../1-ethtool_1%3a6.14-2_arm64.deb ... 105s Unpacking ethtool (1:6.14-2) over (1:6.11-1) ... 105s Preparing to unpack .../2-libevdev2_1.13.4+dfsg-1_arm64.deb ... 105s Unpacking libevdev2:arm64 (1.13.4+dfsg-1) over (1.13.3+dfsg-1) ... 105s Preparing to unpack .../3-libmm-glib0_1.24.0-1_arm64.deb ... 105s Unpacking libmm-glib0:arm64 (1.24.0-1) over (1.23.4-0ubuntu3) ... 105s Preparing to unpack .../4-libpython3.12t64_3.12.10-1_arm64.deb ... 105s Unpacking libpython3.12t64:arm64 (3.12.10-1) over (3.12.8-3) ... 105s Preparing to unpack .../5-libpython3.12-stdlib_3.12.10-1_arm64.deb ... 105s Unpacking libpython3.12-stdlib:arm64 (3.12.10-1) over (3.12.8-3) ... 106s Preparing to unpack .../6-libpython3.12-minimal_3.12.10-1_arm64.deb ... 106s Unpacking libpython3.12-minimal:arm64 (3.12.10-1) over (3.12.8-3) ... 106s Preparing to unpack .../7-patch_2.8-1_arm64.deb ... 106s Unpacking patch (2.8-1) over (2.7.6-7build3) ... 106s Preparing to unpack .../8-zstd_1.5.7+dfsg-1_arm64.deb ... 106s Unpacking zstd (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 106s Setting up libpython3.12-minimal:arm64 (3.12.10-1) ... 106s Setting up libunistring5:arm64 (1.3-2) ... 106s Setting up patch (2.8-1) ... 106s Setting up libmm-glib0:arm64 (1.24.0-1) ... 106s Setting up libevdev2:arm64 (1.13.4+dfsg-1) ... 106s Setting up zstd (1.5.7+dfsg-1) ... 106s Setting up ethtool (1:6.14-2) ... 106s Setting up libpython3.12-stdlib:arm64 (3.12.10-1) ... 106s Setting up libpython3.12t64:arm64 (3.12.10-1) ... 106s Processing triggers for man-db (2.13.0-1) ... 107s Processing triggers for libc-bin (2.41-6ubuntu1) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Starting pkgProblemResolver with broken count: 0 109s Starting 2 pkgProblemResolver with broken count: 0 109s Done 110s Solving dependencies... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [14:58:13]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr 6 14:37:51 UTC 2025 114s autopkgtest [14:58:13]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 117s Get:1 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B] 117s Get:2 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB] 117s Get:3 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB] 117s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC 117s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 117s gpgv: Can't check signature: No public key 117s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found 119s autopkgtest [14:58:18]: testing package ncbi-blast+ version 2.16.0+ds-6build1 119s autopkgtest [14:58:18]: build not needed 125s autopkgtest [14:58:24]: test run-unit-test: preparing testbed 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 127s The following NEW packages will be installed: 127s libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+ 127s ncbi-blast+-legacy ncbi-data 127s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 19.3 MB of archives. 127s After this operation, 90.5 MB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB] 128s Get:2 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB] 128s Get:3 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB] 128s Get:4 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB] 128s Get:5 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 128s Get:6 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB] 128s Get:7 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B] 129s Fetched 19.3 MB in 1s (17.4 MB/s) 129s Selecting previously unselected package libgomp1:arm64. 129s (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 ... 117821 files and directories currently installed.) 129s Preparing to unpack .../0-libgomp1_15-20250404-0ubuntu1_arm64.deb ... 129s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ... 129s Selecting previously unselected package libmbedcrypto16:arm64. 129s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ... 129s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 129s Selecting previously unselected package libmbedx509-7:arm64. 129s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ... 129s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 129s Selecting previously unselected package libmbedtls21:arm64. 129s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ... 129s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 129s Selecting previously unselected package ncbi-data. 129s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 129s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 129s Selecting previously unselected package ncbi-blast+. 129s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_arm64.deb ... 129s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 130s Selecting previously unselected package ncbi-blast+-legacy. 130s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ... 130s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ... 130s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 130s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ... 130s Setting up libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ... 130s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ... 130s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ... 130s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 130s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ... 130s Processing triggers for man-db (2.13.0-1) ... 130s Processing triggers for libc-bin (2.41-6ubuntu1) ... 131s autopkgtest [14:58:30]: test run-unit-test: [----------------------- 132s ---Creating Database-- 132s 132s 132s Building a new DB, current time: 05/04/2025 14:58:31 132s New DB name: /tmp/autopkgtest.GHT9pk/autopkgtest_tmp/testdb 132s New DB title: testdatabase.fa 132s Sequence type: Nucleotide 132s Keep MBits: T 132s Maximum file size: 3000000000B 132s Adding sequences from FASTA; added 3 sequences in 0.181328 seconds. 132s 132s 132s ---Searching Database for Hits--- 132s Warning: [blastn] Examining 5 or more matches is recommended 132s # BLASTN 2.16.0+ 132s # Query: gnl|MYDB|1 this is sequence 1 132s # Database: testdb 132s # Fields: query id, subject id, evalue, bit score 132s # 2 hits found 132s gnl|MYDB|1 gnl2 0.0 1299 132s gnl|MYDB|1 gnl1 0.0 1299 132s # BLAST processed 1 queries 132s ---Search and Fetch An Entry From Database--- 132s >gnl1 132s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 132s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 132s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 132s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 132s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 132s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 132s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 132s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 132s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 132s PASS 132s autopkgtest [14:58:31]: test run-unit-test: -----------------------] 133s autopkgtest [14:58:32]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 133s run-unit-test PASS 133s autopkgtest [14:58:32]: @@@@@@@@@@@@@@@@@@@@ summary 133s run-unit-test PASS 150s nova [W] Using flock in prodstack6-arm64 150s Creating nova instance adt-questing-arm64-ncbi-blast+-20250504-145619-juju-7f2275-prod-proposed-migration-environment-23-55dc71e2-8c07-47a7-a9ce-f1f4b12247fb from image adt/ubuntu-questing-arm64-server-20250504.img (UUID 3e7dda1a-15da-4805-968a-898260235e53)... 150s nova [W] Timed out waiting for 738d76cf-9fd6-4744-a29d-8e8e9f940dd2 to get deleted.