0s autopkgtest [21:08:29]: starting date and time: 2025-05-04 21:08:29+0000
  0s autopkgtest [21:08:29]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production'
  0s autopkgtest [21:08:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ymqi05i7/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sqlite3 --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sqlite3/3.46.1-4 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-2.secgroup --name adt-questing-s390x-ncbi-blast+-20250504-203509-juju-7f2275-prod-proposed-migration-environment-2-8312400c-c603-4d1f-9beb-4fbfd472b1d3 --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/
102s autopkgtest [21:10:11]: testbed dpkg architecture: s390x
102s autopkgtest [21:10:11]: testbed apt version: 3.0.0
103s autopkgtest [21:10:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
103s autopkgtest [21:10:12]: testbed release detected to be: None
103s autopkgtest [21:10:12]: updating testbed package index (apt update)
104s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB]
104s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease
104s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease
104s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease
104s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.9 kB]
104s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1095 kB]
104s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [111 kB]
104s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main s390x Packages [136 kB]
104s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x Packages [1022 kB]
104s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse s390x Packages [28.8 kB]
105s Fetched 2537 kB in 1s (2541 kB/s)
105s Reading package lists...
106s autopkgtest [21:10:15]: upgrading testbed (apt dist-upgrade and autopurge)
106s Reading package lists...
106s Building dependency tree...
106s Reading state information...
106s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
106s Starting 2 pkgProblemResolver with broken count: 0
106s Done
106s Entering ResolveByKeep
106s 
107s Calculating upgrade...
107s The following packages will be upgraded:
107s   base-passwd ethtool libbpf1 libevdev2 libmm-glib0 libnghttp2-14
107s   libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsqlite3-0
107s   libunistring5 libusb-1.0-0 man-db patch usbutils
107s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
107s Need to get 9248 kB of archives.
107s After this operation, 95.2 kB disk space will be freed.
107s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x base-passwd s390x 3.6.7 [54.2 kB]
107s Get:2 http://ftpmaster.internal/ubuntu questing/main s390x libbpf1 s390x 1:1.5.0-3 [188 kB]
107s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main s390x libsqlite3-0 s390x 3.46.1-4 [749 kB]
107s Get:4 http://ftpmaster.internal/ubuntu questing/main s390x libunistring5 s390x 1.3-2 [619 kB]
107s Get:5 http://ftpmaster.internal/ubuntu questing/main s390x ethtool s390x 1:6.14-2 [243 kB]
107s Get:6 http://ftpmaster.internal/ubuntu questing/main s390x libevdev2 s390x 1.13.4+dfsg-1 [36.0 kB]
107s Get:7 http://ftpmaster.internal/ubuntu questing/main s390x libnghttp2-14 s390x 1.64.0-1.1 [77.2 kB]
107s Get:8 http://ftpmaster.internal/ubuntu questing/main s390x libusb-1.0-0 s390x 2:1.0.28-1 [54.4 kB]
107s Get:9 http://ftpmaster.internal/ubuntu questing/main s390x man-db s390x 2.13.1-1 [1386 kB]
107s Get:10 http://ftpmaster.internal/ubuntu questing/main s390x usbutils s390x 1:018-2 [85.6 kB]
107s Get:11 http://ftpmaster.internal/ubuntu questing/main s390x libmm-glib0 s390x 1.24.0-1 [260 kB]
107s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12t64 s390x 3.12.10-1 [2509 kB]
107s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-stdlib s390x 3.12.10-1 [2049 kB]
108s Get:14 http://ftpmaster.internal/ubuntu questing-proposed/universe s390x libpython3.12-minimal s390x 3.12.10-1 [836 kB]
108s Get:15 http://ftpmaster.internal/ubuntu questing/main s390x patch s390x 2.8-1 [101 kB]
108s Preconfiguring packages ...
108s Fetched 9248 kB in 1s (9998 kB/s)
108s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81469 files and directories currently installed.)
108s Preparing to unpack .../base-passwd_3.6.7_s390x.deb ...
108s Unpacking base-passwd (3.6.7) over (3.6.6) ...
108s Setting up base-passwd (3.6.7) ...
108s (Reading database ... 
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 81469 files and directories currently installed.)
108s Preparing to unpack .../00-libbpf1_1%3a1.5.0-3_s390x.deb ...
108s Unpacking libbpf1:s390x (1:1.5.0-3) over (1:1.5.0-2) ...
108s Preparing to unpack .../01-libsqlite3-0_3.46.1-4_s390x.deb ...
108s Unpacking libsqlite3-0:s390x (3.46.1-4) over (3.46.1-3) ...
108s Preparing to unpack .../02-libunistring5_1.3-2_s390x.deb ...
108s Unpacking libunistring5:s390x (1.3-2) over (1.3-1) ...
108s Preparing to unpack .../03-ethtool_1%3a6.14-2_s390x.deb ...
108s Unpacking ethtool (1:6.14-2) over (1:6.11-1) ...
108s Preparing to unpack .../04-libevdev2_1.13.4+dfsg-1_s390x.deb ...
108s Unpacking libevdev2:s390x (1.13.4+dfsg-1) over (1.13.3+dfsg-1) ...
108s Preparing to unpack .../05-libnghttp2-14_1.64.0-1.1_s390x.deb ...
108s Unpacking libnghttp2-14:s390x (1.64.0-1.1) over (1.64.0-1ubuntu1) ...
108s Preparing to unpack .../06-libusb-1.0-0_2%3a1.0.28-1_s390x.deb ...
108s Unpacking libusb-1.0-0:s390x (2:1.0.28-1) over (2:1.0.27-2) ...
108s Preparing to unpack .../07-man-db_2.13.1-1_s390x.deb ...
108s Unpacking man-db (2.13.1-1) over (2.13.0-1) ...
108s Preparing to unpack .../08-usbutils_1%3a018-2_s390x.deb ...
108s Unpacking usbutils (1:018-2) over (1:018-1) ...
108s Preparing to unpack .../09-libmm-glib0_1.24.0-1_s390x.deb ...
108s Unpacking libmm-glib0:s390x (1.24.0-1) over (1.23.4-0ubuntu3) ...
108s Preparing to unpack .../10-libpython3.12t64_3.12.10-1_s390x.deb ...
108s Unpacking libpython3.12t64:s390x (3.12.10-1) over (3.12.8-3) ...
108s Preparing to unpack .../11-libpython3.12-stdlib_3.12.10-1_s390x.deb ...
108s Unpacking libpython3.12-stdlib:s390x (3.12.10-1) over (3.12.8-3) ...
108s Preparing to unpack .../12-libpython3.12-minimal_3.12.10-1_s390x.deb ...
108s Unpacking libpython3.12-minimal:s390x (3.12.10-1) over (3.12.8-3) ...
108s Preparing to unpack .../13-patch_2.8-1_s390x.deb ...
108s Unpacking patch (2.8-1) over (2.7.6-7build3) ...
109s Setting up libsqlite3-0:s390x (3.46.1-4) ...
109s Setting up libpython3.12-minimal:s390x (3.12.10-1) ...
109s Setting up libnghttp2-14:s390x (1.64.0-1.1) ...
109s Setting up man-db (2.13.1-1) ...
109s Updating database of manual pages ...
110s man-db.service is a disabled or a static unit not running, not starting it.
110s Setting up libunistring5:s390x (1.3-2) ...
110s Setting up patch (2.8-1) ...
110s Setting up libmm-glib0:s390x (1.24.0-1) ...
110s Setting up libusb-1.0-0:s390x (2:1.0.28-1) ...
110s Setting up libevdev2:s390x (1.13.4+dfsg-1) ...
110s Setting up libbpf1:s390x (1:1.5.0-3) ...
110s Setting up ethtool (1:6.14-2) ...
110s Setting up libpython3.12-stdlib:s390x (3.12.10-1) ...
110s Setting up usbutils (1:018-2) ...
110s Setting up libpython3.12t64:s390x (3.12.10-1) ...
110s Processing triggers for libc-bin (2.41-6ubuntu1) ...
110s Reading package lists...
110s Building dependency tree...
110s Reading state information...
111s Starting pkgProblemResolver with broken count: 0
111s Starting 2 pkgProblemResolver with broken count: 0
111s Done
111s Solving dependencies...
111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
111s autopkgtest [21:10:20]: rebooting testbed after setup commands that affected boot
129s autopkgtest [21:10:38]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr  6 13:39:00 UTC 2025
131s autopkgtest [21:10:40]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+
134s Get:1 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B]
134s Get:2 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB]
134s Get:3 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB]
134s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC
134s gpgv:                using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D
134s gpgv: Can't check signature: No public key
134s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found
135s autopkgtest [21:10:44]: testing package ncbi-blast+ version 2.16.0+ds-6build1
135s autopkgtest [21:10:44]: build not needed
140s autopkgtest [21:10:49]: test run-unit-test: preparing testbed
140s Reading package lists...
141s Building dependency tree...
141s Reading state information...
141s Starting pkgProblemResolver with broken count: 0
141s Starting 2 pkgProblemResolver with broken count: 0
141s Done
141s The following NEW packages will be installed:
141s   libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+
141s   ncbi-blast+-legacy ncbi-data
141s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
141s Need to get 19.8 MB of archives.
141s After this operation, 87.6 MB of additional disk space will be used.
141s Get:1 http://ftpmaster.internal/ubuntu questing/main s390x libgomp1 s390x 15-20250404-0ubuntu1 [152 kB]
141s Get:2 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedcrypto16 s390x 3.6.2-3ubuntu1 [261 kB]
141s Get:3 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedx509-7 s390x 3.6.2-3ubuntu1 [34.9 kB]
141s Get:4 http://ftpmaster.internal/ubuntu questing/universe s390x libmbedtls21 s390x 3.6.2-3ubuntu1 [122 kB]
141s Get:5 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB]
142s Get:6 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+ s390x 2.16.0+ds-6build1 [15.2 MB]
142s Get:7 http://ftpmaster.internal/ubuntu questing/universe s390x ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B]
142s Fetched 19.8 MB in 1s (19.1 MB/s)
142s Selecting previously unselected package libgomp1:s390x.
142s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 81479 files and directories currently installed.)
142s Preparing to unpack .../0-libgomp1_15-20250404-0ubuntu1_s390x.deb ...
142s Unpacking libgomp1:s390x (15-20250404-0ubuntu1) ...
142s Selecting previously unselected package libmbedcrypto16:s390x.
142s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_s390x.deb ...
142s Unpacking libmbedcrypto16:s390x (3.6.2-3ubuntu1) ...
142s Selecting previously unselected package libmbedx509-7:s390x.
142s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_s390x.deb ...
142s Unpacking libmbedx509-7:s390x (3.6.2-3ubuntu1) ...
142s Selecting previously unselected package libmbedtls21:s390x.
142s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_s390x.deb ...
142s Unpacking libmbedtls21:s390x (3.6.2-3ubuntu1) ...
142s Selecting previously unselected package ncbi-data.
142s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ...
142s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ...
142s Selecting previously unselected package ncbi-blast+.
142s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_s390x.deb ...
142s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ...
143s Selecting previously unselected package ncbi-blast+-legacy.
143s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ...
143s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ...
143s Setting up ncbi-data (6.1.20170106+dfsg2-5) ...
143s Setting up libgomp1:s390x (15-20250404-0ubuntu1) ...
143s Setting up libmbedcrypto16:s390x (3.6.2-3ubuntu1) ...
143s Setting up libmbedx509-7:s390x (3.6.2-3ubuntu1) ...
143s Setting up libmbedtls21:s390x (3.6.2-3ubuntu1) ...
143s Setting up ncbi-blast+ (2.16.0+ds-6build1) ...
143s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ...
143s Processing triggers for man-db (2.13.1-1) ...
143s Processing triggers for libc-bin (2.41-6ubuntu1) ...
144s autopkgtest [21:10:53]: test run-unit-test: [-----------------------
144s ---Creating Database--
144s 
144s 
144s Building a new DB, current time: 05/04/2025 21:12:18
144s New DB name:   /tmp/autopkgtest.KTjhT0/autopkgtest_tmp/testdb
144s New DB title:  testdatabase.fa
144s Sequence type: Nucleotide
144s Keep MBits: T
144s Maximum file size: 3000000000B
145s Adding sequences from FASTA; added 3 sequences in 0.361839 seconds.
145s 
145s 
145s ---Searching Database for Hits---
145s Warning: [blastn] Examining 5 or more matches is recommended
145s # BLASTN 2.16.0+
145s # Query: gnl|MYDB|1 this is sequence 1
145s # Database: testdb
145s # Fields: query id, subject id, evalue, bit score
145s # 2 hits found
145s gnl|MYDB|1	gnl2	0.0	1299
145s gnl|MYDB|1	gnl1	0.0	1299
145s # BLAST processed 1 queries
145s ---Search and Fetch An Entry From Database---
145s >gnl1 
145s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
145s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
145s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
145s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
145s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
145s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
145s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
145s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
145s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
145s PASS
145s autopkgtest [21:10:54]: test run-unit-test: -----------------------]
146s run-unit-test        PASS
146s autopkgtest [21:10:55]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
146s autopkgtest [21:10:55]: @@@@@@@@@@@@@@@@@@@@ summary
146s run-unit-test        PASS
162s nova [W] Using flock in prodstack6-s390x
162s Creating nova instance adt-questing-s390x-ncbi-blast+-20250504-203509-juju-7f2275-prod-proposed-migration-environment-2-8312400c-c603-4d1f-9beb-4fbfd472b1d3 from image adt/ubuntu-questing-s390x-server-20250504.img (UUID b0c8ef7b-1328-4750-b680-0f812c3e85f1)...
162s nova [W] Timed out waiting for 238f523e-4061-4253-ad1b-0a7ed2282f42 to get deleted.