0s autopkgtest [17:09:27]: starting date and time: 2024-05-20 17:09:27+0000 0s autopkgtest [17:09:27]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [17:09:27]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eoy97n8g/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml --apt-upgrade ctdconverter --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-1.secgroup --name adt-oracular-amd64-ctdconverter-20240520-170927-juju-7f2275-prod-proposed-migration-environment-3-88d040ff-e631-473d-bffd-81ff3ca0b445 --image adt/ubuntu-oracular-amd64-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,keyserver.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/ 139s autopkgtest [17:11:46]: testbed dpkg architecture: amd64 139s autopkgtest [17:11:46]: testbed apt version: 2.7.14build2 139s autopkgtest [17:11:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] 140s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [95.2 kB] 140s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1295 kB] 140s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [5972 B] 140s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [1964 B] 140s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [142 kB] 140s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [183 kB] 140s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [7700 B] 140s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [1618 kB] 140s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [682 kB] 140s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [15.6 kB] 140s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [2380 B] 141s Fetched 4123 kB in 1s (6817 kB/s) 141s Reading package lists... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 145s The following packages will be upgraded: 145s apparmor fwupd gir1.2-glib-2.0 less libacl1 libapparmor1 libexpat1 libfwupd2 145s libglib2.0-0t64 libglib2.0-data libgnutls30t64 libgpg-error-l10n 145s libgpg-error0 libpam-modules libpam-modules-bin libpam-runtime libpam0g 145s libtirpc-common libtirpc3t64 python3-blinker python3-httplib2 145s 21 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 9049 kB of archives. 145s After this operation, 352 kB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 libpam0g amd64 1.5.3-7ubuntu1 [67.8 kB] 145s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu1 [51.9 kB] 145s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libpam-modules amd64 1.5.3-7ubuntu1 [284 kB] 145s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libacl1 amd64 2.3.2-2 [16.8 kB] 145s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error-l10n all 1.49-2 [8228 B] 145s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error0 amd64 1.49-2 [70.9 kB] 145s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] 145s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libgnutls30t64 amd64 3.8.5-2ubuntu1 [1009 kB] 145s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 gir1.2-glib-2.0 amd64 2.80.1-0ubuntu2 [183 kB] 145s Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-0t64 amd64 2.80.1-0ubuntu2 [1546 kB] 145s Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 less amd64 590-2ubuntu2.1 [142 kB] 145s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libapparmor1 amd64 4.0.1-0ubuntu1 [49.9 kB] 145s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libexpat1 amd64 2.6.2-1 [86.9 kB] 145s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libglib2.0-data all 2.80.1-0ubuntu2 [48.8 kB] 145s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc-common all 1.3.4+ds-1.3 [8106 B] 145s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.5 kB] 145s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 apparmor amd64 4.0.1-0ubuntu1 [641 kB] 145s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libfwupd2 amd64 1.9.19-1 [136 kB] 145s Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 fwupd amd64 1.9.19-1 [4534 kB] 145s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-blinker all 1.8.2-1 [11.4 kB] 145s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-httplib2 all 0.22.0-1 [30.4 kB] 145s Preconfiguring packages ... 145s Fetched 9049 kB in 0s (95.5 MB/s) 145s (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 ... 74171 files and directories currently installed.) 145s Preparing to unpack .../libpam0g_1.5.3-7ubuntu1_amd64.deb ... 145s Unpacking libpam0g:amd64 (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ... 145s Setting up libpam0g:amd64 (1.5.3-7ubuntu1) ... 146s (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 ... 74171 files and directories currently installed.) 146s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu1_amd64.deb ... 146s Unpacking libpam-modules-bin (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ... 146s Setting up libpam-modules-bin (1.5.3-7ubuntu1) ... 146s pam_namespace.service is a disabled or a static unit not running, not starting it. 146s (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 ... 74171 files and directories currently installed.) 146s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu1_amd64.deb ... 146s Unpacking libpam-modules:amd64 (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ... 146s Setting up libpam-modules:amd64 (1.5.3-7ubuntu1) ... 146s (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 ... 74174 files and directories currently installed.) 146s Preparing to unpack .../libacl1_2.3.2-2_amd64.deb ... 146s Unpacking libacl1:amd64 (2.3.2-2) over (2.3.2-1build1) ... 146s Setting up libacl1:amd64 (2.3.2-2) ... 146s (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 ... 74174 files and directories currently installed.) 146s Preparing to unpack .../libgpg-error-l10n_1.49-2_all.deb ... 146s Unpacking libgpg-error-l10n (1.49-2) over (1.47-3build2) ... 146s Preparing to unpack .../libgpg-error0_1.49-2_amd64.deb ... 146s Unpacking libgpg-error0:amd64 (1.49-2) over (1.47-3build2) ... 146s Setting up libgpg-error0:amd64 (1.49-2) ... 146s (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 ... 74174 files and directories currently installed.) 146s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu1_all.deb ... 146s Unpacking libpam-runtime (1.5.3-7ubuntu1) over (1.5.3-5ubuntu5) ... 147s Setting up libpam-runtime (1.5.3-7ubuntu1) ... 147s (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 ... 74174 files and directories currently installed.) 147s Preparing to unpack .../libgnutls30t64_3.8.5-2ubuntu1_amd64.deb ... 147s Unpacking libgnutls30t64:amd64 (3.8.5-2ubuntu1) over (3.8.3-1.1ubuntu3) ... 147s Setting up libgnutls30t64:amd64 (3.8.5-2ubuntu1) ... 147s (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 ... 74174 files and directories currently installed.) 147s Preparing to unpack .../00-gir1.2-glib-2.0_2.80.1-0ubuntu2_amd64.deb ... 147s Unpacking gir1.2-glib-2.0:amd64 (2.80.1-0ubuntu2) over (2.80.0-6ubuntu1) ... 147s Preparing to unpack .../01-libglib2.0-0t64_2.80.1-0ubuntu2_amd64.deb ... 147s Unpacking libglib2.0-0t64:amd64 (2.80.1-0ubuntu2) over (2.80.0-6ubuntu1) ... 147s Preparing to unpack .../02-less_590-2ubuntu2.1_amd64.deb ... 147s Unpacking less (590-2ubuntu2.1) over (590-2ubuntu2) ... 147s Preparing to unpack .../03-libapparmor1_4.0.1-0ubuntu1_amd64.deb ... 147s Unpacking libapparmor1:amd64 (4.0.1-0ubuntu1) over (4.0.0-beta3-0ubuntu3) ... 147s Preparing to unpack .../04-libexpat1_2.6.2-1_amd64.deb ... 147s Unpacking libexpat1:amd64 (2.6.2-1) over (2.6.1-2build1) ... 147s Preparing to unpack .../05-libglib2.0-data_2.80.1-0ubuntu2_all.deb ... 147s Unpacking libglib2.0-data (2.80.1-0ubuntu2) over (2.80.0-6ubuntu1) ... 147s Preparing to unpack .../06-libtirpc-common_1.3.4+ds-1.3_all.deb ... 147s Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.4+ds-1.1build1) ... 147s Preparing to unpack .../07-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... 147s Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) over (1.3.4+ds-1.1build1) ... 147s Preparing to unpack .../08-apparmor_4.0.1-0ubuntu1_amd64.deb ... 148s Unpacking apparmor (4.0.1-0ubuntu1) over (4.0.0-beta3-0ubuntu3) ... 148s Preparing to unpack .../09-libfwupd2_1.9.19-1_amd64.deb ... 148s Unpacking libfwupd2:amd64 (1.9.19-1) over (1.9.16-1) ... 148s Preparing to unpack .../10-fwupd_1.9.19-1_amd64.deb ... 148s Unpacking fwupd (1.9.19-1) over (1.9.16-1) ... 148s Preparing to unpack .../11-python3-blinker_1.8.2-1_all.deb ... 148s Unpacking python3-blinker (1.8.2-1) over (1.8.1-1) ... 148s Preparing to unpack .../12-python3-httplib2_0.22.0-1_all.deb ... 148s Unpacking python3-httplib2 (0.22.0-1) over (0.20.4-3) ... 149s Setting up libexpat1:amd64 (2.6.2-1) ... 149s Setting up libapparmor1:amd64 (4.0.1-0ubuntu1) ... 149s Setting up libtirpc-common (1.3.4+ds-1.3) ... 149s Setting up less (590-2ubuntu2.1) ... 149s Setting up apparmor (4.0.1-0ubuntu1) ... 149s Installing new version of config file /etc/apparmor.d/abstractions/authentication ... 149s Installing new version of config file /etc/apparmor.d/abstractions/samba ... 149s Installing new version of config file /etc/apparmor.d/firefox ... 150s Reloading AppArmor profiles 150s Setting up libglib2.0-0t64:amd64 (2.80.1-0ubuntu2) ... 150s No schema files found: doing nothing. 150s Setting up libglib2.0-data (2.80.1-0ubuntu2) ... 150s Setting up gir1.2-glib-2.0:amd64 (2.80.1-0ubuntu2) ... 150s Setting up python3-httplib2 (0.22.0-1) ... 150s Setting up libgpg-error-l10n (1.49-2) ... 150s Setting up python3-blinker (1.8.2-1) ... 150s Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... 150s Setting up libfwupd2:amd64 (1.9.19-1) ... 150s Setting up fwupd (1.9.19-1) ... 151s fwupd-offline-update.service is a disabled or a static unit not running, not starting it. 151s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 151s fwupd.service is a disabled or a static unit not running, not starting it. 151s Processing triggers for man-db (2.12.0-4build2) ... 152s Processing triggers for dbus (1.14.10-4ubuntu4) ... 152s Processing triggers for libc-bin (2.39-0ubuntu8) ... 152s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 153s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 153s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 153s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 155s Reading package lists... 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Calculating upgrade... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s autopkgtest [17:12:03]: rebooting testbed after setup commands that affected boot 160s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 170s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 175s autopkgtest [17:12:22]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 176s autopkgtest [17:12:23]: @@@@@@@@@@@@@@@@@@@@ apt-source ctdconverter 177s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (dsc) [2138 B] 177s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (tar) [38.1 kB] 177s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (diff) [7340 B] 178s gpgv: Signature made Thu Jul 13 15:37:57 2023 UTC 178s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 178s gpgv: issuer "tille@debian.org" 178s gpgv: Can't check signature: No public key 178s dpkg-source: warning: cannot verify inline signature for ./ctdconverter_2.1-6.dsc: no acceptable signature found 178s autopkgtest [17:12:25]: testing package ctdconverter version 2.1-6 178s autopkgtest [17:12:25]: build not needed 178s autopkgtest [17:12:25]: test run-unit-test: preparing testbed 178s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Starting pkgProblemResolver with broken count: 1 179s Starting 2 pkgProblemResolver with broken count: 1 179s Investigating (0) python3-ruamel.yaml:amd64 < none -> 0.18.6+ds-3 @un puN Ib > 179s Broken python3-ruamel.yaml:amd64 Depends on python3-ruamel.yaml.clib:amd64 < none | 0.2.8-1build1 @un uH > (>= 0.2.8-2) 179s Considering python3-ruamel.yaml.clib:amd64 0 as a solution to python3-ruamel.yaml:amd64 0 179s Re-Instated python3-ruamel.yaml.clib:amd64 179s Done 179s Some packages could not be installed. This may mean that you have 179s requested an impossible situation or if you are using the unstable 179s distribution that some required packages have not yet been created 179s or been moved out of Incoming. 179s The following information may help to resolve the situation: 179s 179s The following packages have unmet dependencies: 179s python3-ruamel.yaml : Depends: python3-ruamel.yaml.clib (>= 0.2.8-2) but 0.2.8-1build1 is to be installed 179s E: Unable to correct problems, you have held broken packages. 179s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from oracular-proposed 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 180s The following additional packages will be installed: 180s ctdconverter libxslt1.1 python3-ctdopts python3-lxml python3-ruamel.yaml 180s python3-ruamel.yaml.clib 180s Suggested packages: 180s cwl-runner python-lxml-doc 180s Recommended packages: 180s python3-bs4 python3-cssselect python3-html5lib 180s The following NEW packages will be installed: 180s autopkgtest-satdep ctdconverter libxslt1.1 python3-ctdopts python3-lxml 180s python3-ruamel.yaml python3-ruamel.yaml.clib 180s 0 upgraded, 7 newly installed, 0 to remove and 66 not upgraded. 180s Need to get 1720 kB/1721 kB of archives. 180s After this operation, 6591 kB of additional disk space will be used. 180s Get:1 /tmp/autopkgtest.mePm0x/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 180s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ctdopts all 1.5-2 [22.5 kB] 180s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 180s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB] 180s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-ruamel.yaml.clib amd64 0.2.8+ds-1 [133 kB] 180s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 180s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 ctdconverter all 2.1-6 [28.1 kB] 181s Fetched 1720 kB in 0s (31.5 MB/s) 181s Selecting previously unselected package python3-ctdopts. 181s (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 ... 74182 files and directories currently installed.) 181s Preparing to unpack .../0-python3-ctdopts_1.5-2_all.deb ... 181s Unpacking python3-ctdopts (1.5-2) ... 181s Selecting previously unselected package libxslt1.1:amd64. 181s Preparing to unpack .../1-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 181s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 181s Selecting previously unselected package python3-lxml:amd64. 181s Preparing to unpack .../2-python3-lxml_5.2.1-1_amd64.deb ... 181s Unpacking python3-lxml:amd64 (5.2.1-1) ... 181s Selecting previously unselected package python3-ruamel.yaml.clib:amd64. 181s Preparing to unpack .../3-python3-ruamel.yaml.clib_0.2.8+ds-1_amd64.deb ... 181s Unpacking python3-ruamel.yaml.clib:amd64 (0.2.8+ds-1) ... 181s Selecting previously unselected package python3-ruamel.yaml. 181s Preparing to unpack .../4-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 181s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 181s Selecting previously unselected package ctdconverter. 181s Preparing to unpack .../5-ctdconverter_2.1-6_all.deb ... 181s Unpacking ctdconverter (2.1-6) ... 181s Selecting previously unselected package autopkgtest-satdep. 181s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 181s Unpacking autopkgtest-satdep (0) ... 181s Setting up python3-ctdopts (1.5-2) ... 181s Setting up python3-ruamel.yaml.clib:amd64 (0.2.8+ds-1) ... 181s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 182s Setting up libxslt1.1:amd64 (1.1.39-0exp1build1) ... 182s Setting up python3-lxml:amd64 (5.2.1-1) ... 182s Setting up ctdconverter (2.1-6) ... 182s Setting up autopkgtest-satdep (0) ... 182s Processing triggers for man-db (2.12.0-4build2) ... 182s Processing triggers for libc-bin (2.39-0ubuntu8) ... 185s (Reading database ... 74415 files and directories currently installed.) 185s Removing autopkgtest-satdep (0) ... 185s autopkgtest [17:12:32]: test run-unit-test: [----------------------- 185s CTDConverter - A project from the WorkflowConversion family (https://github.com/WorkflowConversion/CTDConverter) 185s 185s Copyright 2017, WorklfowConversion 185s 185s Licensed under the Apache License, Version 2.0 (the "License"); 185s you may not use this file except in compliance with the License. 185s You may obtain a copy of the License at 185s 185s http://www.apache.org/licenses/LICENSE-2.0 185s 185s Unless required by applicable law or agreed to in writing, software 185s distributed under the License is distributed on an "AS IS" BASIS, 185s WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 185s See the License for the specific language governing permissions and 185s limitations under the License. 185s 185s 185s USAGE: 185s 185s $ CTDConverter [FORMAT] [ARGUMENTS ...] 185s 185s FORMAT can be either one of the supported output formats: cwl, galaxy. 185s 185s There is one converter for each supported FORMAT, each taking a different set of arguments. Please consult the detailed 185s documentation for each of the converters. Nevertheless, all converters have the following common parameters/options: 185s 185s 185s I - Parsing a single CTD file and convert it: 185s 185s $ CTDConverter [FORMAT] -i [INPUT_FILE] -o [OUTPUT_FILE] 185s 185s 185s II - Parsing several CTD files, output converted wrappers in a given folder: 185s 185s $ CTDConverter [FORMAT] -i [INPUT_FILES] -o [OUTPUT_DIRECTORY] 185s 185s 185s III - Hardcoding parameters 185s 185s It is possible to hardcode parameters. This makes sense if you want to set a tool in 'quiet' mode or if your tools 185s support multi-threading and accept the number of threads via a parameter, without giving end users the chance to 185s change the values for these parameters. 185s 185s In order to generate hardcoded parameters, you need to provide a simple file. Each line of this file contains 185s two or three columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains 185s the name of the parameter, the second column contains the value that will always be set for this parameter. Only the 185s first two columns are mandatory. 185s 185s If the parameter is to be hardcoded only for a set of tools, then a third column can be added. This column contains 185s a comma-separated list of tool names for which the parameter will be hardcoded. If a third column is not present, 185s then all processed tools containing the given parameter will get a hardcoded value for it. 185s 185s The following is an example of a valid file: 185s 185s ##################################### HARDCODED PARAMETERS example ##################################### 185s # Every line starting with a # will be handled as a comment and will not be parsed. 185s # The first column is the name of the parameter and the second column is the value that will be used. 185s 185s # Parameter name # Value # Tool(s) 185s threads 8 185s mode quiet 185s xtandem_executable xtandem XTandemAdapter 185s verbosity high Foo, Bar 185s 185s ######################################################################################################### 185s 185s Using the above file will produce a command-line similar to: 185s 185s [TOOL] ... -threads 8 -mode quiet ... 185s 185s for all tools. For XTandemAdapter, however, the command-line will look like: 185s 185s XtandemAdapter ... -threads 8 -mode quiet -xtandem_executable xtandem ... 185s 185s And for tools Foo and Bar, the command-line will be similar to: 185s 185s Foo -threads 8 -mode quiet -verbosity high ... 185s 185s 185s IV - Engine-specific parameters 185s 185s i - Galaxy 185s 185s a. Providing file formats, mimetypes 185s 185s Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a 185s certain data format will be able to receive data from a port from the same format. This converter allows you 185s to provide a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. 185s The layout of this file consists of lines, each of either one or four columns separated by any amount of 185s whitespace. The content of each column is as follows: 185s 185s * 1st column: file extension 185s * 2nd column: data type, as listed in Galaxy 185s * 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml 185s * 4th column: mimetype (optional) 185s 185s The following is an example of a valid "file formats" file: 185s 185s ########################################## FILE FORMATS example ########################################## 185s # Every line starting with a # will be handled as a comment and will not be parsed. 185s # The first column is the file format as given in the CTD and second column is the Galaxy data format. The 185s # second, third, fourth and fifth columns can be left empty if the data type has already been registered 185s # in Galaxy, otherwise, all but the mimetype must be provided. 185s 185s # CTD type # Galaxy type # Long Galaxy data type # Mimetype 185s csv tabular galaxy.datatypes.data:Text 185s fasta 185s ini txt galaxy.datatypes.data:Text 185s txt 185s idxml txt galaxy.datatypes.xml:GenericXml application/xml 185s options txt galaxy.datatypes.data:Text 185s grid grid galaxy.datatypes.data:Grid 185s ########################################################################################################## 185s 185s Note that each line consists precisely of either one, three or four columns. In the case of data types already 185s registered in Galaxy (such as fasta and txt in the above example), only the first column is needed. In the 185s case of data types that haven't been yet registered in Galaxy, the first three columns are needed 185s (mimetype is optional). 185s 185s For information about Galaxy data types and subclasses, see the following page: 185s https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes 185s 185s 185s b. Finer control over which tools will be converted 185s 185s Sometimes only a subset of CTDs needs to be converted. It is possible to either explicitly specify which tools 185s will be converted or which tools will not be converted. 185s 185s The value of the -s/--skip-tools parameter is a file in which each line will be interpreted as the name of a 185s tool that will not be converted. Conversely, the value of the -r/--required-tools is a file in which each line 185s will be interpreted as a tool that is required. Only one of these parameters can be specified at a given time. 185s 185s The format of both files is exactly the same. As stated before, each line will be interpreted as the name of a 185s tool. Any line starting with a '#' will be ignored. 185s 185s 185s ii - CWL 185s 185s There are, for now, no CWL-specific parameters or options. 185s 185s 185s 186s autopkgtest [17:12:33]: test run-unit-test: -----------------------] 186s run-unit-test PASS (superficial) 186s autopkgtest [17:12:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 186s autopkgtest [17:12:33]: @@@@@@@@@@@@@@@@@@@@ summary 186s run-unit-test PASS (superficial) 197s flock: timeout while waiting to get lock 197s Creating nova instance adt-oracular-amd64-ctdconverter-20240520-170927-juju-7f2275-prod-proposed-migration-environment-3-88d040ff-e631-473d-bffd-81ff3ca0b445 from image adt/ubuntu-oracular-amd64-server-20240519.img (UUID 34d96c8f-5640-4af4-95e0-3e41e78a0dc7)...