0s autopkgtest [14:30:39]: starting date and time: 2025-03-15 14:30:39+0000 0s autopkgtest [14:30:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [14:30:39]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0bxlywo5/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:glibc --apt-upgrade ncbi-blast+ --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [14:30:59]: testbed dpkg architecture: armhf 22s autopkgtest [14:31:01]: testbed apt version: 2.9.33 26s autopkgtest [14:31:05]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [14:31:07]: testbed release detected to be: None 36s autopkgtest [14:31:15]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [404 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [81.0 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1944 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [326 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [12.1 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3472 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [332 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 40s Get:16 http://ftpmaster.internal/ubuntu plucky/main Sources [1400 kB] 41s Get:17 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 60s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.4 kB] 60s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 60s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.1 MB] 76s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 78s Fetched 41.0 MB in 40s (1021 kB/s) 79s Reading package lists... 85s autopkgtest [14:32:04]: upgrading testbed (apt dist-upgrade and autopurge) 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 88s Starting 2 pkgProblemResolver with broken count: 0 88s Done 89s Entering ResolveByKeep 89s 89s Calculating upgrade... 90s The following packages will be upgraded: 90s libc-bin libc6 locales python3-jinja2 sos strace 90s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 8642 kB of archives. 90s After this operation, 23.6 kB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc6 armhf 2.41-1ubuntu2 [2932 kB] 94s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libc-bin armhf 2.41-1ubuntu2 [545 kB] 94s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf locales all 2.41-1ubuntu2 [4246 kB] 99s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 100s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 100s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 101s Preconfiguring packages ... 101s Fetched 8642 kB in 10s (855 kB/s) 101s (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 ... 64655 files and directories currently installed.) 101s Preparing to unpack .../libc6_2.41-1ubuntu2_armhf.deb ... 101s Unpacking libc6:armhf (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 102s Setting up libc6:armhf (2.41-1ubuntu2) ... 102s (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 ... 64655 files and directories currently installed.) 102s Preparing to unpack .../libc-bin_2.41-1ubuntu2_armhf.deb ... 102s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 102s Setting up libc-bin (2.41-1ubuntu2) ... 102s (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 ... 64655 files and directories currently installed.) 102s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 102s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 103s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 103s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 103s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 103s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 103s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 103s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 104s Setting up sos (4.9.0-5) ... 105s Setting up locales (2.41-1ubuntu2) ... 106s Generating locales (this might take a while)... 107s en_US.UTF-8... done 107s Generation complete. 107s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 108s Setting up strace (6.13+ds-1ubuntu1) ... 108s Processing triggers for man-db (2.13.0-1) ... 109s Processing triggers for systemd (257.3-1ubuntu3) ... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 112s Solving dependencies... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [14:32:34]: rebooting testbed after setup commands that affected boot 154s autopkgtest [14:33:13]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 180s autopkgtest [14:33:39]: @@@@@@@@@@@@@@@@@@@@ apt-source ncbi-blast+ 214s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6build1 (dsc) [2401 B] 214s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6build1 (tar) [18.4 MB] 214s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ncbi-blast+ 2.16.0+ds-6build1 (diff) [40.8 kB] 215s gpgv: Signature made Thu Nov 21 15:47:04 2024 UTC 215s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 215s gpgv: Can't check signature: No public key 215s dpkg-source: warning: cannot verify inline signature for ./ncbi-blast+_2.16.0+ds-6build1.dsc: no acceptable signature found 216s autopkgtest [14:34:15]: testing package ncbi-blast+ version 2.16.0+ds-6build1 218s autopkgtest [14:34:17]: build not needed 226s autopkgtest [14:34:25]: test run-unit-test: preparing testbed 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Starting pkgProblemResolver with broken count: 0 228s Starting 2 pkgProblemResolver with broken count: 0 228s Done 229s The following NEW packages will be installed: 229s libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 ncbi-blast+ 229s ncbi-blast+-legacy ncbi-data 229s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 229s Need to get 19.3 MB of archives. 229s After this operation, 72.9 MB of additional disk space will be used. 229s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 230s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedcrypto16 armhf 3.6.2-3ubuntu1 [226 kB] 230s Get:3 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedx509-7 armhf 3.6.2-3ubuntu1 [30.4 kB] 230s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libmbedtls21 armhf 3.6.2-3ubuntu1 [116 kB] 230s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-data all 6.1.20170106+dfsg2-5 [3966 kB] 234s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-blast+ armhf 2.16.0+ds-6build1 [14.8 MB] 247s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf ncbi-blast+-legacy all 2.16.0+ds-6build1 [4984 B] 248s Fetched 19.3 MB in 18s (1065 kB/s) 248s Selecting previously unselected package libgomp1:armhf. 248s (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 ... 64655 files and directories currently installed.) 248s Preparing to unpack .../0-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 248s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 248s Selecting previously unselected package libmbedcrypto16:armhf. 248s Preparing to unpack .../1-libmbedcrypto16_3.6.2-3ubuntu1_armhf.deb ... 248s Unpacking libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 248s Selecting previously unselected package libmbedx509-7:armhf. 248s Preparing to unpack .../2-libmbedx509-7_3.6.2-3ubuntu1_armhf.deb ... 248s Unpacking libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 248s Selecting previously unselected package libmbedtls21:armhf. 248s Preparing to unpack .../3-libmbedtls21_3.6.2-3ubuntu1_armhf.deb ... 248s Unpacking libmbedtls21:armhf (3.6.2-3ubuntu1) ... 248s Selecting previously unselected package ncbi-data. 248s Preparing to unpack .../4-ncbi-data_6.1.20170106+dfsg2-5_all.deb ... 248s Unpacking ncbi-data (6.1.20170106+dfsg2-5) ... 248s Selecting previously unselected package ncbi-blast+. 248s Preparing to unpack .../5-ncbi-blast+_2.16.0+ds-6build1_armhf.deb ... 248s Unpacking ncbi-blast+ (2.16.0+ds-6build1) ... 248s Selecting previously unselected package ncbi-blast+-legacy. 248s Preparing to unpack .../6-ncbi-blast+-legacy_2.16.0+ds-6build1_all.deb ... 248s Unpacking ncbi-blast+-legacy (2.16.0+ds-6build1) ... 248s Setting up ncbi-data (6.1.20170106+dfsg2-5) ... 248s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 248s Setting up libmbedcrypto16:armhf (3.6.2-3ubuntu1) ... 248s Setting up libmbedx509-7:armhf (3.6.2-3ubuntu1) ... 248s Setting up libmbedtls21:armhf (3.6.2-3ubuntu1) ... 248s Setting up ncbi-blast+ (2.16.0+ds-6build1) ... 248s Setting up ncbi-blast+-legacy (2.16.0+ds-6build1) ... 248s Processing triggers for man-db (2.13.0-1) ... 249s Processing triggers for libc-bin (2.41-1ubuntu2) ... 259s autopkgtest [14:34:58]: test run-unit-test: [----------------------- 261s ---Creating Database-- 261s 261s 261s Building a new DB, current time: 03/15/2025 14:35:00 261s New DB name: /tmp/autopkgtest.s895y7/autopkgtest_tmp/testdb 261s New DB title: testdatabase.fa 261s Sequence type: Nucleotide 261s Keep MBits: T 261s Maximum file size: 3000000000B 261s Adding sequences from FASTA; added 3 sequences in 0.2169 seconds. 261s 261s 261s ---Searching Database for Hits--- 261s Warning: [blastn] Examining 5 or more matches is recommended 261s # BLASTN 2.16.0+ 261s # Query: gnl|MYDB|1 this is sequence 1 261s # Database: testdb 261s # Fields: query id, subject id, evalue, bit score 261s # 2 hits found 261s gnl|MYDB|1 gnl2 0.0 1299 261s gnl|MYDB|1 gnl1 0.0 1299 261s # BLAST processed 1 queries 261s ---Search and Fetch An Entry From Database--- 261s >gnl1 261s GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG 261s TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA 261s GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT 261s GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG 261s GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT 261s TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG 261s CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT 261s TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT 261s CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA 261s PASS 261s autopkgtest [14:35:00]: test run-unit-test: -----------------------] 266s run-unit-test PASS 266s autopkgtest [14:35:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 270s autopkgtest [14:35:09]: @@@@@@@@@@@@@@@@@@@@ summary 270s run-unit-test PASS