0s autopkgtest [14:56:33]: starting date and time: 2025-05-04 14:56:33+0000 0s autopkgtest [14:56:33]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [14:56:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rzhspcqe/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-18.secgroup --name adt-questing-s390x-ncbi-blast+-20250504-145633-juju-7f2275-prod-proposed-migration-environment-2-9ffff603-5b53-4198-ad7f-80826e59d59b --image adt/ubuntu-questing-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 62s autopkgtest [14:57:35]: testbed dpkg architecture: s390x 62s autopkgtest [14:57:35]: testbed apt version: 3.0.0 62s autopkgtest [14:57:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s autopkgtest [14:57:36]: testbed release detected to be: None 63s autopkgtest [14:57:36]: updating testbed package index (apt update) 64s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.3 kB] 64s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1153 kB] 64s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [115 kB] 64s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [143 kB] 64s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1097 kB] 64s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [28.3 kB] 64s Fetched 2680 kB in 1s (2618 kB/s) 65s Reading package lists... 66s autopkgtest [14:57:39]: upgrading testbed (apt dist-upgrade and autopurge) 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 66s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 66s Starting 2 pkgProblemResolver with broken count: 0 66s Done 66s Entering ResolveByKeep 66s 66s Calculating upgrade... 66s The following packages will be upgraded: 66s base-passwd ethtool libevdev2 libmm-glib0 libpython3.12-minimal 66s libpython3.12-stdlib libpython3.12t64 libunistring5 libzstd1 patch zstd 67s 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 7775 kB of archives. 67s After this operation, 138 kB disk space will be freed. 67s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x base-passwd s390x 3.6.7 [54.2 kB] 67s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/main s390x libzstd1 s390x 1.5.7+dfsg-1 [345 kB] 67s Get:3 http://ftpmaster.internal/ubuntu questing/main s390x libunistring5 s390x 1.3-2 [619 kB] 67s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x ethtool s390x 1:6.14-2 [243 kB] 67s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x libevdev2 s390x 1.13.4+dfsg-1 [36.0 kB] 67s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x libmm-glib0 s390x 1.24.0-1 [260 kB] 67s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12t64 s390x 3.12.10-1 [2509 kB] 67s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-stdlib s390x 3.12.10-1 [2049 kB] 67s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-minimal s390x 3.12.10-1 [836 kB] 67s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x patch s390x 2.8-1 [101 kB] 67s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/main s390x zstd s390x 1.5.7+dfsg-1 [722 kB] 67s Preconfiguring packages ... 68s Fetched 7775 kB in 1s (9924 kB/s) 68s (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 ... 81469 files and directories currently installed.) 68s Preparing to unpack .../base-passwd_3.6.7_s390x.deb ... 68s Unpacking base-passwd (3.6.7) over (3.6.6) ... 68s Setting up base-passwd (3.6.7) ... 68s (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 ... 81469 files and directories currently installed.) 68s Preparing to unpack .../libzstd1_1.5.7+dfsg-1_s390x.deb ... 68s Unpacking libzstd1:s390x (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 68s Setting up libzstd1:s390x (1.5.7+dfsg-1) ... 68s (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 ... 81469 files and directories currently installed.) 68s Preparing to unpack .../0-libunistring5_1.3-2_s390x.deb ... 68s Unpacking libunistring5:s390x (1.3-2) over (1.3-1) ... 68s Preparing to unpack .../1-ethtool_1%3a6.14-2_s390x.deb ... 68s Unpacking ethtool (1:6.14-2) over (1:6.11-1) ... 68s Preparing to unpack .../2-libevdev2_1.13.4+dfsg-1_s390x.deb ... 68s Unpacking libevdev2:s390x (1.13.4+dfsg-1) over (1.13.3+dfsg-1) ... 68s Preparing to unpack .../3-libmm-glib0_1.24.0-1_s390x.deb ... 68s Unpacking libmm-glib0:s390x (1.24.0-1) over (1.23.4-0ubuntu3) ... 68s Preparing to unpack .../4-libpython3.12t64_3.12.10-1_s390x.deb ... 68s Unpacking libpython3.12t64:s390x (3.12.10-1) over (3.12.8-3) ... 68s Preparing to unpack .../5-libpython3.12-stdlib_3.12.10-1_s390x.deb ... 68s Unpacking libpython3.12-stdlib:s390x (3.12.10-1) over (3.12.8-3) ... 68s Preparing to unpack .../6-libpython3.12-minimal_3.12.10-1_s390x.deb ... 68s Unpacking libpython3.12-minimal:s390x (3.12.10-1) over (3.12.8-3) ... 68s Preparing to unpack .../7-patch_2.8-1_s390x.deb ... 68s Unpacking patch (2.8-1) over (2.7.6-7build3) ... 68s Preparing to unpack .../8-zstd_1.5.7+dfsg-1_s390x.deb ... 68s Unpacking zstd (1.5.7+dfsg-1) over (1.5.6+dfsg-2) ... 68s Setting up libpython3.12-minimal:s390x (3.12.10-1) ... 68s Setting up libunistring5:s390x (1.3-2) ... 68s Setting up patch (2.8-1) ... 68s Setting up libmm-glib0:s390x (1.24.0-1) ... 68s Setting up libevdev2:s390x (1.13.4+dfsg-1) ... 68s Setting up zstd (1.5.7+dfsg-1) ... 68s Setting up ethtool (1:6.14-2) ... 68s Setting up libpython3.12-stdlib:s390x (3.12.10-1) ... 68s Setting up libpython3.12t64:s390x (3.12.10-1) ... 68s Processing triggers for man-db (2.13.0-1) ... 69s Processing triggers for libc-bin (2.41-6ubuntu1) ... 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Starting pkgProblemResolver with broken count: 0 69s Starting 2 pkgProblemResolver with broken count: 0 69s Done 70s Solving dependencies... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s autopkgtest [14:57:45]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 13:39:00 UTC 2025 72s autopkgtest [14:57:45]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 75s Get:1 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B] 75s Get:2 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB] 75s Get:3 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB] 75s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC 75s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 75s gpgv: Can't check signature: No public key 75s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found 76s autopkgtest [14:57:49]: testing package ncbi-blast+ version 2.16.0+ds-6build1 76s autopkgtest [14:57:49]: build not needed 81s autopkgtest [14:57:54]: test run-unit-test: preparing testbed 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Starting pkgProblemResolver with broken count: 0 82s Starting 2 pkgProblemResolver with broken count: 0 82s Done 82s The following NEW packages will be installed: 82s libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+ 82s ncbi-blast+-legacy ncbi-data 82s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 19.8 MB of archives. 82s After this operation, 87.6 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB] 82s Get:2 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB] 82s Get:3 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB] 82s Get:4 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB] 82s Get:5 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 82s Get:6 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB] 83s Get:7 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B] 83s Fetched 19.8 MB in 1s (18.8 MB/s) 83s Selecting previously unselected package libgomp1:s390x. 83s (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 ... 81470 files and directories currently installed.) 83s Preparing to unpack .../0-libgomp1_15-20250404-0ubuntu1_s390x.deb ... 83s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ... 83s Selecting previously unselected package libmbedcrypto16:s390x. 83s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ... 83s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 83s Selecting previously unselected package libmbedx509-7:s390x. 83s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ... 83s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 83s Selecting previously unselected package libmbedtls21:s390x. 83s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ... 83s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ... 83s Selecting previously unselected package ncbi-data. 83s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 83s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 83s Selecting previously unselected package ncbi-blast+. 83s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ... 83s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 83s Selecting previously unselected package ncbi-blast+-legacy. 83s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ... 83s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ... 83s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 83s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ... 83s Setting up libmbedcrypto16:s390x (3.6.2-3ubuntu1) ... 83s Setting up libmbedx509-7:s390x (3.6.2-3ubuntu1) ... 83s Setting up libmbedtls21:s390x (3.6.2-3ubuntu1) ... 83s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 83s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ... 83s Processing triggers for man-db (2.13.0-1) ... 84s Processing triggers for libc-bin (2.41-6ubuntu1) ... 85s autopkgtest [14:57:58]: test run-unit-test: [----------------------- 85s ---Creating Database-- 85s 85s 85s Building a new DB, current time: 05/04/2025 14:57:58 85s New DB name: /tmp/autopkgtest.Iah4kc/autopkgtest_tmp/testdb 85s New DB title: testdatabase.fa 85s Sequence type: Nucleotide 85s Keep MBits: T 85s Maximum file size: 3000000000B 85s Adding sequences from FASTA; added 3 sequences in 0.319133 seconds. 85s 85s 85s ---Searching Database for Hits--- 85s Warning: [blastn] Examining 5 or more matches is recommended 85s # BLASTN 2.16.0+ 85s # Query: gnl|MYDB|1 this is sequence 1 85s # Database: testdb 85s # Fields: query id, subject id, evalue, bit score 85s # 2 hits found 85s gnl|MYDB|1 gnl2 0.0 1299 85s gnl|MYDB|1 gnl1 0.0 1299 85s # BLAST processed 1 queries 85s ---Search and Fetch An Entry From Database--- 86s >gnl1 86s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 86s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 86s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 86s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 86s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 86s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 86s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 86s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 86s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 86s PASS 86s autopkgtest [14:57:59]: test run-unit-test: -----------------------] 86s run-unit-test PASS 86s autopkgtest [14:57:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 87s autopkgtest [14:58:00]: @@@@@@@@@@@@@@@@@@@@ summary 87s run-unit-test PASS 91s nova [W] Using flock in prodstack6-s390x 91s Creating nova instance adt-questing-s390x-ncbi-blast+-20250504-145633-juju-7f2275-prod-proposed-migration-environment-2-9ffff603-5b53-4198-ad7f-80826e59d59b from image adt/ubuntu-questing-s390x-server-20250504.img (UUID b0c8ef7b-1328-4750-b680-0f812c3e85f1)... 91s nova [W] Timed out waiting for 82286e2d-d8ad-4834-b56e-6dbb27e558b7 to get deleted.