0s autopkgtest [02:09:29]: starting date and time: 2024-03-18 02:09:29+0000 0s autopkgtest [02:09:29]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [02:09:29]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.sw4e15mn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:ncbi-blast+,src:mbedtls --apt-upgrade ruby-crb-blast --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ncbi-blast+/2.12.0+ds-4build1 mbedtls/2.28.7-1.1ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-16.secgroup --name adt-noble-arm64-ruby-crb-blast-20240318-020928-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 98s autopkgtest [02:11:07]: testbed dpkg architecture: arm64 98s autopkgtest [02:11:07]: testbed apt version: 2.7.12 98s autopkgtest [02:11:07]: @@@@@@@@@@@@@@@@@@@@ test bed setup 98s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 99s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3710 kB] 100s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 100s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 100s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 100s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [654 kB] 100s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 100s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 100s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 100s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4065 kB] 100s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 100s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.3 kB] 100s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 102s Fetched 9189 kB in 2s (3885 kB/s) 102s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s Calculating upgrade... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s sh: Attempting to set up Debian/Ubuntu apt sources automatically 107s sh: Distribution appears to be Ubuntu 108s Reading package lists... 109s Building dependency tree... 109s Reading state information... 109s eatmydata is already the newest version (131-1). 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s dbus is already the newest version (1.14.10-4ubuntu1). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s rng-tools-debian is already the newest version (2.4). 110s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s The following packages will be REMOVED: 111s cloud-init* python3-configobj* python3-debconf* 112s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 112s After this operation, 3252 kB disk space will be freed. 112s (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 ... 74758 files and directories currently installed.) 112s Removing cloud-init (24.1.1-0ubuntu1) ... 112s Removing python3-configobj (5.0.8-3) ... 112s Removing python3-debconf (1.5.86) ... 112s Processing triggers for man-db (2.12.0-3) ... 113s (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 ... 74369 files and directories currently installed.) 113s Purging configuration files for cloud-init (24.1.1-0ubuntu1) ... 114s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 114s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 114s invoke-rc.d: policy-rc.d denied execution of try-restart. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s linux-generic is already the newest version (6.8.0-11.11+1). 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 115s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 115s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 118s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s Calculating upgrade... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [02:11:29]: rebooting testbed after setup commands that affected boot 272s autopkgtest [02:14:01]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 275s autopkgtest [02:14:04]: @@@@@@@@@@@@@@@@@@@@ apt-source ruby-crb-blast 277s Get:1 http://ftpmaster.internal/ubuntu noble/universe ruby-crb-blast 0.6.9-5 (dsc) [2166 B] 277s Get:2 http://ftpmaster.internal/ubuntu noble/universe ruby-crb-blast 0.6.9-5 (tar) [37.2 kB] 277s Get:3 http://ftpmaster.internal/ubuntu noble/universe ruby-crb-blast 0.6.9-5 (diff) [5740 B] 277s gpgv: Signature made Mon Aug 21 21:53:37 2023 UTC 277s gpgv: using RSA key 8ED6C3F8BAC9DB7FC130A870F823A2729883C97C 277s gpgv: issuer "kanashiro@debian.org" 277s gpgv: Can't check signature: No public key 277s dpkg-source: warning: cannot verify inline signature for ./ruby-crb-blast_0.6.9-5.dsc: no acceptable signature found 278s autopkgtest [02:14:07]: testing package ruby-crb-blast version 0.6.9-5 278s autopkgtest [02:14:07]: build not needed 278s autopkgtest [02:14:07]: test gem2deb-test-runner: preparing testbed 280s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Starting pkgProblemResolver with broken count: 0 280s Starting 2 pkgProblemResolver with broken count: 0 280s Done 281s The following additional packages will be installed: 281s gem2deb-test-runner help2man libgomp1 libmbedcrypto7 libmbedtls14 281s libmbedx509-1 libruby libruby3.1 ncbi-blast+ ncbi-data rake ruby 281s ruby-activesupport ruby-bio ruby-concurrent ruby-crb-blast ruby-facade 281s ruby-fixwhich ruby-i18n ruby-net-telnet ruby-pathname2 ruby-rubygems 281s ruby-sdbm ruby-shoulda ruby-shoulda-context ruby-shoulda-matchers 281s ruby-threach ruby-trollop ruby-tzinfo ruby-webrick ruby-xmlrpc ruby-zeitwerk 281s ruby3.1 rubygems-integration 281s Suggested packages: 281s ri ruby-dev clustalw emboss bundler 281s Recommended packages: 281s zip blast2 hmmer mafft muscle probcons sim4 t-coffee fonts-lato libjs-jquery 281s The following NEW packages will be installed: 281s autopkgtest-satdep gem2deb-test-runner help2man libgomp1 libmbedcrypto7 281s libmbedtls14 libmbedx509-1 libruby libruby3.1 ncbi-blast+ ncbi-data rake 281s ruby ruby-activesupport ruby-bio ruby-concurrent ruby-crb-blast ruby-facade 281s ruby-fixwhich ruby-i18n ruby-net-telnet ruby-pathname2 ruby-rubygems 281s ruby-sdbm ruby-shoulda ruby-shoulda-context ruby-shoulda-matchers 281s ruby-threach ruby-trollop ruby-tzinfo ruby-webrick ruby-xmlrpc ruby-zeitwerk 281s ruby3.1 rubygems-integration 281s 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. 281s Need to get 24.1 MB/24.1 MB of archives. 281s After this operation, 115 MB of additional disk space will be used. 281s Get:1 /tmp/autopkgtest.RKyX5E/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [776 B] 281s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 rubygems-integration all 1.18 [5336 B] 281s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ruby-net-telnet all 0.2.0-1 [13.3 kB] 281s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ruby-webrick all 1.8.1-1 [52.3 kB] 281s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] 281s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libruby arm64 1:3.1+1 [4640 B] 281s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 ruby-sdbm arm64 1.0.0-5build3 [17.9 kB] 281s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libruby3.1 arm64 3.1.2-7ubuntu4 [5115 kB] 282s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 ruby3.1 arm64 3.1.2-7ubuntu4 [49.0 kB] 282s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 ruby-rubygems all 3.4.20-1 [238 kB] 282s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 ruby arm64 1:3.1+1 [3464 B] 282s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 rake all 13.0.6-3 [61.6 kB] 282s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 gem2deb-test-runner arm64 2.2.2 [18.2 kB] 282s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 help2man arm64 1.49.3 [201 kB] 282s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 282s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedcrypto7 arm64 2.28.7-1ubuntu1 [206 kB] 282s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedx509-1 arm64 2.28.7-1ubuntu1 [46.8 kB] 282s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 libmbedtls14 arm64 2.28.7-1ubuntu1 [82.0 kB] 282s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 282s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 ncbi-blast+ arm64 2.12.0+ds-4 [12.1 MB] 282s Get:21 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-concurrent all 1.1.6+dfsg-5build3 [212 kB] 282s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-i18n all 1.14.1-1 [42.0 kB] 282s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-tzinfo all 2.0.6-1 [55.2 kB] 282s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-zeitwerk all 2.6.8-1 [36.0 kB] 282s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-activesupport all 2:6.1.7.3+dfsg-3 [198 kB] 282s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-bio all 2.0.5-1 [656 kB] 282s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-trollop all 2.0-2.1 [14.9 kB] 282s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-facade all 1.2.1-1 [8272 B] 282s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-pathname2 all 1.8.2-2 [15.0 kB] 282s Get:30 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-fixwhich all 1.0.2-2 [4328 B] 282s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-threach all 0.2.0-2 [5364 B] 282s Get:32 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-crb-blast all 0.6.9-5 [12.4 kB] 282s Get:33 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-shoulda-context all 2.0.0-2 [16.4 kB] 282s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-shoulda-matchers all 4.3.0-2 [72.8 kB] 282s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 ruby-shoulda all 4.0.0-3 [5972 B] 283s Fetched 24.1 MB in 2s (15.8 MB/s) 283s Selecting previously unselected package rubygems-integration. 283s (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 ... 74314 files and directories currently installed.) 283s Preparing to unpack .../00-rubygems-integration_1.18_all.deb ... 283s Unpacking rubygems-integration (1.18) ... 283s Selecting previously unselected package ruby-net-telnet. 283s Preparing to unpack .../01-ruby-net-telnet_0.2.0-1_all.deb ... 283s Unpacking ruby-net-telnet (0.2.0-1) ... 283s Selecting previously unselected package ruby-webrick. 283s Preparing to unpack .../02-ruby-webrick_1.8.1-1_all.deb ... 283s Unpacking ruby-webrick (1.8.1-1) ... 283s Selecting previously unselected package ruby-xmlrpc. 283s Preparing to unpack .../03-ruby-xmlrpc_0.3.2-2_all.deb ... 283s Unpacking ruby-xmlrpc (0.3.2-2) ... 283s Selecting previously unselected package libruby:arm64. 283s Preparing to unpack .../04-libruby_1%3a3.1+1_arm64.deb ... 283s Unpacking libruby:arm64 (1:3.1+1) ... 283s Selecting previously unselected package ruby-sdbm:arm64. 283s Preparing to unpack .../05-ruby-sdbm_1.0.0-5build3_arm64.deb ... 283s Unpacking ruby-sdbm:arm64 (1.0.0-5build3) ... 283s Selecting previously unselected package libruby3.1:arm64. 283s Preparing to unpack .../06-libruby3.1_3.1.2-7ubuntu4_arm64.deb ... 283s Unpacking libruby3.1:arm64 (3.1.2-7ubuntu4) ... 284s Selecting previously unselected package ruby3.1. 284s Preparing to unpack .../07-ruby3.1_3.1.2-7ubuntu4_arm64.deb ... 284s Unpacking ruby3.1 (3.1.2-7ubuntu4) ... 284s Selecting previously unselected package ruby-rubygems. 284s Preparing to unpack .../08-ruby-rubygems_3.4.20-1_all.deb ... 284s Unpacking ruby-rubygems (3.4.20-1) ... 284s Selecting previously unselected package ruby. 284s Preparing to unpack .../09-ruby_1%3a3.1+1_arm64.deb ... 284s Unpacking ruby (1:3.1+1) ... 284s Selecting previously unselected package rake. 284s Preparing to unpack .../10-rake_13.0.6-3_all.deb ... 284s Unpacking rake (13.0.6-3) ... 284s Selecting previously unselected package gem2deb-test-runner. 284s Preparing to unpack .../11-gem2deb-test-runner_2.2.2_arm64.deb ... 284s Unpacking gem2deb-test-runner (2.2.2) ... 284s Selecting previously unselected package help2man. 284s Preparing to unpack .../12-help2man_1.49.3_arm64.deb ... 284s Unpacking help2man (1.49.3) ... 284s Selecting previously unselected package libgomp1:arm64. 284s Preparing to unpack .../13-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 284s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 284s Selecting previously unselected package libmbedcrypto7:arm64. 284s Preparing to unpack .../14-libmbedcrypto7_2.28.7-1ubuntu1_arm64.deb ... 284s Unpacking libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 284s Selecting previously unselected package libmbedx509-1:arm64. 284s Preparing to unpack .../15-libmbedx509-1_2.28.7-1ubuntu1_arm64.deb ... 284s Unpacking libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 284s Selecting previously unselected package libmbedtls14:arm64. 284s Preparing to unpack .../16-libmbedtls14_2.28.7-1ubuntu1_arm64.deb ... 284s Unpacking libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 284s Selecting previously unselected package ncbi-data. 284s Preparing to unpack .../17-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 284s Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... 284s Selecting previously unselected package ncbi-blast+. 284s Preparing to unpack .../18-ncbi-blast+_2.12.0+ds-4_arm64.deb ... 284s Unpacking ncbi-blast+ (2.12.0+ds-4) ... 285s Selecting previously unselected package ruby-concurrent. 285s Preparing to unpack .../19-ruby-concurrent_1.1.6+dfsg-5build3_all.deb ... 285s Unpacking ruby-concurrent (1.1.6+dfsg-5build3) ... 285s Selecting previously unselected package ruby-i18n. 285s Preparing to unpack .../20-ruby-i18n_1.14.1-1_all.deb ... 285s Unpacking ruby-i18n (1.14.1-1) ... 285s Selecting previously unselected package ruby-tzinfo. 285s Preparing to unpack .../21-ruby-tzinfo_2.0.6-1_all.deb ... 285s Unpacking ruby-tzinfo (2.0.6-1) ... 285s Selecting previously unselected package ruby-zeitwerk. 285s Preparing to unpack .../22-ruby-zeitwerk_2.6.8-1_all.deb ... 285s Unpacking ruby-zeitwerk (2.6.8-1) ... 285s Selecting previously unselected package ruby-activesupport. 285s Preparing to unpack .../23-ruby-activesupport_2%3a6.1.7.3+dfsg-3_all.deb ... 285s Unpacking ruby-activesupport (2:6.1.7.3+dfsg-3) ... 285s Selecting previously unselected package ruby-bio. 285s Preparing to unpack .../24-ruby-bio_2.0.5-1_all.deb ... 285s Unpacking ruby-bio (2.0.5-1) ... 285s Selecting previously unselected package ruby-trollop. 285s Preparing to unpack .../25-ruby-trollop_2.0-2.1_all.deb ... 285s Unpacking ruby-trollop (2.0-2.1) ... 285s Selecting previously unselected package ruby-facade. 285s Preparing to unpack .../26-ruby-facade_1.2.1-1_all.deb ... 285s Unpacking ruby-facade (1.2.1-1) ... 285s Selecting previously unselected package ruby-pathname2. 285s Preparing to unpack .../27-ruby-pathname2_1.8.2-2_all.deb ... 285s Unpacking ruby-pathname2 (1.8.2-2) ... 285s Selecting previously unselected package ruby-fixwhich. 285s Preparing to unpack .../28-ruby-fixwhich_1.0.2-2_all.deb ... 285s Unpacking ruby-fixwhich (1.0.2-2) ... 285s Selecting previously unselected package ruby-threach. 286s Preparing to unpack .../29-ruby-threach_0.2.0-2_all.deb ... 286s Unpacking ruby-threach (0.2.0-2) ... 286s Selecting previously unselected package ruby-crb-blast. 286s Preparing to unpack .../30-ruby-crb-blast_0.6.9-5_all.deb ... 286s Unpacking ruby-crb-blast (0.6.9-5) ... 286s Selecting previously unselected package ruby-shoulda-context. 286s Preparing to unpack .../31-ruby-shoulda-context_2.0.0-2_all.deb ... 286s Unpacking ruby-shoulda-context (2.0.0-2) ... 286s Selecting previously unselected package ruby-shoulda-matchers. 286s Preparing to unpack .../32-ruby-shoulda-matchers_4.3.0-2_all.deb ... 286s Unpacking ruby-shoulda-matchers (4.3.0-2) ... 286s Selecting previously unselected package ruby-shoulda. 286s Preparing to unpack .../33-ruby-shoulda_4.0.0-3_all.deb ... 286s Unpacking ruby-shoulda (4.0.0-3) ... 286s Selecting previously unselected package autopkgtest-satdep. 286s Preparing to unpack .../34-1-autopkgtest-satdep.deb ... 286s Unpacking autopkgtest-satdep (0) ... 286s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 286s Setting up ruby-facade (1.2.1-1) ... 286s Setting up rubygems-integration (1.18) ... 286s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 286s Setting up ruby-concurrent (1.1.6+dfsg-5build3) ... 286s Setting up help2man (1.49.3) ... 286s Setting up libmbedcrypto7:arm64 (2.28.7-1ubuntu1) ... 286s Setting up ruby-net-telnet (0.2.0-1) ... 286s Setting up ruby-i18n (1.14.1-1) ... 286s Setting up ruby-webrick (1.8.1-1) ... 286s Setting up ruby-pathname2 (1.8.2-2) ... 286s Setting up ruby-xmlrpc (0.3.2-2) ... 286s Setting up ruby-zeitwerk (2.6.8-1) ... 286s Setting up ruby-bio (2.0.5-1) ... 286s Setting up libmbedx509-1:arm64 (2.28.7-1ubuntu1) ... 286s Setting up libmbedtls14:arm64 (2.28.7-1ubuntu1) ... 286s Setting up ruby-tzinfo (2.0.6-1) ... 286s Setting up ncbi-blast+ (2.12.0+ds-4) ... 286s Setting up rake (13.0.6-3) ... 286s Setting up libruby3.1:arm64 (3.1.2-7ubuntu4) ... 286s Setting up libruby:arm64 (1:3.1+1) ... 286s Setting up ruby-rubygems (3.4.20-1) ... 286s Setting up ruby3.1 (3.1.2-7ubuntu4) ... 286s Setting up ruby-sdbm:arm64 (1.0.0-5build3) ... 286s Setting up ruby (1:3.1+1) ... 286s Setting up ruby-threach (0.2.0-2) ... 286s Setting up ruby-fixwhich (1.0.2-2) ... 286s Setting up ruby-activesupport (2:6.1.7.3+dfsg-3) ... 286s Setting up ruby-shoulda-context (2.0.0-2) ... 286s Setting up ruby-trollop (2.0-2.1) ... 286s Setting up gem2deb-test-runner (2.2.2) ... 286s Setting up ruby-crb-blast (0.6.9-5) ... 286s Setting up ruby-shoulda-matchers (4.3.0-2) ... 286s Setting up ruby-shoulda (4.0.0-3) ... 286s Setting up autopkgtest-satdep (0) ... 286s Processing triggers for libc-bin (2.39-0ubuntu2) ... 286s Processing triggers for man-db (2.12.0-3) ... 287s Processing triggers for install-info (7.1-3) ... 291s (Reading database ... 78860 files and directories currently installed.) 291s Removing autopkgtest-satdep (0) ... 291s autopkgtest [02:14:20]: test gem2deb-test-runner: gem2deb-test-runner --autopkgtest --check-dependencies 2>&1 291s autopkgtest [02:14:20]: test gem2deb-test-runner: [----------------------- 292s 292s ┌──────────────────────────────────────────────────────────────────────────────┐ 292s │ Checking Rubygems dependency resolution on ruby3.1 │ 292s └──────────────────────────────────────────────────────────────────────────────┘ 292s 292s RUBYLIB=. GEM_PATH= ruby3.1 -e gem\ \"crb-blast\" 292s mv lib ./.gem2deb.lib 292s mv ./.gem2deb.lib lib 292s 292s ┌──────────────────────────────────────────────────────────────────────────────┐ 292s │ Run tests for ruby3.1 from debian/ruby-tests.rake │ 292s └──────────────────────────────────────────────────────────────────────────────┘ 292s 292s RUBYLIB=. GEM_PATH= ruby3.1 -S rake --rakelibdir /gem2deb-nonexistent -f debian/ruby-tests.rake 292s mv lib ./.gem2deb.lib 292s /usr/bin/ruby3.1 -w -I"test" /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader.rb "test/test_test.rb" "test/test_bin.rb" "test/test_test.rb" "test/test_test2.rb" "test/test_test3.rb" -v 292s /usr/lib/ruby/vendor_ruby/fixwhich.rb:3: warning: assigned but unused variable - e 292s /usr/lib/ruby/vendor_ruby/pathname2.rb:211: warning: method redefined; discarding old children 292s /usr/share/rubygems-integration/all/gems/facade-1.2.1/lib/facade.rb:40: warning: previous definition of children was here 292s /usr/lib/ruby/vendor_ruby/threach.rb:7: warning: `*' interpreted as argument prefix 292s /tmp/autopkgtest.RKyX5E/build.Sd2/src/test/test_test3.rb:29: warning: assigned but unused variable - blaster 292s /tmp/autopkgtest.RKyX5E/build.Sd2/src/test/test_test3.rb:45: warning: assigned but unused variable - dbs 292s /tmp/autopkgtest.RKyX5E/build.Sd2/src/test/test_test3.rb:46: warning: assigned but unused variable - run 292s /tmp/autopkgtest.RKyX5E/build.Sd2/src/test/test_test3.rb:47: warning: assigned but unused variable - load 292s Loaded suite /usr/lib/ruby/gems/3.1.0/gems/rake-13.0.6/lib/rake/rake_test_loader 292s Started 292s Test2CRBBlast: 293s test: crb-blast should add secondary hits. : .: (0.656521) 293s test: crb-blast should break input file into no more pieces than there are sequences. : .: (0.349307) 294s test: crb-blast should break input file into pieces. :.: (0.300919) 294s test: crb-blast should find reciprocals. : .: (0.297909) 294s test: crb-blast should get non reciprocal hits. : .: (0.429776) 295s test: crb-blast should load output should check if the databases exist. : .: (0.521701) 295s test: crb-blast should run blast should check if the databases exist yet. : .: (0.339646) 296s test: crb-blast should setup2 should run ok. : .: (0.425711) 296s Test3CRBBlast: 296s test: crb-blast should raise error when files don't exist. : .: (0.001147) 296s test: crb-blast should run. : .: (0.400106) 296s test: crb-blast should work for query sequences with pipes. : .: (0.312836) 296s TestBinary: 297s test: crb-blast should run binary. : .: (0.155412) 297s TestCRBBlast: 297s test: crb-blast should check if contig has reciprocal hit. : .: (0.868306) 298s test: crb-blast should determine that the target is a protein sequence. : .: (0.664239) 298s test: crb-blast should find reciprocals. : .: (0.387824) 299s test: crb-blast should get number of reciprocals. : .: (0.344427) 299s test: crb-blast should get query results. : .: (0.398879) 300s test: crb-blast should load outputs. : .: (0.430007) 300s test: crb-blast should not find fake scaffold name. : .: (0.478833) 301s test: crb-blast should output all reciprocal hits. : .: (0.426795) 301s test: crb-blast should run blast. : .: (0.351090) 301s test: crb-blast should setup should run ok. : .: (0.303913) 301s 301s Finished in 8.84954104 seconds. 301s ------------------------------------------------------------------------------- 301s 22 tests, 42 assertions, 0 failures, 0 errors, 0 pendings, 0 omissions, 0 notifications 301s 100% passed 301s ------------------------------------------------------------------------------- 301s 2.49 tests/s, 4.75 assertions/s 301s mv ./.gem2deb.lib lib 302s autopkgtest [02:14:31]: test gem2deb-test-runner: -----------------------] 302s autopkgtest [02:14:31]: test gem2deb-test-runner: - - - - - - - - - - results - - - - - - - - - - 302s gem2deb-test-runner PASS 302s autopkgtest [02:14:31]: @@@@@@@@@@@@@@@@@@@@ summary 302s gem2deb-test-runner PASS 313s Creating nova instance adt-noble-arm64-ruby-crb-blast-20240318-020928-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240318.img (UUID 6b9ea2ac-1792-4f95-a56d-e128e96ab6e9)...