0s autopkgtest [05:05:18]: starting date and time: 2025-02-22 05:05:18+0000
  0s autopkgtest [05:05:18]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [05:05:18]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rzj716cs/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glib2.0 --apt-upgrade exonerate --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glib2.0/2.83.4-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-8.secgroup --name adt-plucky-ppc64el-exonerate-20250222-050518-juju-7f2275-prod-proposed-migration-environment-20-3982d604-9274-433c-93c2-2badfbbffb92 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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,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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 96s autopkgtest [05:06:54]: testbed dpkg architecture: ppc64el
 96s autopkgtest [05:06:54]: testbed apt version: 2.9.30ubuntu1
 96s autopkgtest [05:06:54]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 97s autopkgtest [05:06:55]: testbed release detected to be: None
 97s autopkgtest [05:06:55]: updating testbed package index (apt update)
 98s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB]
 98s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 98s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 98s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 98s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [80.1 kB]
 98s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [508 kB]
 98s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B]
 98s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB]
 98s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [125 kB]
 98s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [760 B]
 98s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [434 kB]
 98s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [3292 B]
 98s Fetched 1279 kB in 1s (1337 kB/s)
 99s Reading package lists...
100s Reading package lists...
100s Building dependency tree...
100s Reading state information...
100s Calculating upgrade...
100s Calculating upgrade...
100s The following packages will be upgraded:
100s   apparmor apport apport-core-dump-handler base-files cloud-init
100s   cloud-init-base gcc-14-base libapparmor1 libclang-cpp18 libclang1-19
100s   libgnutls30t64 libllvm18 libllvm19 liblsof0 libnss3 libperl5.40 lsof
100s   motd-news-config perl perl-base perl-modules-5.40 python3-apport
100s   python3-problem-report ucf vim-common vim-tiny xxd
101s 27 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
101s Need to get 99.0 MB of archives.
101s After this operation, 56.3 kB disk space will be freed.
101s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el motd-news-config all 13.6ubuntu1 [5168 B]
101s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el base-files ppc64el 13.6ubuntu1 [75.6 kB]
101s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el perl-modules-5.40 all 5.40.1-2 [3217 kB]
103s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libperl5.40 ppc64el 5.40.1-2 [4948 kB]
105s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el perl ppc64el 5.40.1-2 [262 kB]
105s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el perl-base ppc64el 5.40.1-2 [1923 kB]
106s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-problem-report all 2.31.0+git20250220-0ubuntu1 [26.0 kB]
106s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-apport all 2.31.0+git20250220-0ubuntu1 [93.5 kB]
106s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el apport-core-dump-handler all 2.31.0+git20250220-0ubuntu1 [18.7 kB]
106s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el apport all 2.31.0+git20250220-0ubuntu1 [83.1 kB]
106s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-base ppc64el 14.2.0-17ubuntu3 [53.6 kB]
106s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libapparmor1 ppc64el 4.1.0~beta5-0ubuntu5 [58.8 kB]
106s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.9-2ubuntu2 [1079 kB]
107s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el ucf all 3.0050 [43.5 kB]
107s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el vim-tiny ppc64el 2:9.1.0967-1ubuntu2 [1079 kB]
107s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el vim-common all 2:9.1.0967-1ubuntu2 [396 kB]
108s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el xxd ppc64el 2:9.1.0967-1ubuntu2 [68.4 kB]
108s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el apparmor ppc64el 4.1.0~beta5-0ubuntu5 [806 kB]
108s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el lsof ppc64el 4.99.4+dfsg-2 [256 kB]
108s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsof0 ppc64el 4.99.4+dfsg-2 [68.5 kB]
108s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el cloud-init-base all 25.1-0ubuntu1 [616 kB]
109s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libclang-cpp18 ppc64el 1:18.1.8-16build1 [14.4 MB]
113s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el libllvm18 ppc64el 1:18.1.8-16build1 [28.6 MB]
115s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el libllvm19 ppc64el 1:19.1.7-1ubuntu2 [29.8 MB]
117s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libclang1-19 ppc64el 1:19.1.7-1ubuntu2 [9141 kB]
117s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnss3 ppc64el 2:3.108-1ubuntu1 [1869 kB]
117s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el cloud-init all 25.1-0ubuntu1 [2088 B]
118s Preconfiguring packages ...
118s Fetched 99.0 MB in 17s (5820 kB/s)
118s (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 ... 106370 files and directories currently installed.)
118s Preparing to unpack .../motd-news-config_13.6ubuntu1_all.deb ...
118s Unpacking motd-news-config (13.6ubuntu1) over (13.5ubuntu3) ...
118s Preparing to unpack .../base-files_13.6ubuntu1_ppc64el.deb ...
118s Unpacking base-files (13.6ubuntu1) over (13.5ubuntu3) ...
118s Setting up base-files (13.6ubuntu1) ...
118s Updating /root/.profile to current default.
119s motd-news.service is a disabled or a static unit not running, not starting it.
119s (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 ... 106370 files and directories currently installed.)
119s Preparing to unpack .../perl_5.40.1-2_ppc64el.deb ...
119s Unpacking perl (5.40.1-2) over (5.40.0-8) ...
119s Preparing to unpack .../perl-modules-5.40_5.40.1-2_all.deb ...
119s Unpacking perl-modules-5.40 (5.40.1-2) over (5.40.0-8) ...
119s Preparing to unpack .../libperl5.40_5.40.1-2_ppc64el.deb ...
119s Unpacking libperl5.40:ppc64el (5.40.1-2) over (5.40.0-8) ...
120s Preparing to unpack .../perl-base_5.40.1-2_ppc64el.deb ...
120s Unpacking perl-base (5.40.1-2) over (5.40.0-8) ...
120s Setting up perl-base (5.40.1-2) ...
120s (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 ... 106370 files and directories currently installed.)
120s Preparing to unpack .../00-python3-problem-report_2.31.0+git20250220-0ubuntu1_all.deb ...
120s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead.
120s   for fn in glob1(directory, "%s.*" % fname):
120s Unpacking python3-problem-report (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ...
120s Preparing to unpack .../01-python3-apport_2.31.0+git20250220-0ubuntu1_all.deb ...
120s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead.
120s   for fn in glob1(directory, "%s.*" % fname):
120s Unpacking python3-apport (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ...
120s Preparing to unpack .../02-apport-core-dump-handler_2.31.0+git20250220-0ubuntu1_all.deb ...
120s Unpacking apport-core-dump-handler (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ...
120s Preparing to unpack .../03-apport_2.31.0+git20250220-0ubuntu1_all.deb ...
120s Unpacking apport (2.31.0+git20250220-0ubuntu1) over (2.31.0-0ubuntu5) ...
120s Preparing to unpack .../04-gcc-14-base_14.2.0-17ubuntu3_ppc64el.deb ...
120s Unpacking gcc-14-base:ppc64el (14.2.0-17ubuntu3) over (14.2.0-17ubuntu1) ...
120s Preparing to unpack .../05-libapparmor1_4.1.0~beta5-0ubuntu5_ppc64el.deb ...
120s Unpacking libapparmor1:ppc64el (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ...
120s Preparing to unpack .../06-libgnutls30t64_3.8.9-2ubuntu2_ppc64el.deb ...
120s Unpacking libgnutls30t64:ppc64el (3.8.9-2ubuntu2) over (3.8.9-2ubuntu1) ...
120s Preparing to unpack .../07-ucf_3.0050_all.deb ...
120s Unpacking ucf (3.0050) over (3.0049) ...
120s Preparing to unpack .../08-vim-tiny_2%3a9.1.0967-1ubuntu2_ppc64el.deb ...
120s Unpacking vim-tiny (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ...
120s Preparing to unpack .../09-vim-common_2%3a9.1.0967-1ubuntu2_all.deb ...
120s Unpacking vim-common (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ...
120s Preparing to unpack .../10-xxd_2%3a9.1.0967-1ubuntu2_ppc64el.deb ...
120s Unpacking xxd (2:9.1.0967-1ubuntu2) over (2:9.1.0861-1ubuntu1) ...
120s Preparing to unpack .../11-apparmor_4.1.0~beta5-0ubuntu5_ppc64el.deb ...
121s Unpacking apparmor (4.1.0~beta5-0ubuntu5) over (4.1.0~beta5-0ubuntu4) ...
121s Preparing to unpack .../12-lsof_4.99.4+dfsg-2_ppc64el.deb ...
121s Unpacking lsof (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ...
121s Preparing to unpack .../13-liblsof0_4.99.4+dfsg-2_ppc64el.deb ...
121s Unpacking liblsof0 (4.99.4+dfsg-2) over (4.99.4+dfsg-1) ...
121s Preparing to unpack .../14-cloud-init-base_25.1-0ubuntu1_all.deb ...
121s /usr/bin/py3clean:101: DeprecationWarning: glob.glob1 is deprecated and will be removed in Python 3.15. Use glob.glob and pass a directory to its root_dir argument instead.
121s   for fn in glob1(directory, "%s.*" % fname):
121s Unpacking cloud-init-base (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ...
121s Preparing to unpack .../15-libclang-cpp18_1%3a18.1.8-16build1_ppc64el.deb ...
121s Unpacking libclang-cpp18 (1:18.1.8-16build1) over (1:18.1.8-15) ...
122s Preparing to unpack .../16-libllvm18_1%3a18.1.8-16build1_ppc64el.deb ...
122s Unpacking libllvm18:ppc64el (1:18.1.8-16build1) over (1:18.1.8-15) ...
122s Preparing to unpack .../17-libllvm19_1%3a19.1.7-1ubuntu2_ppc64el.deb ...
122s Unpacking libllvm19:ppc64el (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ...
123s Preparing to unpack .../18-libclang1-19_1%3a19.1.7-1ubuntu2_ppc64el.deb ...
123s Unpacking libclang1-19 (1:19.1.7-1ubuntu2) over (1:19.1.7-1ubuntu1) ...
123s Preparing to unpack .../19-libnss3_2%3a3.108-1ubuntu1_ppc64el.deb ...
123s Unpacking libnss3:ppc64el (2:3.108-1ubuntu1) over (2:3.107-1ubuntu1) ...
123s Preparing to unpack .../20-cloud-init_25.1-0ubuntu1_all.deb ...
123s Unpacking cloud-init (25.1-0ubuntu1) over (25.1~3geb1965a4-0ubuntu1) ...
123s Setting up libgnutls30t64:ppc64el (3.8.9-2ubuntu2) ...
123s Setting up motd-news-config (13.6ubuntu1) ...
123s Setting up libllvm19:ppc64el (1:19.1.7-1ubuntu2) ...
123s Setting up libapparmor1:ppc64el (4.1.0~beta5-0ubuntu5) ...
123s Setting up libclang1-19 (1:19.1.7-1ubuntu2) ...
123s Setting up gcc-14-base:ppc64el (14.2.0-17ubuntu3) ...
123s Setting up python3-problem-report (2.31.0+git20250220-0ubuntu1) ...
123s Setting up liblsof0 (4.99.4+dfsg-2) ...
123s Setting up libnss3:ppc64el (2:3.108-1ubuntu1) ...
123s Setting up cloud-init-base (25.1-0ubuntu1) ...
125s Setting up xxd (2:9.1.0967-1ubuntu2) ...
125s Setting up python3-apport (2.31.0+git20250220-0ubuntu1) ...
125s Setting up apparmor (4.1.0~beta5-0ubuntu5) ...
125s Installing new version of config file /etc/apparmor.d/fusermount3 ...
126s Reloading AppArmor profiles 
128s Setting up vim-common (2:9.1.0967-1ubuntu2) ...
128s Setting up ucf (3.0050) ...
128s Setting up lsof (4.99.4+dfsg-2) ...
128s Setting up perl-modules-5.40 (5.40.1-2) ...
128s Setting up libllvm18:ppc64el (1:18.1.8-16build1) ...
128s Setting up cloud-init (25.1-0ubuntu1) ...
128s Setting up vim-tiny (2:9.1.0967-1ubuntu2) ...
128s Setting up libperl5.40:ppc64el (5.40.1-2) ...
128s Setting up perl (5.40.1-2) ...
128s Setting up libclang-cpp18 (1:18.1.8-16build1) ...
128s Setting up apport-core-dump-handler (2.31.0+git20250220-0ubuntu1) ...
129s Setting up apport (2.31.0+git20250220-0ubuntu1) ...
130s apport-autoreport.service is a disabled or a static unit not running, not starting it.
130s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-2ubuntu5) ...
130s Processing triggers for install-info (7.1.1-1) ...
130s Processing triggers for libc-bin (2.40-4ubuntu1) ...
130s Processing triggers for rsyslog (8.2412.0-2ubuntu1) ...
130s Processing triggers for systemd (257.2-3ubuntu1) ...
130s Processing triggers for man-db (2.13.0-1) ...
132s Processing triggers for initramfs-tools (0.145ubuntu2) ...
132s update-initramfs: Generating /boot/initrd.img-6.12.0-15-generic
132s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
142s Reading package lists...autopkgtest [05:07:38]: upgrading testbed (apt dist-upgrade and autopurge)
142s 
142s Building dependency tree...
142s Reading state information...
142s Solving dependencies...
142s 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
142s Reading package lists...
142s Building dependency tree...
142s Reading state information...
142s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
142s Starting 2 pkgProblemResolver with broken count: 0
142s Done
142s Entering ResolveByKeep
142s 
142s Calculating upgrade...
142s The following packages will be upgraded:
142s   gir1.2-glib-2.0 libglib2.0-0t64 libglib2.0-data
142s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
142s Need to get 2038 kB of archives.
142s After this operation, 2048 B of additional disk space will be used.
142s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el gir1.2-glib-2.0 ppc64el 2.83.4-1 [184 kB]
142s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libglib2.0-0t64 ppc64el 2.83.4-1 [1801 kB]
143s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libglib2.0-data all 2.83.4-1 [52.9 kB]
143s Fetched 2038 kB in 2s (1165 kB/s)
144s (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 ... 106371 files and directories currently installed.)
144s Preparing to unpack .../gir1.2-glib-2.0_2.83.4-1_ppc64el.deb ...
144s Unpacking gir1.2-glib-2.0:ppc64el (2.83.4-1) over (2.83.3-2) ...
144s Preparing to unpack .../libglib2.0-0t64_2.83.4-1_ppc64el.deb ...
144s Unpacking libglib2.0-0t64:ppc64el (2.83.4-1) over (2.83.3-2) ...
144s Preparing to unpack .../libglib2.0-data_2.83.4-1_all.deb ...
144s Unpacking libglib2.0-data (2.83.4-1) over (2.83.3-2) ...
144s Setting up libglib2.0-0t64:ppc64el (2.83.4-1) ...
144s No schema files found: doing nothing.
144s Setting up libglib2.0-data (2.83.4-1) ...
144s Setting up gir1.2-glib-2.0:ppc64el (2.83.4-1) ...
144s Processing triggers for libc-bin (2.40-4ubuntu1) ...
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
144s Starting pkgProblemResolver with broken count: 0
145s Starting 2 pkgProblemResolver with broken count: 0
145s Done
145s Solving dependencies...
145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s autopkgtest [05:07:43]: rebooting testbed after setup commands that affected boot
175s autopkgtest [05:08:13]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP Tue Feb  4 16:32:08 UTC 2025
178s autopkgtest [05:08:16]: @@@@@@@@@@@@@@@@@@@@ apt-source exonerate
180s Get:1 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (dsc) [2187 B]
180s Get:2 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (tar) [521 kB]
180s Get:3 http://ftpmaster.internal/ubuntu plucky/universe exonerate 2.4.0-5build2 (diff) [9364 B]
180s gpgv: Signature made Mon Apr  1 05:47:10 2024 UTC
180s gpgv:                using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984
180s gpgv: Can't check signature: No public key
180s dpkg-source: warning: cannot verify inline signature for ./exonerate_2.4.0-5build2.dsc: no acceptable signature found
180s autopkgtest [05:08:18]: testing package exonerate version 2.4.0-5build2
181s autopkgtest [05:08:19]: build not needed
181s autopkgtest [05:08:19]: test run-unit-test: preparing testbed
182s Reading package lists...
182s Building dependency tree...
182s Reading state information...
182s Starting pkgProblemResolver with broken count: 0
182s Starting 2 pkgProblemResolver with broken count: 0
182s Done
182s The following NEW packages will be installed:
182s   exonerate
182s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
182s Need to get 2050 kB of archives.
182s After this operation, 8839 kB of additional disk space will be used.
182s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ppc64el exonerate ppc64el 2.4.0-5build2 [2050 kB]
184s Fetched 2050 kB in 1s (1465 kB/s)
184s Selecting previously unselected package exonerate.
184s (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 ... 106371 files and directories currently installed.)
184s Preparing to unpack .../exonerate_2.4.0-5build2_ppc64el.deb ...
184s Unpacking exonerate (2.4.0-5build2) ...
184s Setting up exonerate (2.4.0-5build2) ...
184s Processing triggers for man-db (2.13.0-1) ...
186s autopkgtest [05:08:24]: test run-unit-test: [-----------------------
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/ipcress/ipcress.simple.test.sh
186s ** Message: 05:08:24.547: Loaded [1] experiments
186s Ipcress run successfully
186s Found 1 product, as expected
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaremove.test.sh
186s Have calmodulin in input
186s ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN]
186s exiting ...
186s Calmodulin successfully removed
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastadiff.test.sh
186s fastadiff: id mismatch: CALM_HUMAN P53_HUMAN
186s Different seqs recognised as different
186s Identity test OK
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastatranslate.test.sh
186s Extraced CDS for translation
186s Tranlated sequence
186s Tranlsated sequence correct
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastalength.test.sh
186s 149 CALM_HUMAN
186s Calmodulin length OK
186s Calmodulin identifier OK
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastanrdb.test.sh
186s Made input file for fastanrdb
186s Successfully ran fastanrdb on: fastanrdb.input.test.fasta
186s Expected number of seqs in output: 4
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaclip.test.sh
186s Clipped OK
186s >test:subseq(0,4)
186s ACGT
186s Clipped input correctly
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastasort.test.sh
186s Sorted CALM_HUMAN 149
186s Sorted P53_HUMAN 393
186s Sorted TUBE_DROME 462
186s Sorted AF01595 1132
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: odd_length length (7) not divisible by 3
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: too_short length (4) not divisible by 3
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: no_start missing start codon (has:AAA)
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: no_end missing stop codon (has:TTT)
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: in_frame_stop contains in-frame stop codon (pos:9, codon:TAG)
186s 
186s ** (process:1530): WARNING **: 05:08:24.586: non_acgt_base contains non-ACGT base: [pos: 5 base: N]
186s ** FATAL ERROR **: Could not find identifier [A_MISSING_FROM_START] (missing -F ?)
186s exiting ...
186s ** FATAL ERROR **: Could not find identifier [M_MISSING_FROM_MIDDLE] (missing -F ?)
186s exiting ...
186s ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END] (missing -F ?)
186s exiting ...
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastarefomat.test.sh
186s Reformatted OK
186s >test
186s ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT
186s Reformatted length consistent
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastavalidcds.test.sh
186s Validiated CDS sequences OK
186s >valid_seq
186s ATGAAACCCGGGTTTTAA
186s Validated correctly a single seq from input
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaclean.test.sh
186s >CALM_HUMAN:filter(clean)
186s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
186s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
186s EFVQMMTAK
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaoverlap.test.sh
186s /usr/bin/fastaoverlap working OK
186s Generated 15
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaexpode.test.sh
186s Made input file for fastaexplode
186s Make output directory for fastaexplode
186s Successfully ran fastaexplode on: fastaexplode.test.fasta
186s Expected number of seqs in output: 4
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastasubseq.test.sh
186s Generated correct subseq
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastaindex.fastafetch.test.sh
186s Made index fastafetch.test.idx
186s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx CALM_HUMAN
186s expect 0
186s >CALM_HUMAN
186s MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
186s TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
186s EFVQMMTAK
186s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx P53_HUMAN
186s expect 0
186s >P53_HUMAN
186s MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
186s PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
186s CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
186s TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR
186s DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
186s KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
186s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx A_MISSING_FROM_START
186s expect 1
186s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx M_MISSING_FROM_MIDDLE
186s expect 1
186s /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx z_MISSING_FROM_END
186s expect 1
186s fastaindex fastafetch test OK
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastacomposition.test.sh
186s Calmodulin cDNA composition correct
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastasoftmask.fastahardmask.test.sh
186s Softmasked OK
186s >test
186s ACGNAACCGGNNAAACCCGGGNNNAAAACCCCGGGGNNNN
186s Hardmasked OK
186s Hardmasked file is same as original masked file
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastarevcomp.test.sh
186s Reverse complement created : ./data/cdna/calm.human.dna.fasta
186s Reverse complement created : fastarevcomp.rc.test.fasta
186s RC length is the same
186s RC length is the same
186s 2nd reverse complement same as original
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/util/fastasplit.test.sh
186s Split fastasplit.test.fasta OK
186s Split into two files as expected
186s Input len 2136
186s Output len 2136
186s Input and output lengths match
186s 
186s /tmp/autopkgtest.7lk3HY/autopkgtest_tmp/exonerate/exonerate.simple.test.sh
186s Exonerate simple test OK
186s Score as expected: 10875
186s PASS
186s autopkgtest [05:08:24]: test run-unit-test: -----------------------]
187s run-unit-test        PASS
187s autopkgtest [05:08:25]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
187s autopkgtest [05:08:25]: @@@@@@@@@@@@@@@@@@@@ summary
187s run-unit-test        PASS
192s nova [W] Using flock in prodstack6-ppc64el
192s Creating nova instance adt-plucky-ppc64el-exonerate-20250222-050518-juju-7f2275-prod-proposed-migration-environment-20-3982d604-9274-433c-93c2-2badfbbffb92 from image adt/ubuntu-plucky-ppc64el-server-20250221.img (UUID 2f98d860-9c02-405f-ad5b-1c2fc9874794)...
192s nova [W] Timed out waiting for 5bf043fe-1a6f-4f5f-a8e5-b824dd2588a0 to get deleted.