0s autopkgtest [20:34:13]: starting date and time: 2025-05-04 20:34:13+0000
  0s autopkgtest [20:34:13]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production'
  0s autopkgtest [20:34:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5381uqf6/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-11.secgroup --name adt-questing-arm64-ncbi-blast+-20250504-203413-juju-7f2275-prod-proposed-migration-environment-2-f48c1b27-2d39-4c92-94d2-5d59cf645d01 --image adt/ubuntu-questing-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
173s autopkgtest [20:37:06]: testbed dpkg architecture: arm64
173s autopkgtest [20:37:06]: testbed apt version: 3.0.0
173s autopkgtest [20:37:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup
173s autopkgtest [20:37:06]: testbed release detected to be: None
174s autopkgtest [20:37:07]: updating testbed package index (apt update)
174s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [110 kB]
175s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease
175s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease
175s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease
175s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [111 kB]
175s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [1095 kB]
175s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [33.9 kB]
175s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 Packages [143 kB]
175s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 Packages [1104 kB]
175s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/multiverse arm64 Packages [30.1 kB]
175s Fetched 2627 kB in 1s (2582 kB/s)
176s Reading package lists...
177s autopkgtest [20:37:10]: upgrading testbed (apt dist-upgrade and autopurge)
177s Reading package lists...
177s Building dependency tree...
177s Reading state information...
178s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
178s Starting 2 pkgProblemResolver with broken count: 0
178s Done
178s Entering ResolveByKeep
179s 
179s Calculating upgrade...
179s The following packages will be upgraded:
179s   base-passwd ethtool libbpf1 libevdev2 libmm-glib0 libnghttp2-14
179s   libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsqlite3-0
179s   libunistring5 libusb-1.0-0 man-db patch usbutils
179s 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
179s Need to get 8938 kB of archives.
179s After this operation, 133 kB disk space will be freed.
179s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 base-passwd arm64 3.6.7 [54.2 kB]
180s Get:2 http://ftpmaster.internal/ubuntu questing/main arm64 libbpf1 arm64 1:1.5.0-3 [182 kB]
180s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/main arm64 libsqlite3-0 arm64 3.46.1-4 [707 kB]
180s Get:4 http://ftpmaster.internal/ubuntu questing/main arm64 libunistring5 arm64 1.3-2 [601 kB]
180s Get:5 http://ftpmaster.internal/ubuntu questing/main arm64 ethtool arm64 1:6.14-2 [242 kB]
180s Get:6 http://ftpmaster.internal/ubuntu questing/main arm64 libevdev2 arm64 1.13.4+dfsg-1 [35.8 kB]
180s Get:7 http://ftpmaster.internal/ubuntu questing/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [74.6 kB]
180s Get:8 http://ftpmaster.internal/ubuntu questing/main arm64 libusb-1.0-0 arm64 2:1.0.28-1 [54.8 kB]
180s Get:9 http://ftpmaster.internal/ubuntu questing/main arm64 man-db arm64 2.13.1-1 [1369 kB]
180s Get:10 http://ftpmaster.internal/ubuntu questing/main arm64 usbutils arm64 1:018-2 [81.5 kB]
180s Get:11 http://ftpmaster.internal/ubuntu questing/main arm64 libmm-glib0 arm64 1.24.0-1 [262 kB]
180s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12t64 arm64 3.12.10-1 [2314 kB]
180s Get:13 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-stdlib arm64 3.12.10-1 [2029 kB]
180s Get:14 http://ftpmaster.internal/ubuntu questing-proposed/universe arm64 libpython3.12-minimal arm64 3.12.10-1 [836 kB]
180s Get:15 http://ftpmaster.internal/ubuntu questing/main arm64 patch arm64 2.8-1 [94.0 kB]
180s Preconfiguring packages ...
181s Fetched 8938 kB in 1s (9737 kB/s)
181s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117820 files and directories currently installed.)
181s Preparing to unpack .../base-passwd_3.6.7_arm64.deb ...
181s Unpacking base-passwd (3.6.7) over (3.6.6) ...
181s Setting up base-passwd (3.6.7) ...
181s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 117820 files and directories currently installed.)
181s Preparing to unpack .../00-libbpf1_1%3a1.5.0-3_arm64.deb ...
181s Unpacking libbpf1:arm64 (1:1.5.0-3) over (1:1.5.0-2) ...
181s Preparing to unpack .../01-libsqlite3-0_3.46.1-4_arm64.deb ...
181s Unpacking libsqlite3-0:arm64 (3.46.1-4) over (3.46.1-3) ...
181s Preparing to unpack .../02-libunistring5_1.3-2_arm64.deb ...
181s Unpacking libunistring5:arm64 (1.3-2) over (1.3-1) ...
181s Preparing to unpack .../03-ethtool_1%3a6.14-2_arm64.deb ...
181s Unpacking ethtool (1:6.14-2) over (1:6.11-1) ...
181s Preparing to unpack .../04-libevdev2_1.13.4+dfsg-1_arm64.deb ...
181s Unpacking libevdev2:arm64 (1.13.4+dfsg-1) over (1.13.3+dfsg-1) ...
181s Preparing to unpack .../05-libnghttp2-14_1.64.0-1.1_arm64.deb ...
181s Unpacking libnghttp2-14:arm64 (1.64.0-1.1) over (1.64.0-1ubuntu1) ...
181s Preparing to unpack .../06-libusb-1.0-0_2%3a1.0.28-1_arm64.deb ...
181s Unpacking libusb-1.0-0:arm64 (2:1.0.28-1) over (2:1.0.27-2) ...
181s Preparing to unpack .../07-man-db_2.13.1-1_arm64.deb ...
181s Unpacking man-db (2.13.1-1) over (2.13.0-1) ...
182s Preparing to unpack .../08-usbutils_1%3a018-2_arm64.deb ...
182s Unpacking usbutils (1:018-2) over (1:018-1) ...
182s Preparing to unpack .../09-libmm-glib0_1.24.0-1_arm64.deb ...
182s Unpacking libmm-glib0:arm64 (1.24.0-1) over (1.23.4-0ubuntu3) ...
182s Preparing to unpack .../10-libpython3.12t64_3.12.10-1_arm64.deb ...
182s Unpacking libpython3.12t64:arm64 (3.12.10-1) over (3.12.8-3) ...
182s Preparing to unpack .../11-libpython3.12-stdlib_3.12.10-1_arm64.deb ...
182s Unpacking libpython3.12-stdlib:arm64 (3.12.10-1) over (3.12.8-3) ...
182s Preparing to unpack .../12-libpython3.12-minimal_3.12.10-1_arm64.deb ...
182s Unpacking libpython3.12-minimal:arm64 (3.12.10-1) over (3.12.8-3) ...
182s Preparing to unpack .../13-patch_2.8-1_arm64.deb ...
182s Unpacking patch (2.8-1) over (2.7.6-7build3) ...
182s Setting up libsqlite3-0:arm64 (3.46.1-4) ...
182s Setting up libpython3.12-minimal:arm64 (3.12.10-1) ...
182s Setting up libnghttp2-14:arm64 (1.64.0-1.1) ...
182s Setting up man-db (2.13.1-1) ...
182s Updating database of manual pages ...
185s man-db.service is a disabled or a static unit not running, not starting it.
185s Setting up libunistring5:arm64 (1.3-2) ...
185s Setting up patch (2.8-1) ...
185s Setting up libmm-glib0:arm64 (1.24.0-1) ...
185s Setting up libusb-1.0-0:arm64 (2:1.0.28-1) ...
185s Setting up libevdev2:arm64 (1.13.4+dfsg-1) ...
185s Setting up libbpf1:arm64 (1:1.5.0-3) ...
185s Setting up ethtool (1:6.14-2) ...
185s Setting up libpython3.12-stdlib:arm64 (3.12.10-1) ...
185s Setting up usbutils (1:018-2) ...
185s Setting up libpython3.12t64:arm64 (3.12.10-1) ...
185s Processing triggers for libc-bin (2.41-6ubuntu1) ...
185s Reading package lists...
185s Building dependency tree...
185s Reading state information...
186s Starting pkgProblemResolver with broken count: 0
186s Starting 2 pkgProblemResolver with broken count: 0
186s Done
186s Solving dependencies...
187s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
187s autopkgtest [20:37:20]: rebooting testbed after setup commands that affected boot
210s autopkgtest [20:37:43]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Sun Apr  6 14:37:51 UTC 2025
213s autopkgtest [20:37:46]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+
217s Get:1 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B]
217s Get:2 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB]
217s Get:3 http://ftpmaster.internal/ubuntu questing/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB]
217s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC
217s gpgv:                using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D
217s gpgv: Can't check signature: No public key
217s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found
218s autopkgtest [20:37:51]: testing package ncbi-blast+ version 2.16.0+ds-6build1
219s autopkgtest [20:37:52]: build not needed
224s autopkgtest [20:37:57]: test run-unit-test: preparing testbed
224s Reading package lists...
224s Building dependency tree...
224s Reading state information...
224s Starting pkgProblemResolver with broken count: 0
225s Starting 2 pkgProblemResolver with broken count: 0
225s Done
225s The following NEW packages will be installed:
225s   libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+
225s   ncbi-blast+-legacy ncbi-data
225s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
225s Need to get 19.3 MB of archives.
225s After this operation, 90.5 MB of additional disk space will be used.
225s Get:1 http://ftpmaster.internal/ubuntu questing/main arm64 libgomp1 arm64 15-20250404-0ubuntu1 [147 kB]
226s Get:2 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedcrypto16 arm64 3.6.2-3ubuntu1 [258 kB]
226s Get:3 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedx509-7 arm64 3.6.2-3ubuntu1 [35.7 kB]
226s Get:4 http://ftpmaster.internal/ubuntu questing/universe arm64 libmbedtls21 arm64 3.6.2-3ubuntu1 [122 kB]
226s Get:5 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB]
226s Get:6 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+ arm64 2.16.0+ds-6build1 [14.8 MB]
227s Get:7 http://ftpmaster.internal/ubuntu questing/universe arm64 ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B]
227s Fetched 19.3 MB in 1s (14.0 MB/s)
227s Selecting previously unselected package libgomp1:arm64.
227s (Reading database ... 
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(Reading database ... 117830 files and directories currently installed.)
227s Preparing to unpack .../0-libgomp1_15-20250404-0ubuntu1_arm64.deb ...
227s Unpacking libgomp1:arm64 (15-20250404-0ubuntu1) ...
227s Selecting previously unselected package libmbedcrypto16:arm64.
228s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_arm64.deb ...
228s Unpacking libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ...
228s Selecting previously unselected package libmbedx509-7:arm64.
228s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_arm64.deb ...
228s Unpacking libmbedx509-7:arm64 (3.6.2-3ubuntu1) ...
228s Selecting previously unselected package libmbedtls21:arm64.
228s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_arm64.deb ...
228s Unpacking libmbedtls21:arm64 (3.6.2-3ubuntu1) ...
228s Selecting previously unselected package ncbi-data.
228s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ...
228s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ...
228s Selecting previously unselected package ncbi-blast+.
228s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_arm64.deb ...
228s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ...
228s Selecting previously unselected package ncbi-blast+-legacy.
228s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ...
228s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ...
228s Setting up ncbi-data (6.1.20170106+dfsg2-5) ...
228s Setting up libgomp1:arm64 (15-20250404-0ubuntu1) ...
228s Setting up libmbedcrypto16:arm64 (3.6.2-3ubuntu1) ...
228s Setting up libmbedx509-7:arm64 (3.6.2-3ubuntu1) ...
228s Setting up libmbedtls21:arm64 (3.6.2-3ubuntu1) ...
228s Setting up ncbi-blast+ (2.16.0+ds-6build1) ...
228s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ...
228s Processing triggers for man-db (2.13.1-1) ...
229s Processing triggers for libc-bin (2.41-6ubuntu1) ...
230s autopkgtest [20:38:03]: test run-unit-test: [-----------------------
231s ---Creating Database--
231s 
231s 
231s Building a new DB, current time: 05/04/2025 20:38:04
231s New DB name:   /tmp/autopkgtest.Ob4Koo/autopkgtest_tmp/testdb
231s New DB title:  testdatabase.fa
231s Sequence type: Nucleotide
231s Keep MBits: T
231s Maximum file size: 3000000000B
231s Adding sequences from FASTA; added 3 sequences in 0.181117 seconds.
231s 
231s 
231s ---Searching Database for Hits---
231s Warning: [blastn] Examining 5 or more matches is recommended
231s # BLASTN 2.16.0+
231s # Query: gnl|MYDB|1 this is sequence 1
231s # Database: testdb
231s # Fields: query id, subject id, evalue, bit score
231s # 2 hits found
231s gnl|MYDB|1	gnl2	0.0	1299
231s gnl|MYDB|1	gnl1	0.0	1299
231s # BLAST processed 1 queries
231s ---Search and Fetch An Entry From Database---
231s >gnl1 
231s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
231s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
231s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
231s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
231s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
231s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
231s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
231s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
231s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
231s PASS
232s autopkgtest [20:38:05]: test run-unit-test: -----------------------]
232s autopkgtest [20:38:05]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
232s run-unit-test        PASS
232s autopkgtest [20:38:05]: @@@@@@@@@@@@@@@@@@@@ summary
232s run-unit-test        PASS
250s nova [W] Using flock in prodstack6-arm64
250s flock: timeout while waiting to get lock
250s Creating nova instance adt-questing-arm64-ncbi-blast+-20250504-203413-juju-7f2275-prod-proposed-migration-environment-2-f48c1b27-2d39-4c92-94d2-5d59cf645d01 from image adt/ubuntu-questing-arm64-server-20250504.img (UUID 3e7dda1a-15da-4805-968a-898260235e53)...
250s nova [W] Timed out waiting for 5908f1fe-9c53-4323-ba3f-1b118ccf5d45 to get deleted.