0s autopkgtest [19:45:08]: starting date: 2024-02-23 0s autopkgtest [19:45:08]: git checkout: d9c0295 adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [19:45:08]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h5lp6guf/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:ruby-defaults,src:genomethreader --apt-upgrade genomethreader --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ruby-defaults/1:3.2~ubuntu1 genomethreader/1.7.3+dfsg-8ubuntu1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-4.secgroup --name adt-noble-amd64-genomethreader-20240223-194508-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 63s autopkgtest [19:46:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 63s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [819 kB] 63s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [13.8 kB] 63s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [92.5 kB] 63s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [9872 B] 63s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [120 kB] 63s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [202 kB] 63s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 63s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [4976 B] 63s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [52.6 kB] 63s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 63s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [333 kB] 63s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [971 kB] 63s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 63s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [10.2 kB] 63s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [2392 B] 63s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 64s Fetched 2761 kB in 0s (5943 kB/s) 64s Reading package lists... 66s Reading package lists... 66s Building dependency tree... 66s Reading state information... 67s Calculating upgrade... 67s The following packages were automatically installed and are no longer required: 67s irqbalance libnuma1 67s Use 'sudo apt autoremove' to remove them. 67s The following packages will be upgraded: 67s apport apport-core-dump-handler apt apt-utils base-files bash binutils 67s binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 67s coreutils dash debconf debconf-i18n eject fdisk gzip hostname 67s inetutils-telnet libapt-pkg6.0 libbinutils libblkid1 libbz2-1.0 libc-bin 67s libc6 libcap2 libcap2-bin libctf-nobfd0 libctf0 libfdisk1 libffi8 67s libgprofng0 libmount1 libnuma1 libpam-cap libpam-modules libpam-modules-bin 67s libpam-runtime libpam0g libsframe1 libsmartcols1 libuuid1 libxml2 locales 67s login lto-disabled-list motd-news-config mount passwd python-apt-common 67s python3-apport python3-apt python3-debconf python3-problem-report 67s python3-pyrsistent sysvinit-utils telnet ubuntu-minimal ubuntu-standard 67s util-linux uuid-runtime 67s 63 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 23.1 MB of archives. 67s After this operation, 164 kB disk space will be freed. 67s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 motd-news-config all 13ubuntu7 [5080 B] 67s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 locales all 2.39-0ubuntu2 [4230 kB] 67s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.39-0ubuntu2 [3262 kB] 67s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.39-0ubuntu2 [682 kB] 67s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] 67s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 python3-debconf all 1.5.86 [4160 B] 67s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] 67s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu7 [74.2 kB] 67s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu2 [794 kB] 67s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.3-6ubuntu2 [94.6 kB] 67s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 coreutils amd64 9.4-2ubuntu4 [1412 kB] 67s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu3 [89.7 kB] 67s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] 67s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] 67s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] 67s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.3-6ubuntu2 [1127 kB] 67s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] 67s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5ubuntu1 [34.6 kB] 67s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5ubuntu1 [34.4 kB] 67s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libapt-pkg6.0 amd64 2.7.12 [982 kB] 67s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 apt amd64 2.7.12 [1377 kB] 67s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 apt-utils amd64 2.7.12 [217 kB] 67s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.2-9.1ubuntu3 [65.9 kB] 67s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu3 [48.1 kB] 67s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu3 [285 kB] 67s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.3-6ubuntu2 [118 kB] 67s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.3-6ubuntu2 [64.1 kB] 67s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.3-6ubuntu2 [34.5 kB] 67s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.3-6ubuntu2 [33.0 kB] 67s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 python-apt-common all 2.7.6 [19.7 kB] 67s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 python3-apt amd64 2.7.6 [206 kB] 67s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 python3-problem-report all 2.28.0-0ubuntu1 [23.6 kB] 67s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 python3-apport all 2.28.0-0ubuntu1 [92.0 kB] 67s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 apport-core-dump-handler all 2.28.0-0ubuntu1 [16.6 kB] 67s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 apport all 2.28.0-0ubuntu1 [83.9 kB] 67s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.3-6ubuntu2 [122 kB] 67s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] 67s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.3-6ubuntu2 [134 kB] 67s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.2-9.1ubuntu3 [40.4 kB] 67s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] 67s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] 67s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 eject amd64 2.39.3-6ubuntu2 [26.3 kB] 67s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-cap amd64 1:2.66-5ubuntu1 [12.4 kB] 67s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2-bin amd64 1:2.66-5ubuntu1 [34.2 kB] 67s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.3-6ubuntu2 [146 kB] 67s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu1 [762 kB] 67s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-minimal amd64 1.532 [10.3 kB] 67s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.3-6ubuntu2 [73.7 kB] 67s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 inetutils-telnet amd64 2:2.5-3ubuntu1 [99.5 kB] 67s Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libnuma1 amd64 2.0.18-1 [23.2 kB] 67s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 telnet all 0.17+2.5-3ubuntu1 [3682 B] 67s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-standard amd64 1.532 [10.3 kB] 67s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-3ubuntu1 [851 kB] 67s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-3ubuntu1 [94.5 kB] 67s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-3ubuntu1 [97.1 kB] 67s Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-3ubuntu1 [2469 kB] 67s Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-3ubuntu1 [18.0 kB] 67s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-3ubuntu1 [573 kB] 67s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-3ubuntu1 [239 kB] 67s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-3ubuntu1 [14.9 kB] 67s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 fdisk amd64 2.39.3-6ubuntu2 [121 kB] 67s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] 67s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 python3-pyrsistent amd64 0.20.0-1 [59.2 kB] 68s Preconfiguring packages ... 68s Fetched 23.1 MB in 0s (123 MB/s) 68s (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 ... 70450 files and directories currently installed.) 68s Preparing to unpack .../motd-news-config_13ubuntu7_all.deb ... 68s Unpacking motd-news-config (13ubuntu7) over (13ubuntu6) ... 68s Preparing to unpack .../locales_2.39-0ubuntu2_all.deb ... 68s Unpacking locales (2.39-0ubuntu2) over (2.38-3ubuntu1) ... 68s Preparing to unpack .../libc6_2.39-0ubuntu2_amd64.deb ... 68s Checking for services that may need to be restarted... 68s Checking init scripts... 68s Checking for services that may need to be restarted... 68s Checking init scripts... 68s Stopping some services possibly affected by the upgrade (will be restarted later): 68s cron: stopping...done. 68s 68s Unpacking libc6:amd64 (2.39-0ubuntu2) over (2.38-3ubuntu1) ... 69s Setting up libc6:amd64 (2.39-0ubuntu2) ... 69s Checking for services that may need to be restarted... 69s Checking init scripts... 69s Restarting services possibly affected by the upgrade: 69s cron: restarting...done. 69s 69s Services restarted successfully. 69s (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 ... 70461 files and directories currently installed.) 69s Preparing to unpack .../libc-bin_2.39-0ubuntu2_amd64.deb ... 69s Unpacking libc-bin (2.39-0ubuntu2) over (2.38-3ubuntu1) ... 69s Setting up libc-bin (2.39-0ubuntu2) ... 69s (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 ... 70461 files and directories currently installed.) 69s Preparing to unpack .../debconf-i18n_1.5.86_all.deb ... 69s Unpacking debconf-i18n (1.5.86) over (1.5.82) ... 69s Preparing to unpack .../python3-debconf_1.5.86_all.deb ... 69s Unpacking python3-debconf (1.5.86) over (1.5.82) ... 70s Preparing to unpack .../debconf_1.5.86_all.deb ... 70s Unpacking debconf (1.5.86) over (1.5.82) ... 70s Setting up debconf (1.5.86) ... 70s Installing new version of config file /etc/debconf.conf ... 70s (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 ... 70460 files and directories currently installed.) 70s Preparing to unpack .../base-files_13ubuntu7_amd64.deb ... 70s Unpacking base-files (13ubuntu7) over (13ubuntu6) ... 70s Setting up base-files (13ubuntu7) ... 71s motd-news.service is a disabled or a static unit not running, not starting it. 71s (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 ... 70467 files and directories currently installed.) 71s Preparing to unpack .../bash_5.2.21-2ubuntu2_amd64.deb ... 71s Unpacking bash (5.2.21-2ubuntu2) over (5.2.21-2ubuntu1) ... 71s Setting up bash (5.2.21-2ubuntu2) ... 71s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 71s (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 ... 70467 files and directories currently installed.) 71s Preparing to unpack .../bsdutils_1%3a2.39.3-6ubuntu2_amd64.deb ... 71s Unpacking bsdutils (1:2.39.3-6ubuntu2) over (1:2.39.2-6ubuntu1) ... 71s Setting up bsdutils (1:2.39.3-6ubuntu2) ... 71s (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 ... 70467 files and directories currently installed.) 71s Preparing to unpack .../coreutils_9.4-2ubuntu4_amd64.deb ... 71s Unpacking coreutils (9.4-2ubuntu4) over (9.4-2ubuntu2) ... 71s Setting up coreutils (9.4-2ubuntu4) ... 71s (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 ... 70467 files and directories currently installed.) 71s Preparing to unpack .../dash_0.5.12-6ubuntu3_amd64.deb ... 71s Unpacking dash (0.5.12-6ubuntu3) over (0.5.12-6ubuntu1) ... 71s Setting up dash (0.5.12-6ubuntu3) ... 71s (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 ... 70466 files and directories currently installed.) 71s Preparing to unpack .../gzip_1.12-1ubuntu2_amd64.deb ... 71s Unpacking gzip (1.12-1ubuntu2) over (1.12-1ubuntu1) ... 71s dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') 71s dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') 71s Setting up gzip (1.12-1ubuntu2) ... 71s (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 ... 70466 files and directories currently installed.) 71s Preparing to unpack .../hostname_3.23+nmu2ubuntu1_amd64.deb ... 71s Unpacking hostname (3.23+nmu2ubuntu1) over (3.23+nmu1ubuntu1) ... 71s Setting up hostname (3.23+nmu2ubuntu1) ... 71s (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 ... 70466 files and directories currently installed.) 71s Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu1_amd64.deb ... 71s Unpacking login (1:4.13+dfsg1-4ubuntu1) over (1:4.13+dfsg1-3ubuntu1) ... 71s Setting up login (1:4.13+dfsg1-4ubuntu1) ... 72s (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 ... 70466 files and directories currently installed.) 72s Preparing to unpack .../util-linux_2.39.3-6ubuntu2_amd64.deb ... 72s Unpacking util-linux (2.39.3-6ubuntu2) over (2.39.2-6ubuntu1) ... 72s Setting up util-linux (2.39.3-6ubuntu2) ... 72s fstrim.service is a disabled or a static unit not running, not starting it. 72s (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 ... 70467 files and directories currently installed.) 72s Preparing to unpack .../sysvinit-utils_3.08-6ubuntu2_amd64.deb ... 72s Unpacking sysvinit-utils (3.08-6ubuntu2) over (3.08-3ubuntu1) ... 72s dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty 72s dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty 72s dpkg: warning: unable to delete old directory '/lib/init': Directory not empty 72s Setting up sysvinit-utils (3.08-6ubuntu2) ... 72s (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 ... 70465 files and directories currently installed.) 72s Preparing to unpack .../bzip2_1.0.8-5ubuntu1_amd64.deb ... 72s Unpacking bzip2 (1.0.8-5ubuntu1) over (1.0.8-5build1) ... 72s dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') 72s dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') 72s dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') 72s dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') 72s dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') 72s dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') 72s Preparing to unpack .../libbz2-1.0_1.0.8-5ubuntu1_amd64.deb ... 72s Unpacking libbz2-1.0:amd64 (1.0.8-5ubuntu1) over (1.0.8-5build1) ... 73s Setting up libbz2-1.0:amd64 (1.0.8-5ubuntu1) ... 73s (Reading database ... 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unpack .../02-libcap2-bin_1%3a2.66-5ubuntu1_amd64.deb ... 76s Unpacking libcap2-bin (1:2.66-5ubuntu1) over (1:2.66-4ubuntu1) ... 76s Preparing to unpack .../03-libfdisk1_2.39.3-6ubuntu2_amd64.deb ... 76s Unpacking libfdisk1:amd64 (2.39.3-6ubuntu2) over (2.39.2-6ubuntu1) ... 76s Preparing to unpack .../04-libxml2_2.9.14+dfsg-1.3ubuntu1_amd64.deb ... 76s Unpacking libxml2:amd64 (2.9.14+dfsg-1.3ubuntu1) over (2.9.14+dfsg-1.3build3) ... 76s Preparing to unpack .../05-ubuntu-minimal_1.532_amd64.deb ... 76s Unpacking ubuntu-minimal (1.532) over (1.531) ... 76s Preparing to unpack .../06-bsdextrautils_2.39.3-6ubuntu2_amd64.deb ... 76s Unpacking bsdextrautils (2.39.3-6ubuntu2) over (2.39.2-6ubuntu1) ... 76s Preparing to unpack .../07-inetutils-telnet_2%3a2.5-3ubuntu1_amd64.deb ... 76s Unpacking inetutils-telnet (2:2.5-3ubuntu1) over (2:2.4-3ubuntu1) ... 76s Preparing to unpack .../08-libnuma1_2.0.18-1_amd64.deb ... 76s Unpacking libnuma1:amd64 (2.0.18-1) over (2.0.16-1) ... 76s Preparing to unpack .../09-telnet_0.17+2.5-3ubuntu1_all.deb ... 76s Unpacking telnet (0.17+2.5-3ubuntu1) over (0.17+2.4-3ubuntu1) ... 76s Preparing to unpack .../10-ubuntu-standard_1.532_amd64.deb ... 76s Unpacking ubuntu-standard (1.532) over (1.531) ... 76s Preparing to unpack .../11-libgprofng0_2.42-3ubuntu1_amd64.deb ... 76s Unpacking libgprofng0:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 76s Preparing to unpack .../12-libctf0_2.42-3ubuntu1_amd64.deb ... 76s Unpacking libctf0:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 76s Preparing to unpack .../13-libctf-nobfd0_2.42-3ubuntu1_amd64.deb ... 76s Unpacking libctf-nobfd0:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 76s Preparing to unpack .../14-binutils-x86-64-linux-gnu_2.42-3ubuntu1_amd64.deb ... 76s Unpacking binutils-x86-64-linux-gnu (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 76s Preparing to unpack .../15-binutils_2.42-3ubuntu1_amd64.deb ... 76s Unpacking binutils (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 76s Preparing to unpack .../16-libbinutils_2.42-3ubuntu1_amd64.deb ... 76s Unpacking libbinutils:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 77s Preparing to unpack .../17-binutils-common_2.42-3ubuntu1_amd64.deb ... 77s Unpacking binutils-common:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 77s Preparing to unpack .../18-libsframe1_2.42-3ubuntu1_amd64.deb ... 77s Unpacking libsframe1:amd64 (2.42-3ubuntu1) over (2.42-2ubuntu1) ... 77s Preparing to unpack .../19-fdisk_2.39.3-6ubuntu2_amd64.deb ... 77s Unpacking fdisk (2.39.3-6ubuntu2) over (2.39.2-6ubuntu1) ... 77s Preparing to unpack .../20-lto-disabled-list_47_all.deb ... 77s Unpacking lto-disabled-list (47) over (46) ... 77s Preparing to unpack .../21-python3-pyrsistent_0.20.0-1_amd64.deb ... 77s Unpacking python3-pyrsistent:amd64 (0.20.0-1) over (0.18.1-1build5) ... 77s Setting up motd-news-config (13ubuntu7) ... 77s Setting up lto-disabled-list (47) ... 77s Setting up apt-utils (2.7.12) ... 77s Setting up bsdextrautils (2.39.3-6ubuntu2) ... 77s Setting up python3-problem-report (2.28.0-0ubuntu1) ... 77s Setting up python3-debconf (1.5.86) ... 77s Setting up binutils-common:amd64 (2.42-3ubuntu1) ... 77s Setting up inetutils-telnet (2:2.5-3ubuntu1) ... 77s Setting up libctf-nobfd0:amd64 (2.42-3ubuntu1) ... 77s Setting up debconf-i18n (1.5.86) ... 77s Setting up ubuntu-standard (1.532) ... 77s Setting up bzip2 (1.0.8-5ubuntu1) ... 77s Setting up locales (2.39-0ubuntu2) ... 77s Installing new version of config file /etc/locale.alias ... 78s Generating locales (this might take a while)... 79s en_US.UTF-8... done 79s Generation complete. 79s Setting up libsframe1:amd64 (2.42-3ubuntu1) ... 79s Setting up libcap2-bin (1:2.66-5ubuntu1) ... 79s Setting up eject (2.39.3-6ubuntu2) ... 79s Setting up libfdisk1:amd64 (2.39.3-6ubuntu2) ... 79s Setting up libnuma1:amd64 (2.0.18-1) ... 79s Setting up python3-pyrsistent:amd64 (0.20.0-1) ... 79s Setting up python-apt-common (2.7.6) ... 79s Setting up mount (2.39.3-6ubuntu2) ... 79s Setting up uuid-runtime (2.39.3-6ubuntu2) ... 80s uuidd.service is a disabled or a static unit not running, not starting it. 80s Setting up libbinutils:amd64 (2.42-3ubuntu1) ... 80s Setting up libpam-cap:amd64 (1:2.66-5ubuntu1) ... 80s Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu1) ... 80s Setting up libctf0:amd64 (2.42-3ubuntu1) ... 80s Setting up telnet (0.17+2.5-3ubuntu1) ... 80s Setting up ubuntu-minimal (1.532) ... 80s Setting up python3-apt (2.7.6) ... 80s Setting up fdisk (2.39.3-6ubuntu2) ... 80s Setting up python3-apport (2.28.0-0ubuntu1) ... 80s Setting up libgprofng0:amd64 (2.42-3ubuntu1) ... 80s Setting up binutils-x86-64-linux-gnu (2.42-3ubuntu1) ... 80s Setting up binutils (2.42-3ubuntu1) ... 80s Setting up apport (2.28.0-0ubuntu1) ... 81s apport-autoreport.service is a disabled or a static unit not running, not starting it. 81s Setting up apport-core-dump-handler (2.28.0-0ubuntu1) ... 82s Processing triggers for man-db (2.12.0-3) ... 84s Processing triggers for plymouth-theme-ubuntu-text (24.004.60-1ubuntu3) ... 84s update-initramfs: deferring update (trigger activated) 84s Processing triggers for debianutils (5.16) ... 84s Processing triggers for install-info (7.1-3) ... 84s Processing triggers for libc-bin (2.39-0ubuntu2) ... 84s Processing triggers for initramfs-tools (0.142ubuntu19) ... 84s update-initramfs: Generating /boot/initrd.img-6.6.0-14-generic 84s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s The following packages will be REMOVED: 94s irqbalance* libnuma1* 94s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 94s After this operation, 213 kB disk space will be freed. 94s (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 ... 70467 files and directories currently installed.) 94s Removing irqbalance (1.9.3-2ubuntu2) ... 94s Removing libnuma1:amd64 (2.0.18-1) ... 94s Processing triggers for man-db (2.12.0-3) ... 94s Processing triggers for libc-bin (2.39-0ubuntu2) ... 94s (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 ... 70453 files and directories currently installed.) 94s Purging configuration files for irqbalance (1.9.3-2ubuntu2) ... 95s sh: Attempting to set up Debian/Ubuntu apt sources automatically 95s sh: Distribution appears to be Ubuntu 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s eatmydata is already the newest version (131-1). 96s dbus is already the newest version (1.14.10-3ubuntu1). 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s rng-tools-debian is already the newest version (2.4). 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s The following additional packages will be installed: 97s libhavege2 97s The following NEW packages will be installed: 97s haveged libhavege2 97s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 57.3 kB of archives. 97s After this operation, 220 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 libhavege2 amd64 1.9.14-1ubuntu1 [23.8 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble/universe amd64 haveged amd64 1.9.14-1ubuntu1 [33.6 kB] 97s Fetched 57.3 kB in 0s (2876 kB/s) 97s Selecting previously unselected package libhavege2:amd64. 97s (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 ... 70451 files and directories currently installed.) 97s Preparing to unpack .../libhavege2_1.9.14-1ubuntu1_amd64.deb ... 97s Unpacking libhavege2:amd64 (1.9.14-1ubuntu1) ... 97s Selecting previously unselected package haveged. 97s Preparing to unpack .../haveged_1.9.14-1ubuntu1_amd64.deb ... 97s Unpacking haveged (1.9.14-1ubuntu1) ... 98s Setting up libhavege2:amd64 (1.9.14-1ubuntu1) ... 98s Setting up haveged (1.9.14-1ubuntu1) ... 98s Created symlink /etc/systemd/system/sysinit.target.wants/haveged.service → /usr/lib/systemd/system/haveged.service. 98s Processing triggers for man-db (2.12.0-3) ... 99s Processing triggers for libc-bin (2.39-0ubuntu2) ... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s The following packages will be REMOVED: 100s cloud-init* python3-configobj* python3-debconf* 100s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 100s After this operation, 3228 kB disk space will be freed. 100s (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 ... 70467 files and directories currently installed.) 100s Removing cloud-init (24.1~6ga4140119-0ubuntu1) ... 101s Removing python3-configobj (5.0.8-3) ... 101s Removing python3-debconf (1.5.86) ... 101s Processing triggers for man-db (2.12.0-3) ... 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 ... 70079 files and directories currently installed.) 101s Purging configuration files for cloud-init (24.1~6ga4140119-0ubuntu1) ... 102s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 102s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 102s Reading package lists... 103s Building dependency tree... 103s Reading state information... 103s linux-generic is already the newest version (6.6.0-14.14). 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 103s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 103s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 103s Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 103s Get:5 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 103s Get:6 http://ftpmaster.internal/ubuntu noble/main Sources [1383 kB] 103s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1430 kB] 104s Get:8 http://ftpmaster.internal/ubuntu noble/main i386 Packages [1057 kB] 104s Get:9 http://ftpmaster.internal/ubuntu noble/universe i386 Packages [8496 kB] 104s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.1 MB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [816 kB] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [977 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [333 kB] 109s Fetched 49.8 MB in 6s (9023 kB/s) 110s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 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... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s autopkgtest [19:46:59]: rebooting testbed after setup commands that affected boot 131s autopkgtest [19:47:19]: testbed running kernel: Linux 6.6.0-14-generic #14-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 30 10:27:29 UTC 2023 131s autopkgtest [19:47:19]: testbed dpkg architecture: amd64 132s autopkgtest [19:47:20]: @@@@@@@@@@@@@@@@@@@@ apt-source genomethreader 133s Get:1 http://ftpmaster.internal/ubuntu noble/universe genomethreader 1.7.3+dfsg-8ubuntu1 (dsc) [2364 B] 133s Get:2 http://ftpmaster.internal/ubuntu noble/universe genomethreader 1.7.3+dfsg-8ubuntu1 (tar) [40.0 MB] 133s Get:3 http://ftpmaster.internal/ubuntu noble/universe genomethreader 1.7.3+dfsg-8ubuntu1 (diff) [14.2 kB] 133s gpgv: Signature made Fri Feb 23 03:38:20 2024 UTC 133s gpgv: using RSA key 8ED6C3F8BAC9DB7FC130A870F823A2729883C97C 133s gpgv: issuer "kanashiro@ubuntu.com" 133s gpgv: Can't check signature: No public key 133s dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-8ubuntu1.dsc: no acceptable signature found 134s autopkgtest [19:47:22]: testing package genomethreader version 1.7.3+dfsg-8ubuntu1 134s autopkgtest [19:47:22]: build not needed 135s autopkgtest [19:47:23]: test run-testsuite: preparing testbed 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 140s Starting 2 pkgProblemResolver with broken count: 0 140s Done 140s Done 140s Starting pkgProblemResolver with broken count: 0 140s Starting 2 pkgProblemResolver with broken count: 0 140s Done 141s The following additional packages will be installed: 141s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 141s genomethreader genometools genometools-common libcairo2 libdatrie1 141s libfontconfig1 libgenometools0 libgraphite2-3 libharfbuzz0b liblua5.1-0 141s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpixman-1-0 libruby 141s libruby3.2 libthai-data libthai0 libtre5 libxcb-render0 libxcb-shm0 141s libxrender1 lua-filesystem lua-lpeg lua-md5 rake ruby ruby-net-telnet 141s ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 141s rubygems-integration 141s Suggested packages: 141s tre-agrep ri ruby-dev bundler 141s Recommended packages: 141s zip fonts-lato libjs-jquery 141s The following NEW packages will be installed: 141s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 141s genomethreader genometools genometools-common libcairo2 libdatrie1 141s libfontconfig1 libgenometools0 libgraphite2-3 libharfbuzz0b liblua5.1-0 141s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpixman-1-0 libruby 141s libruby3.2 libthai-data libthai0 libtre5 libxcb-render0 libxcb-shm0 141s libxrender1 lua-filesystem lua-lpeg lua-md5 rake ruby ruby-net-telnet 141s ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 141s rubygems-integration 141s 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. 141s 1 not fully installed or removed. 141s Need to get 14.4 MB of archives. 141s After this operation, 59.2 MB of additional disk space will be used. 141s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 141s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 141s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.14.2-6ubuntu1 [36.2 kB] 141s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.14.2-6ubuntu1 [136 kB] 141s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 141s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 141s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 141s Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 141s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 141s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 liblua5.1-0 amd64 5.1.5-9 [122 kB] 141s Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.14.2-6ubuntu1 [180 kB] 141s Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 141s Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 141s Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 141s Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 141s Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 141s Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 141s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 141s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 141s Get:20 http://ftpmaster.internal/ubuntu noble/universe amd64 libtre5 amd64 0.8.0-7 [50.1 kB] 141s Get:21 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-md5 amd64 1.2+git+1+8d87fee-2 [14.0 kB] 141s Get:22 http://ftpmaster.internal/ubuntu noble/universe amd64 genometools-common all 1.6.5+ds-2 [194 kB] 141s Get:23 http://ftpmaster.internal/ubuntu noble/universe amd64 libgenometools0 amd64 1.6.5+ds-2 [548 kB] 141s Get:24 http://ftpmaster.internal/ubuntu noble/universe amd64 genomethreader amd64 1.7.3+dfsg-8ubuntu1 [1969 kB] 141s Get:25 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-filesystem amd64 1.8.0-3 [13.0 kB] 141s Get:26 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-lpeg amd64 1.0.2-2 [38.6 kB] 141s Get:27 http://ftpmaster.internal/ubuntu noble/universe amd64 genometools amd64 1.6.5+ds-2 [1975 kB] 141s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 rubygems-integration all 1.18 [5336 B] 141s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 rake all 13.0.6-3 [61.6 kB] 141s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-net-telnet all 0.2.0-1 [13.3 kB] 141s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-webrick all 1.8.1-1 [52.3 kB] 141s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] 141s Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libruby amd64 1:3.2~ubuntu1 [4694 B] 141s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-sdbm amd64 1.0.0-5build3 [18.6 kB] 141s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libruby3.2 amd64 3.2.3-1 [5339 kB] 141s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 ruby3.2 amd64 3.2.3-1 [50.7 kB] 141s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-rubygems all 3.4.20-1 [238 kB] 141s Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ruby amd64 1:3.2~ubuntu1 [3466 B] 141s Fetched 14.4 MB in 0s (90.7 MB/s) 141s Selecting previously unselected package fonts-dejavu-mono. 141s (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 ... 70024 files and directories currently installed.) 141s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 141s Unpacking fonts-dejavu-mono (2.37-8) ... 141s Selecting previously unselected package fonts-dejavu-core. 141s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 142s Unpacking fonts-dejavu-core (2.37-8) ... 142s Selecting previously unselected package fontconfig-config. 142s Preparing to unpack .../02-fontconfig-config_2.14.2-6ubuntu1_amd64.deb ... 142s Unpacking fontconfig-config (2.14.2-6ubuntu1) ... 142s Selecting previously unselected package libfontconfig1:amd64. 142s Preparing to unpack .../03-libfontconfig1_2.14.2-6ubuntu1_amd64.deb ... 142s Unpacking libfontconfig1:amd64 (2.14.2-6ubuntu1) ... 142s Selecting previously unselected package libpixman-1-0:amd64. 142s Preparing to unpack .../04-libpixman-1-0_0.42.2-1_amd64.deb ... 142s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 142s Selecting previously unselected package libxcb-render0:amd64. 142s Preparing to unpack .../05-libxcb-render0_1.15-1_amd64.deb ... 142s Unpacking libxcb-render0:amd64 (1.15-1) ... 142s Selecting previously unselected package libxcb-shm0:amd64. 142s Preparing to unpack .../06-libxcb-shm0_1.15-1_amd64.deb ... 142s Unpacking libxcb-shm0:amd64 (1.15-1) ... 142s Selecting previously unselected package libxrender1:amd64. 142s Preparing to unpack .../07-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 142s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 142s Selecting previously unselected package libcairo2:amd64. 142s Preparing to unpack .../08-libcairo2_1.18.0-1_amd64.deb ... 142s Unpacking libcairo2:amd64 (1.18.0-1) ... 142s Selecting previously unselected package liblua5.1-0:amd64. 142s Preparing to unpack .../09-liblua5.1-0_5.1.5-9_amd64.deb ... 142s Unpacking liblua5.1-0:amd64 (5.1.5-9) ... 142s Selecting previously unselected package fontconfig. 142s Preparing to unpack .../10-fontconfig_2.14.2-6ubuntu1_amd64.deb ... 142s Unpacking fontconfig (2.14.2-6ubuntu1) ... 142s Selecting previously unselected package libgraphite2-3:amd64. 142s Preparing to unpack .../11-libgraphite2-3_1.3.14-2_amd64.deb ... 142s Unpacking libgraphite2-3:amd64 (1.3.14-2) ... 142s Selecting previously unselected package libharfbuzz0b:amd64. 142s Preparing to unpack .../12-libharfbuzz0b_8.3.0-2_amd64.deb ... 142s Unpacking libharfbuzz0b:amd64 (8.3.0-2) ... 142s Selecting previously unselected package libthai-data. 142s Preparing to unpack .../13-libthai-data_0.1.29-2_all.deb ... 142s Unpacking libthai-data (0.1.29-2) ... 142s Selecting previously unselected package libdatrie1:amd64. 142s Preparing to unpack .../14-libdatrie1_0.2.13-3_amd64.deb ... 142s Unpacking libdatrie1:amd64 (0.2.13-3) ... 142s Selecting previously unselected package libthai0:amd64. 142s Preparing to unpack .../15-libthai0_0.1.29-2_amd64.deb ... 142s Unpacking libthai0:amd64 (0.1.29-2) ... 142s Selecting previously unselected package libpango-1.0-0:amd64. 142s Preparing to unpack .../16-libpango-1.0-0_1.51.0+ds-4_amd64.deb ... 142s Unpacking libpango-1.0-0:amd64 (1.51.0+ds-4) ... 142s Selecting previously unselected package libpangoft2-1.0-0:amd64. 142s Preparing to unpack .../17-libpangoft2-1.0-0_1.51.0+ds-4_amd64.deb ... 142s Unpacking libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 142s Selecting previously unselected package libpangocairo-1.0-0:amd64. 142s Preparing to unpack .../18-libpangocairo-1.0-0_1.51.0+ds-4_amd64.deb ... 142s Unpacking libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 142s Selecting previously unselected package libtre5:amd64. 142s Preparing to unpack .../19-libtre5_0.8.0-7_amd64.deb ... 142s Unpacking libtre5:amd64 (0.8.0-7) ... 142s Selecting previously unselected package lua-md5:amd64. 142s Preparing to unpack .../20-lua-md5_1.2+git+1+8d87fee-2_amd64.deb ... 142s Unpacking lua-md5:amd64 (1.2+git+1+8d87fee-2) ... 142s Selecting previously unselected package genometools-common. 142s Preparing to unpack .../21-genometools-common_1.6.5+ds-2_all.deb ... 142s Unpacking genometools-common (1.6.5+ds-2) ... 142s Selecting previously unselected package libgenometools0. 142s Preparing to unpack .../22-libgenometools0_1.6.5+ds-2_amd64.deb ... 142s Unpacking libgenometools0 (1.6.5+ds-2) ... 142s Selecting previously unselected package genomethreader. 142s Preparing to unpack .../23-genomethreader_1.7.3+dfsg-8ubuntu1_amd64.deb ... 142s Unpacking genomethreader (1.7.3+dfsg-8ubuntu1) ... 142s Selecting previously unselected package lua-filesystem:amd64. 142s Preparing to unpack .../24-lua-filesystem_1.8.0-3_amd64.deb ... 142s Unpacking lua-filesystem:amd64 (1.8.0-3) ... 142s Selecting previously unselected package lua-lpeg:amd64. 142s Preparing to unpack .../25-lua-lpeg_1.0.2-2_amd64.deb ... 142s Unpacking lua-lpeg:amd64 (1.0.2-2) ... 142s Selecting previously unselected package genometools. 142s Preparing to unpack .../26-genometools_1.6.5+ds-2_amd64.deb ... 142s Unpacking genometools (1.6.5+ds-2) ... 142s Selecting previously unselected package rubygems-integration. 142s Preparing to unpack .../27-rubygems-integration_1.18_all.deb ... 142s Unpacking rubygems-integration (1.18) ... 142s Selecting previously unselected package rake. 143s Preparing to unpack .../28-rake_13.0.6-3_all.deb ... 143s Unpacking rake (13.0.6-3) ... 143s Selecting previously unselected package ruby-net-telnet. 143s Preparing to unpack .../29-ruby-net-telnet_0.2.0-1_all.deb ... 143s Unpacking ruby-net-telnet (0.2.0-1) ... 143s Selecting previously unselected package ruby-webrick. 143s Preparing to unpack .../30-ruby-webrick_1.8.1-1_all.deb ... 143s Unpacking ruby-webrick (1.8.1-1) ... 143s Selecting previously unselected package ruby-xmlrpc. 143s Preparing to unpack .../31-ruby-xmlrpc_0.3.2-2_all.deb ... 143s Unpacking ruby-xmlrpc (0.3.2-2) ... 143s Selecting previously unselected package libruby:amd64. 143s Preparing to unpack .../32-libruby_1%3a3.2~ubuntu1_amd64.deb ... 143s Unpacking libruby:amd64 (1:3.2~ubuntu1) ... 143s Selecting previously unselected package ruby-sdbm:amd64. 143s Preparing to unpack .../33-ruby-sdbm_1.0.0-5build3_amd64.deb ... 143s Unpacking ruby-sdbm:amd64 (1.0.0-5build3) ... 143s Selecting previously unselected package libruby3.2:amd64. 143s Preparing to unpack .../34-libruby3.2_3.2.3-1_amd64.deb ... 143s Unpacking libruby3.2:amd64 (3.2.3-1) ... 143s Selecting previously unselected package ruby3.2. 143s Preparing to unpack .../35-ruby3.2_3.2.3-1_amd64.deb ... 143s Unpacking ruby3.2 (3.2.3-1) ... 143s Selecting previously unselected package ruby-rubygems. 143s Preparing to unpack .../36-ruby-rubygems_3.4.20-1_all.deb ... 143s Unpacking ruby-rubygems (3.4.20-1) ... 143s Selecting previously unselected package ruby. 143s Preparing to unpack .../37-ruby_1%3a3.2~ubuntu1_amd64.deb ... 143s Unpacking ruby (1:3.2~ubuntu1) ... 143s Setting up libgraphite2-3:amd64 (1.3.14-2) ... 143s Setting up libpixman-1-0:amd64 (0.42.2-1) ... 143s Setting up lua-lpeg:amd64 (1.0.2-2) ... 143s Setting up libtre5:amd64 (0.8.0-7) ... 143s Setting up libxrender1:amd64 (1:0.9.10-1.1) ... 143s Setting up libdatrie1:amd64 (0.2.13-3) ... 143s Setting up libxcb-render0:amd64 (1.15-1) ... 143s Setting up rubygems-integration (1.18) ... 143s Setting up libxcb-shm0:amd64 (1.15-1) ... 143s Setting up lua-filesystem:amd64 (1.8.0-3) ... 143s Setting up lua-md5:amd64 (1.2+git+1+8d87fee-2) ... 143s Setting up ruby-net-telnet (0.2.0-1) ... 143s Setting up fonts-dejavu-mono (2.37-8) ... 143s Setting up fonts-dejavu-core (2.37-8) ... 143s Setting up ruby-webrick (1.8.1-1) ... 143s Setting up liblua5.1-0:amd64 (5.1.5-9) ... 143s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 143s Setting up libthai-data (0.1.29-2) ... 143s Setting up ruby-xmlrpc (0.3.2-2) ... 143s Setting up fontconfig-config (2.14.2-6ubuntu1) ... 143s Setting up libthai0:amd64 (0.1.29-2) ... 143s Setting up libfontconfig1:amd64 (2.14.2-6ubuntu1) ... 143s Setting up fontconfig (2.14.2-6ubuntu1) ... 145s Regenerating fonts cache... done. 145s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... 145s Setting up libcairo2:amd64 (1.18.0-1) ... 145s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 145s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 145s Setting up genometools-common (1.6.5+ds-2) ... 145s Setting up libgenometools0 (1.6.5+ds-2) ... 145s Setting up genomethreader (1.7.3+dfsg-8ubuntu1) ... 145s Setting up genometools (1.6.5+ds-2) ... 145s Setting up ruby-rubygems (3.4.20-1) ... 145s Setting up ruby3.2 (3.2.3-1) ... 145s Setting up ruby (1:3.2~ubuntu1) ... 145s Setting up rake (13.0.6-3) ... 145s Setting up autopkgtest-satdep (0) ... 145s Setting up libruby3.2:amd64 (3.2.3-1) ... 145s Setting up libruby:amd64 (1:3.2~ubuntu1) ... 145s Setting up ruby-sdbm:amd64 (1.0.0-5build3) ... 145s Processing triggers for libc-bin (2.39-0ubuntu2) ... 145s Processing triggers for man-db (2.12.0-3) ... 148s (Reading database ... 73683 files and directories currently installed.) 148s Removing autopkgtest-satdep (0) ... 149s autopkgtest [19:47:37]: test run-testsuite: [----------------------- 149s 1: gth : ok 149s 2: gth -help : ok 149s 3: gth -help+ : ok 150s 4: gth -version : ok 150s 5: gth regression test (assertion in gthsafilter) : ok 151s 6: gth regression test (-gff3out -intermediate) : ok 151s 8: gth regression test (-gff3out -skipalignmentout) : ok 151s 10: gth regression test (-gff3out -intermediate -o) : ok 151s 11: gth regression test (-gff3out -skipalignmentout -o) : ok 151s 12: gthconsensus regression test (-gff3out -intermediate) : ok 151s 13: gthconsensus regression test (-gff3out -skipalignmentout) : ok 152s 14: gthconsensus regression test (-gff3out -intermediate -o) : ok 152s 15: gthconsensus regression test (-gff3out -skipalignmentout -o): ok 152s 16: gth regression test (-exondistri) : ok 152s 17: gth regression test (-introndistri) : ok 152s 18: gth regression test (-refseqcovdistri) : ok 152s 19: gth regression test (all distributions) : ok 153s 20: gth regression test (-skipindexcheck) : ok 153s 21: gth regression test (index reconstruction) : ok 153s 22: gth regression test (-createindicesonly & -noautoindex) : ok 153s 23: gth regression test (coverage assertion) : ok 154s 24: gth -gff3out -intermediate (long intron files) : ok 155s 25: gth -gff3out -skipalignmentout (long intron files) : ok 155s 26: gth -gff3out -frompos (correct positions in sequence region): ok 155s 27: gth -gff3out -intermediate (correct reverse positions) : ok 160s 28: gth arabidopsis : ok 160s 29: gth illegal character in protein file : ok 160s 30: align_dna : ok 161s 31: gth -gff3descranges (single exon) : ok 161s 32: gthconsensus -help : ok 161s 33: gthconsensus -help+ : ok 161s 34: gthconsensus empty_file : ok 161s 35: gthconsensus empty_file.gz : ok 161s 36: gthconsensus empty_file.bz2 : ok 162s 37: gthbssmfileinfo (arabidopsis) : ok 162s 38: gthbssmfileinfo (human) : ok 163s 39: gthbssmprint (arabidopsis) : ok 163s 40: gthbssmprint (human) : ok 163s 41: gthbssmrmsd (arabidopsis) : ok 172s 42: gthbssmtrain (examples from manual) : ok 172s 43: gthbssmtrain (file, no introns) : ok 173s 44: gthbssmtrain (file, introns) : ok 173s 45: gthbssmtrain (stdin, no introns) : ok 173s 46: gthbssmtrain (stdin, introns) : ok 173s 47: gthbssmtrain (short intron) : ok 174s autopkgtest [19:48:02]: test run-testsuite: -----------------------] 174s run-testsuite PASS 174s autopkgtest [19:48:02]: test run-testsuite: - - - - - - - - - - results - - - - - - - - - - 174s autopkgtest [19:48:02]: @@@@@@@@@@@@@@@@@@@@ summary 174s run-testsuite PASS 186s Creating nova instance adt-noble-amd64-genomethreader-20240223-194508-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240221.img (UUID 057b5928-448e-4dd4-ac28-971d6ccdd38d)...