0s autopkgtest [16:03:56]: starting date and time: 2024-07-26 16:03:56+0000 0s autopkgtest [16:03:56]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [16:03:56]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gqn2o80l/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:gffread --apt-upgrade gffread --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=gffread/0.12.7-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-13.secgroup --name adt-oracular-s390x-gffread-20240726-160356-juju-7f2275-prod-proposed-migration-environment-2-fab9632e-e3ef-4c05-bc3b-fc3dca37e4d0 --image adt/ubuntu-oracular-s390x-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,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/ 81s autopkgtest [16:05:17]: testbed dpkg architecture: s390x 81s autopkgtest [16:05:17]: testbed apt version: 2.9.6 81s autopkgtest [16:05:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 82s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 82s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [50.6 kB] 82s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [4288 B] 82s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [436 kB] 83s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 83s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [66.8 kB] 83s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x c-n-f Metadata [2112 B] 83s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1368 B] 83s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x c-n-f Metadata [120 B] 83s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [397 kB] 83s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x c-n-f Metadata [8372 B] 83s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [2072 B] 83s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x c-n-f Metadata [120 B] 83s Fetched 1104 kB in 1s (1402 kB/s) 83s Reading package lists... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Calculating upgrade... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 86s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 87s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 87s Reading package lists... 87s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 91s autopkgtest [16:05:27]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:14:26 UTC 2024 91s autopkgtest [16:05:27]: @@@@@@@@@@@@@@@@@@@@ apt-source gffread 93s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/universe gffread 0.12.7-6 (dsc) [2434 B] 93s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe gffread 0.12.7-6 (tar) [404 kB] 93s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe gffread 0.12.7-6 (diff) [9024 B] 93s gpgv: Signature made Tue Jul 9 11:19:40 2024 UTC 93s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./gffread_0.12.7-6.dsc: no acceptable signature found 93s autopkgtest [16:05:29]: testing package gffread version 0.12.7-6 93s autopkgtest [16:05:29]: build not needed 94s autopkgtest [16:05:30]: test run-tests: preparing testbed 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 96s Starting pkgProblemResolver with broken count: 1 96s Starting 2 pkgProblemResolver with broken count: 1 96s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib > 96s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.6.3-2ubuntu1 @un uH > 96s Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 0 96s Re-Instated fonts-lyx:s390x 96s Re-Instated python-matplotlib-data:s390x 96s Re-Instated python3-six:s390x 96s Re-Instated python3-dateutil:s390x 96s Re-Instated tk8.6-blt2.5:s390x 96s Re-Instated blt:s390x 96s Re-Instated python3-tk:s390x 96s Re-Instated python3-pil.imagetk:s390x 96s Re-Instated python3-contourpy:s390x 96s Re-Instated python3-cycler:s390x 96s Re-Instated python3-brotli:s390x 96s Re-Instated python3-decorator:s390x 96s Re-Instated liblbfgsb0:s390x 96s Re-Instated python3-scipy:s390x 96s Re-Instated python3-ufolib2:s390x 96s Re-Instated python3-mpmath:s390x 96s Re-Instated python3-sympy:s390x 96s Re-Instated python3-tz:s390x 96s Re-Instated python3-appdirs:s390x 96s Re-Instated python3-fs:s390x 96s Re-Instated libxslt1.1:s390x 96s Re-Instated python3-lxml:s390x 96s Re-Instated python3-lz4:s390x 96s Re-Instated python3-unicodedata2:s390x 96s Re-Instated unicode-data:s390x 96s Re-Instated python3-fonttools:s390x 96s Re-Instated python3-kiwisolver:s390x 96s Re-Instated python3-packaging:s390x 96s Re-Instated libqhull-r8.0:s390x 96s Re-Instated python3-matplotlib:s390x 96s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.1.4+dfsg-8 @un uH > 96s Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 0 96s Re-Instated python3-pandas-lib:s390x 96s Re-Instated python3-pandas:s390x 96s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH > 96s Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 0 96s Re-Instated python3-joblib:s390x 96s Re-Instated python3-networkx:s390x 96s Re-Instated python3-pomegranate:s390x 96s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H > 96s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-3 @un uH > 96s Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 0 96s Re-Instated python3-threadpoolctl:s390x 96s Re-Instated python3-sklearn-lib:s390x 96s Re-Instated python3-sklearn:s390x 96s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.76.0-1 @un uH > 96s Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 0 96s Re-Instated r-bioc-dnacopy:s390x 96s Done 96s Some packages could not be installed. This may mean that you have 96s requested an impossible situation or if you are using the unstable 96s distribution that some required packages have not yet been created 96s or been moved out of Incoming. 96s The following information may help to resolve the situation: 96s 96s The following packages have unmet dependencies: 96s cnvkit : Depends: python3-pysam but it is not installable 96s E: Unable to correct problems, you have held broken packages. 96s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from oracular-proposed 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Starting pkgProblemResolver with broken count: 1 97s Starting 2 pkgProblemResolver with broken count: 1 97s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib > 97s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.6.3-2ubuntu1 @un uH > 97s Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 0 97s Re-Instated fonts-lyx:s390x 97s Re-Instated python-matplotlib-data:s390x 97s Re-Instated python3-six:s390x 97s Re-Instated python3-dateutil:s390x 97s Re-Instated python3-minimal:s390x 97s Re-Instated libpython3-stdlib:s390x 97s Re-Instated python3:s390x 97s Re-Instated tk8.6-blt2.5:s390x 97s Re-Instated blt:s390x 97s Re-Instated python3-tk:s390x 97s Re-Instated python3-pil.imagetk:s390x 97s Re-Instated python3-contourpy:s390x 97s Re-Instated python3-cycler:s390x 97s Re-Instated python3-brotli:s390x 97s Re-Instated python3-decorator:s390x 97s Re-Instated liblbfgsb0:s390x 97s Re-Instated python3-scipy:s390x 97s Re-Instated python3-ufolib2:s390x 97s Re-Instated python3-mpmath:s390x 97s Re-Instated python3-sympy:s390x 97s Re-Instated python3-tz:s390x 97s Re-Instated python3-appdirs:s390x 97s Re-Instated python3-fs:s390x 97s Re-Instated libxslt1.1:s390x 97s Re-Instated python3-lxml:s390x 97s Re-Instated python3-lz4:s390x 97s Re-Instated python3-unicodedata2:s390x 97s Re-Instated unicode-data:s390x 97s Re-Instated python3-fonttools:s390x 97s Re-Instated python3-kiwisolver:s390x 97s Re-Instated python3-packaging:s390x 97s Re-Instated libqhull-r8.0:s390x 97s Re-Instated python3-matplotlib:s390x 97s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.2.2+dfsg-4 @un uH > 97s Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 0 97s Re-Instated python3-pandas-lib:s390x 97s Re-Instated python3-pandas:s390x 97s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH > 97s Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 0 97s Re-Instated python3-joblib:s390x 97s Re-Instated python3-networkx:s390x 97s Re-Instated python3-pomegranate:s390x 97s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H > 97s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-3 @un uH > 97s Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 0 97s Re-Instated python3-threadpoolctl:s390x 97s Re-Instated python3-sklearn-lib:s390x 97s Re-Instated python3-sklearn:s390x 97s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.76.0-1 @un uH > 97s Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 0 97s Re-Instated r-bioc-dnacopy:s390x 97s Done 97s Some packages could not be installed. This may mean that you have 97s requested an impossible situation or if you are using the unstable 97s distribution that some required packages have not yet been created 97s or been moved out of Incoming. 97s The following information may help to resolve the situation: 97s 97s The following packages have unmet dependencies: 97s cnvkit : Depends: python3-pysam but it is not installable 97s E: Unable to correct problems, you have held broken packages. 97s autopkgtest: WARNING: Test dependencies are unsatisfiable - calling apt install on test deps directly for further data about failing dependencies in test logs 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s Starting pkgProblemResolver with broken count: 1 98s Starting 2 pkgProblemResolver with broken count: 1 98s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib > 98s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.6.3-2ubuntu1 @un uH > 98s Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 9999 98s Re-Instated fonts-lyx:s390x 98s Re-Instated python-matplotlib-data:s390x 98s Re-Instated python3-six:s390x 98s Re-Instated python3-dateutil:s390x 98s Re-Instated python3-minimal:s390x 98s Re-Instated libpython3-stdlib:s390x 98s Re-Instated python3:s390x 98s Re-Instated tk8.6-blt2.5:s390x 98s Re-Instated blt:s390x 98s Re-Instated python3-tk:s390x 98s Re-Instated python3-pil.imagetk:s390x 98s Re-Instated python3-contourpy:s390x 98s Re-Instated python3-cycler:s390x 98s Re-Instated python3-brotli:s390x 98s Re-Instated python3-decorator:s390x 98s Re-Instated liblbfgsb0:s390x 98s Re-Instated python3-scipy:s390x 98s Re-Instated python3-ufolib2:s390x 98s Re-Instated python3-mpmath:s390x 98s Re-Instated python3-sympy:s390x 98s Re-Instated python3-tz:s390x 98s Re-Instated python3-appdirs:s390x 98s Re-Instated python3-fs:s390x 98s Re-Instated libxslt1.1:s390x 98s Re-Instated python3-lxml:s390x 98s Re-Instated python3-lz4:s390x 98s Re-Instated python3-unicodedata2:s390x 98s Re-Instated unicode-data:s390x 98s Re-Instated python3-fonttools:s390x 98s Re-Instated python3-kiwisolver:s390x 98s Re-Instated python3-packaging:s390x 98s Re-Instated libqhull-r8.0:s390x 98s Re-Instated python3-matplotlib:s390x 98s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.2.2+dfsg-4 @un uH > 98s Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 9999 98s Re-Instated python3-pandas-lib:s390x 98s Re-Instated python3-pandas:s390x 98s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH > 98s Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 9999 98s Re-Instated python3-joblib:s390x 98s Re-Instated python3-networkx:s390x 98s Re-Instated python3-pomegranate:s390x 98s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H > 98s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-3 @un uH > 98s Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 9999 98s Re-Instated python3-threadpoolctl:s390x 98s Re-Instated python3-sklearn-lib:s390x 98s Re-Instated python3-sklearn:s390x 98s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.76.0-1 @un uH > 98s Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 9999 98s Re-Instated r-bioc-dnacopy:s390x 98s Done 98s bash is already the newest version (5.2.21-2.1ubuntu1). 98s dpkg-dev is already the newest version (1.22.6ubuntu14). 98s Some packages could not be installed. This may mean that you have 98s requested an impossible situation or if you are using the unstable 98s distribution that some required packages have not yet been created 98s or been moved out of Incoming. 98s The following information may help to resolve the situation: 98s 98s The following packages have unmet dependencies: 98s cnvkit : Depends: python3-pysam but it is not installable 98s E: Unable to correct problems, you have held broken packages. 98s run-tests FAIL badpkg 98s blame: gffread 98s badpkg: Test dependencies are unsatisfiable. A common reason is that your testbed is out of date with respect to the archive, and you need to use a current testbed or run apt-get update or use -U. 98s autopkgtest [16:05:34]: @@@@@@@@@@@@@@@@@@@@ summary 98s run-tests FAIL badpkg 98s blame: gffread 98s badpkg: Test dependencies are unsatisfiable. A common reason is that your testbed is out of date with respect to the archive, and you need to use a current testbed or run apt-get update or use -U. 119s nova [W] Using flock in scalingstack-bos02-s390x 119s Creating nova instance adt-oracular-s390x-gffread-20240726-160356-juju-7f2275-prod-proposed-migration-environment-2-fab9632e-e3ef-4c05-bc3b-fc3dca37e4d0 from image adt/ubuntu-oracular-s390x-server-20240726.img (UUID 1d18c6e9-51cf-4c36-8ceb-449d0bc81f1d)...