0s autopkgtest [10:37:39]: starting date and time: 2024-11-13 10:37:39+0000
  0s autopkgtest [10:37:39]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [10:37:39]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nquy1nqn/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-16.secgroup --name adt-plucky-s390x-cnvkit-20241113-103738-juju-7f2275-prod-proposed-migration-environment-15-e888ad8c-508a-4da6-a362-b8fe10396024 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/
130s autopkgtest [10:39:49]: testbed dpkg architecture: s390x
131s autopkgtest [10:39:50]: testbed apt version: 2.9.8
131s autopkgtest [10:39:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup
131s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
132s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
132s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
132s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
132s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
132s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [85.8 kB]
132s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [565 kB]
132s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [16.6 kB]
132s Fetched 1689 kB in 1s (2003 kB/s)
132s Reading package lists...
135s Reading package lists...
135s Building dependency tree...
135s Reading state information...
135s Calculating upgrade...
135s The following NEW packages will be installed:
135s   python3.13-gdbm
135s The following packages will be upgraded:
135s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
135s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
135s Need to get 252 kB of archives.
135s After this operation, 98.3 kB of additional disk space will be used.
135s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB]
135s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB]
135s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB]
135s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB]
136s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B]
136s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB]
136s Fetched 252 kB in 1s (498 kB/s)
136s (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 ... 55510 files and directories currently installed.)
136s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ...
136s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
136s Setting up python3-minimal (3.12.7-1) ...
136s (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 ... 55510 files and directories currently installed.)
136s Preparing to unpack .../python3_3.12.7-1_s390x.deb ...
136s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
136s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ...
136s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ...
136s Selecting previously unselected package python3.13-gdbm.
136s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ...
136s Unpacking python3.13-gdbm (3.13.0-2) ...
136s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ...
136s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ...
136s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ...
136s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
136s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ...
136s Setting up python3.13-gdbm (3.13.0-2) ...
136s Setting up libpython3-stdlib:s390x (3.12.7-1) ...
136s Setting up python3 (3.12.7-1) ...
136s Setting up python3-gdbm:s390x (3.12.7-1) ...
136s Processing triggers for man-db (2.12.1-3) ...
137s Processing triggers for libc-bin (2.40-1ubuntu3) ...
137s Reading package lists...
137s Building dependency tree...
137s Reading state information...
137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
138s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
138s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
138s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
138s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
138s Reading package lists...
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s Calculating upgrade...
139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
139s Reading package lists...
139s Building dependency tree...
139s Reading state information...
139s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
143s autopkgtest [10:40:02]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024
144s autopkgtest [10:40:03]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit
149s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (dsc) [2449 B]
149s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (tar) [23.7 MB]
149s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.10-2 (diff) [17.7 kB]
149s gpgv: Signature made Mon Apr  8 08:42:55 2024 UTC
149s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
149s gpgv: Can't check signature: No public key
149s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found
149s autopkgtest [10:40:08]: testing package cnvkit version 0.9.10-2
151s autopkgtest [10:40:10]: build not needed
156s autopkgtest [10:40:15]: test run-unit-test: preparing testbed
163s Reading package lists...
163s Building dependency tree...
163s Reading state information...
163s Starting pkgProblemResolver with broken count: 1
163s Starting 2 pkgProblemResolver with broken count: 1
163s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib >
163s Broken cnvkit:s390x Depends on python3-biopython:s390x < none | 1.84+dfsg-4 @un uH >
163s   Considering python3-biopython:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated libblas3:s390x
163s   Re-Instated libgfortran5:s390x
163s   Re-Instated liblapack3:s390x
163s   Re-Instated python3-numpy:s390x
163s   Re-Instated libgomp1:s390x
163s   Re-Instated libimagequant0:s390x
163s   Re-Instated libgraphite2-3:s390x
163s   Re-Instated libharfbuzz0b:s390x
163s   Re-Instated libraqm0:s390x
163s   Re-Instated libwebpdemux2:s390x
163s   Re-Instated libwebpmux3:s390x
163s   Re-Instated python3-pil:s390x
163s   Re-Instated python3-cairo:s390x
163s   Re-Instated python3-freetype:s390x
163s   Re-Instated python3-rlpycairo:s390x
163s   Re-Instated libfontenc1:s390x
163s   Re-Instated x11-common:s390x
163s   Re-Instated xfonts-encodings:s390x
163s   Re-Instated xfonts-utils:s390x
163s   Re-Instated fonts-urw-base35:s390x
163s   Re-Instated python3-reportlab:s390x
163s   Re-Instated sgml-base:s390x
163s   Re-Instated xml-core:s390x
163s   Re-Instated w3c-sgml-lib:s390x
163s   Re-Instated python3-biopython:s390x
163s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.8.3-3 @un uH >
163s   Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated libjs-jquery:s390x
163s   Re-Instated libjs-jquery-ui:s390x
163s   Re-Instated fonts-lyx:s390x
163s   Re-Instated python-matplotlib-data:s390x
163s   Re-Instated python3-six:s390x
163s   Re-Instated python3-dateutil:s390x
163s   Re-Instated libtcl8.6:s390x
163s   Re-Instated libxft2:s390x
163s   Re-Instated libxss1:s390x
163s   Re-Instated libtk8.6:s390x
163s   Re-Instated python3.12-tk:s390x
163s   Re-Instated python3.13-tk:s390x
163s   Re-Instated tk8.6-blt2.5:s390x
163s   Re-Instated blt:s390x
163s   Re-Instated python3-tk:s390x
163s   Re-Instated python3-pil.imagetk:s390x
163s   Re-Instated python3-contourpy:s390x
163s   Re-Instated python3-cycler:s390x
163s   Re-Instated python3-brotli:s390x
163s   Re-Instated python3-decorator:s390x
163s   Re-Instated liblbfgsb0:s390x
163s   Re-Instated python3-scipy:s390x
163s   Re-Instated python3-ufolib2:s390x
163s   Re-Instated python3-mpmath:s390x
163s   Re-Instated python3-sympy:s390x
163s   Re-Instated python3-tz:s390x
163s   Re-Instated python3-appdirs:s390x
163s   Re-Instated python3-fs:s390x
163s   Re-Instated libxslt1.1:s390x
163s   Re-Instated python3-lxml:s390x
163s   Re-Instated python3-lz4:s390x
163s   Re-Instated python3-unicodedata2:s390x
163s   Re-Instated unicode-data:s390x
163s   Re-Instated python3-fonttools:s390x
163s   Re-Instated python3-kiwisolver:s390x
163s   Re-Instated python3-packaging:s390x
163s   Re-Instated libqhull-r8.0:s390x
163s   Re-Instated python3-matplotlib:s390x
163s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.2.3+dfsg-5 @un uH >
163s   Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated python3-pandas-lib:s390x
163s   Re-Instated python3-pandas:s390x
163s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH >
163s   Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated python3-joblib:s390x
163s   Re-Instated python3-networkx:s390x
163s   Re-Instated python3-pomegranate:s390x
163s Broken cnvkit:s390x Depends on python3-pyfaidx:s390x < none | 0.8.1.3-1 @un uH >
163s   Considering python3-pyfaidx:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated python3-importlib-metadata:s390x
163s   Re-Instated python3-pyfaidx:s390x
163s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H >
163s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-6 @un uH >
163s   Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated python3-threadpoolctl:s390x
163s   Re-Instated python3-sklearn-lib:s390x
163s   Re-Instated python3-sklearn:s390x
163s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.78.0-1 @un uH >
163s   Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 0
163s   Re-Instated zip:s390x
163s   Re-Instated unzip:s390x
163s   Re-Instated libpaper1:s390x
163s   Re-Instated libpaper-utils:s390x
163s   Re-Instated xdg-utils:s390x
163s   Re-Instated fontconfig:s390x
163s   Re-Instated libthai-data:s390x
163s   Re-Instated libdatrie1:s390x
163s   Re-Instated libthai0:s390x
163s   Re-Instated libpango-1.0-0:s390x
163s   Re-Instated libpangoft2-1.0-0:s390x
163s   Re-Instated libpangocairo-1.0-0:s390x
163s   Re-Instated libice6:s390x
163s   Re-Instated libsm6:s390x
163s   Re-Instated libxt6t64:s390x
163s   Re-Instated r-base-core:s390x
163s   Re-Instated r-bioc-biocgenerics:s390x
163s   Re-Instated r-bioc-dnacopy:s390x
163s Done
163s Some packages could not be installed. This may mean that you have
163s requested an impossible situation or if you are using the unstable
163s distribution that some required packages have not yet been created
163s or been moved out of Incoming.
163s The following information may help to resolve the situation:
163s 
163s The following packages have unmet dependencies:
163s  cnvkit : Depends: python3-pysam but it is not installable
163s E: Unable to correct problems, you have held broken packages.
163s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from plucky-proposed
164s Reading package lists...
164s Building dependency tree...
164s Reading state information...
164s Starting pkgProblemResolver with broken count: 1
164s Starting 2 pkgProblemResolver with broken count: 1
164s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib >
164s Broken cnvkit:s390x Depends on python3-biopython:s390x < none | 1.84+dfsg-4 @un uH >
164s   Considering python3-biopython:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated libblas3:s390x
164s   Re-Instated libgfortran5:s390x
164s   Re-Instated liblapack3:s390x
164s   Re-Instated python3-numpy:s390x
164s   Re-Instated libgomp1:s390x
164s   Re-Instated libimagequant0:s390x
164s   Re-Instated libgraphite2-3:s390x
164s   Re-Instated libharfbuzz0b:s390x
164s   Re-Instated libraqm0:s390x
164s   Re-Instated libwebpdemux2:s390x
164s   Re-Instated libwebpmux3:s390x
164s   Re-Instated python3-pil:s390x
164s   Re-Instated python3-cairo:s390x
164s   Re-Instated python3-freetype:s390x
164s   Re-Instated python3-rlpycairo:s390x
164s   Re-Instated libfontenc1:s390x
164s   Re-Instated x11-common:s390x
164s   Re-Instated xfonts-encodings:s390x
164s   Re-Instated xfonts-utils:s390x
164s   Re-Instated fonts-urw-base35:s390x
164s   Re-Instated python3-reportlab:s390x
164s   Re-Instated sgml-base:s390x
164s   Re-Instated xml-core:s390x
164s   Re-Instated w3c-sgml-lib:s390x
164s   Re-Instated python3-biopython:s390x
164s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.8.3-3 @un uH >
164s   Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated libjs-jquery:s390x
164s   Re-Instated libjs-jquery-ui:s390x
164s   Re-Instated fonts-lyx:s390x
164s   Re-Instated python-matplotlib-data:s390x
164s   Re-Instated python3-dateutil:s390x
164s   Re-Instated libtcl8.6:s390x
164s   Re-Instated libxft2:s390x
164s   Re-Instated libxss1:s390x
164s   Re-Instated libtk8.6:s390x
164s   Re-Instated python3.12-tk:s390x
164s   Re-Instated python3.13-tk:s390x
164s   Re-Instated tk8.6-blt2.5:s390x
164s   Re-Instated blt:s390x
164s   Re-Instated python3-tk:s390x
164s   Re-Instated python3-pil.imagetk:s390x
164s   Re-Instated python3-contourpy:s390x
164s   Re-Instated python3-cycler:s390x
164s   Re-Instated python3-brotli:s390x
164s   Re-Instated python3-decorator:s390x
164s   Re-Instated liblbfgsb0:s390x
164s   Re-Instated python3-scipy:s390x
164s   Re-Instated python3-ufolib2:s390x
164s   Re-Instated python3-mpmath:s390x
164s   Re-Instated python3-sympy:s390x
164s   Re-Instated python3-tz:s390x
164s   Re-Instated python3-six:s390x
164s   Re-Instated python3-appdirs:s390x
164s   Re-Instated python3-fs:s390x
164s   Re-Instated libxslt1.1:s390x
164s   Re-Instated python3-lxml:s390x
164s   Re-Instated python3-lz4:s390x
164s   Re-Instated python3-unicodedata2:s390x
164s   Re-Instated unicode-data:s390x
164s   Re-Instated python3-fonttools:s390x
164s   Re-Instated python3-kiwisolver:s390x
164s   Re-Instated python3-packaging:s390x
164s   Re-Instated libqhull-r8.0:s390x
164s   Re-Instated python3-matplotlib:s390x
164s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.2.3+dfsg-5 @un uH >
164s   Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated python3-pandas-lib:s390x
164s   Re-Instated python3-pandas:s390x
164s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH >
164s   Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated python3-joblib:s390x
164s   Re-Instated python3-networkx:s390x
164s   Re-Instated python3-pomegranate:s390x
164s Broken cnvkit:s390x Depends on python3-pyfaidx:s390x < none | 0.8.1.3-1 @un uH >
164s   Considering python3-pyfaidx:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated python3-importlib-metadata:s390x
164s   Re-Instated python3-pyfaidx:s390x
164s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H >
164s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-6 @un uH >
164s   Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated python3-threadpoolctl:s390x
164s   Re-Instated python3-sklearn-lib:s390x
164s   Re-Instated python3-sklearn:s390x
164s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.78.0-1 @un uH >
164s   Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 0
164s   Re-Instated zip:s390x
164s   Re-Instated unzip:s390x
164s   Re-Instated libpaper1:s390x
164s   Re-Instated libpaper-utils:s390x
164s   Re-Instated xdg-utils:s390x
164s   Re-Instated fontconfig:s390x
164s   Re-Instated libthai-data:s390x
164s   Re-Instated libdatrie1:s390x
164s   Re-Instated libthai0:s390x
164s   Re-Instated libpango-1.0-0:s390x
164s   Re-Instated libpangoft2-1.0-0:s390x
164s   Re-Instated libpangocairo-1.0-0:s390x
164s   Re-Instated libice6:s390x
164s   Re-Instated libsm6:s390x
164s   Re-Instated libxt6t64:s390x
164s   Re-Instated r-base-core:s390x
164s   Re-Instated r-bioc-biocgenerics:s390x
164s   Re-Instated r-bioc-dnacopy:s390x
164s Done
164s Some packages could not be installed. This may mean that you have
164s requested an impossible situation or if you are using the unstable
164s distribution that some required packages have not yet been created
164s or been moved out of Incoming.
164s The following information may help to resolve the situation:
164s 
164s The following packages have unmet dependencies:
164s  cnvkit : Depends: python3-pysam but it is not installable
164s E: Unable to correct problems, you have held broken packages.
164s autopkgtest: WARNING: Test dependencies are unsatisfiable - calling apt install on test deps directly for further data about failing dependencies in test logs
164s Reading package lists...
164s Building dependency tree...
164s Reading state information...
164s Starting pkgProblemResolver with broken count: 1
164s Starting 2 pkgProblemResolver with broken count: 1
164s Investigating (0) cnvkit:s390x < none -> 0.9.10-2 @un puN Ib >
164s Broken cnvkit:s390x Depends on python3-biopython:s390x < none | 1.84+dfsg-4 @un uH >
164s   Considering python3-biopython:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated libblas3:s390x
164s   Re-Instated libgfortran5:s390x
164s   Re-Instated liblapack3:s390x
164s   Re-Instated python3-numpy:s390x
164s   Re-Instated libgomp1:s390x
164s   Re-Instated libimagequant0:s390x
164s   Re-Instated libgraphite2-3:s390x
164s   Re-Instated libharfbuzz0b:s390x
164s   Re-Instated libraqm0:s390x
164s   Re-Instated libwebpdemux2:s390x
164s   Re-Instated libwebpmux3:s390x
164s   Re-Instated python3-pil:s390x
164s   Re-Instated python3-cairo:s390x
164s   Re-Instated python3-freetype:s390x
164s   Re-Instated python3-rlpycairo:s390x
164s   Re-Instated libfontenc1:s390x
164s   Re-Instated x11-common:s390x
164s   Re-Instated xfonts-encodings:s390x
164s   Re-Instated xfonts-utils:s390x
164s   Re-Instated fonts-urw-base35:s390x
164s   Re-Instated python3-reportlab:s390x
164s   Re-Instated sgml-base:s390x
164s   Re-Instated xml-core:s390x
164s   Re-Instated w3c-sgml-lib:s390x
164s   Re-Instated python3-biopython:s390x
164s Broken cnvkit:s390x Depends on python3-matplotlib:s390x < none | 3.8.3-3 @un uH >
164s   Considering python3-matplotlib:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated libjs-jquery:s390x
164s   Re-Instated libjs-jquery-ui:s390x
164s   Re-Instated fonts-lyx:s390x
164s   Re-Instated python-matplotlib-data:s390x
164s   Re-Instated python3-dateutil:s390x
164s   Re-Instated libtcl8.6:s390x
164s   Re-Instated libxft2:s390x
164s   Re-Instated libxss1:s390x
164s   Re-Instated libtk8.6:s390x
164s   Re-Instated python3.12-tk:s390x
164s   Re-Instated python3.13-tk:s390x
164s   Re-Instated tk8.6-blt2.5:s390x
164s   Re-Instated blt:s390x
164s   Re-Instated python3-tk:s390x
164s   Re-Instated python3-pil.imagetk:s390x
164s   Re-Instated python3-contourpy:s390x
164s   Re-Instated python3-cycler:s390x
164s   Re-Instated python3-brotli:s390x
164s   Re-Instated python3-decorator:s390x
164s   Re-Instated liblbfgsb0:s390x
164s   Re-Instated python3-scipy:s390x
164s   Re-Instated python3-ufolib2:s390x
164s   Re-Instated python3-mpmath:s390x
164s   Re-Instated python3-sympy:s390x
164s   Re-Instated python3-tz:s390x
164s   Re-Instated python3-six:s390x
164s   Re-Instated python3-appdirs:s390x
164s   Re-Instated python3-fs:s390x
164s   Re-Instated libxslt1.1:s390x
164s   Re-Instated python3-lxml:s390x
164s   Re-Instated python3-lz4:s390x
164s   Re-Instated python3-unicodedata2:s390x
164s   Re-Instated unicode-data:s390x
164s   Re-Instated python3-fonttools:s390x
164s   Re-Instated python3-kiwisolver:s390x
164s   Re-Instated python3-packaging:s390x
164s   Re-Instated libqhull-r8.0:s390x
164s   Re-Instated python3-matplotlib:s390x
164s Broken cnvkit:s390x Depends on python3-pandas:s390x < none | 2.2.3+dfsg-5 @un uH >
164s   Considering python3-pandas:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated python3-pandas-lib:s390x
164s   Re-Instated python3-pandas:s390x
164s Broken cnvkit:s390x Depends on python3-pomegranate:s390x < none | 0.14.8-6 @un uH >
164s   Considering python3-pomegranate:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated python3-joblib:s390x
164s   Re-Instated python3-networkx:s390x
164s   Re-Instated python3-pomegranate:s390x
164s Broken cnvkit:s390x Depends on python3-pyfaidx:s390x < none | 0.8.1.3-1 @un uH >
164s   Considering python3-pyfaidx:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated python3-importlib-metadata:s390x
164s   Re-Instated python3-pyfaidx:s390x
164s Broken cnvkit:s390x Depends on python3-pysam:s390x < none @un H >
164s Broken cnvkit:s390x Depends on python3-sklearn:s390x < none | 1.4.2+dfsg-6 @un uH >
164s   Considering python3-sklearn:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated python3-threadpoolctl:s390x
164s   Re-Instated python3-sklearn-lib:s390x
164s   Re-Instated python3-sklearn:s390x
164s Broken cnvkit:s390x Depends on r-bioc-dnacopy:s390x < none | 1.78.0-1 @un uH >
164s   Considering r-bioc-dnacopy:s390x 1 as a solution to cnvkit:s390x 9999
164s   Re-Instated zip:s390x
164s   Re-Instated unzip:s390x
164s   Re-Instated libpaper1:s390x
164s   Re-Instated libpaper-utils:s390x
164s   Re-Instated xdg-utils:s390x
164s   Re-Instated fontconfig:s390x
164s   Re-Instated libthai-data:s390x
164s   Re-Instated libdatrie1:s390x
164s   Re-Instated libthai0:s390x
164s   Re-Instated libpango-1.0-0:s390x
164s   Re-Instated libpangoft2-1.0-0:s390x
164s   Re-Instated libpangocairo-1.0-0:s390x
164s   Re-Instated libice6:s390x
164s   Re-Instated libsm6:s390x
164s   Re-Instated libxt6t64:s390x
164s   Re-Instated r-base-core:s390x
164s   Re-Instated r-bioc-biocgenerics:s390x
164s   Re-Instated r-bioc-dnacopy:s390x
164s Done
164s Some packages could not be installed. This may mean that you have
164s requested an impossible situation or if you are using the unstable
164s distribution that some required packages have not yet been created
164s or been moved out of Incoming.
164s The following information may help to resolve the situation:
164s 
164s The following packages have unmet dependencies:
164s  cnvkit : Depends: python3-pysam but it is not installable
164s E: Unable to correct problems, you have held broken packages.
165s run-unit-test        SKIP installation fails and skip-not-installable set
165s autopkgtest [10:40:24]: test pybuild-autopkgtest: preparing testbed
168s Reading package lists...
168s Building dependency tree...
168s Reading state information...
168s Starting pkgProblemResolver with broken count: 1
168s Starting 2 pkgProblemResolver with broken count: 1
168s Investigating (0) autopkgtest-satdep:s390x < none -> 0 @un puN Ib >
168s Broken autopkgtest-satdep:s390x Depends on cnvkit:s390x < none | 0.9.10-2 @un uH >
168s   Considering cnvkit:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated libblas3:s390x
168s   Re-Instated libgfortran5:s390x
168s   Re-Instated liblapack3:s390x
168s   Re-Instated python3-numpy:s390x
168s   Re-Instated libfreetype6:s390x
168s   Re-Instated libgomp1:s390x
168s   Re-Instated libimagequant0:s390x
168s   Re-Instated libjpeg-turbo8:s390x
168s   Re-Instated libjpeg8:s390x
168s   Re-Instated liblcms2-2:s390x
168s   Re-Instated libopenjp2-7:s390x
168s   Re-Instated libgraphite2-3:s390x
168s   Re-Instated libharfbuzz0b:s390x
168s   Re-Instated libraqm0:s390x
168s   Re-Instated libdeflate0:s390x
168s   Re-Instated libjbig0:s390x
168s   Re-Instated libsharpyuv0:s390x
168s   Re-Instated libwebp7:s390x
168s   Re-Instated libtiff6:s390x
168s   Re-Instated libwebpdemux2:s390x
168s   Re-Instated libwebpmux3:s390x
168s   Re-Instated python3-pil:s390x
168s   Re-Instated fonts-dejavu-mono:s390x
168s   Re-Instated fonts-dejavu-core:s390x
168s   Re-Instated fontconfig-config:s390x
168s   Re-Instated libfontconfig1:s390x
168s   Re-Instated libpixman-1-0:s390x
168s   Re-Instated libxcb-render0:s390x
168s   Re-Instated libxcb-shm0:s390x
168s   Re-Instated libxrender1:s390x
168s   Re-Instated libcairo2:s390x
168s   Re-Instated python3-cairo:s390x
168s   Re-Instated python3-freetype:s390x
168s   Re-Instated python3-rlpycairo:s390x
168s   Re-Instated libfontenc1:s390x
168s   Re-Instated x11-common:s390x
168s   Re-Instated xfonts-encodings:s390x
168s   Re-Instated xfonts-utils:s390x
168s   Re-Instated fonts-urw-base35:s390x
168s   Re-Instated python3-reportlab:s390x
168s   Re-Instated sgml-base:s390x
168s   Re-Instated xml-core:s390x
168s   Re-Instated w3c-sgml-lib:s390x
168s   Re-Instated python3-biopython:s390x
168s   Re-Instated libjs-jquery:s390x
168s   Re-Instated libjs-jquery-ui:s390x
168s   Re-Instated fonts-lyx:s390x
168s   Re-Instated python-matplotlib-data:s390x
168s   Re-Instated python3-dateutil:s390x
168s   Re-Instated libtcl8.6:s390x
168s   Re-Instated libxft2:s390x
168s   Re-Instated libxss1:s390x
168s   Re-Instated libtk8.6:s390x
168s   Re-Instated python3.12-tk:s390x
168s   Re-Instated python3.13-tk:s390x
168s   Re-Instated tk8.6-blt2.5:s390x
168s   Re-Instated blt:s390x
168s   Re-Instated python3-tk:s390x
168s   Re-Instated python3-pil.imagetk:s390x
168s   Re-Instated python3-contourpy:s390x
168s   Re-Instated python3-cycler:s390x
168s   Re-Instated python3-brotli:s390x
168s   Re-Instated python3-decorator:s390x
168s   Re-Instated liblbfgsb0:s390x
168s   Re-Instated python3-scipy:s390x
168s   Re-Instated python3-ufolib2:s390x
168s   Re-Instated python3-mpmath:s390x
168s   Re-Instated python3-sympy:s390x
168s   Re-Instated python3-tz:s390x
168s   Re-Instated python3-six:s390x
168s   Re-Instated python3-appdirs:s390x
168s   Re-Instated python3-fs:s390x
168s   Re-Instated libxslt1.1:s390x
168s   Re-Instated python3-lxml:s390x
168s   Re-Instated python3-lz4:s390x
168s   Re-Instated python3-unicodedata2:s390x
168s   Re-Instated unicode-data:s390x
168s   Re-Instated python3-fonttools:s390x
168s   Re-Instated python3-kiwisolver:s390x
168s   Re-Instated python3-packaging:s390x
168s   Re-Instated libqhull-r8.0:s390x
168s   Re-Instated python3-matplotlib:s390x
168s   Re-Instated python3-pandas-lib:s390x
168s   Re-Instated python3-pandas:s390x
168s   Re-Instated python3-joblib:s390x
168s   Re-Instated python3-networkx:s390x
168s   Re-Instated python3-pomegranate:s390x
168s   Re-Instated python3-importlib-metadata:s390x
168s   Re-Instated python3-pyfaidx:s390x
168s     Reinst Failed early because of python3-pysam:s390x
168s Broken autopkgtest-satdep:s390x Depends on pybuild-plugin-autopkgtest:s390x < none | 6.20241024 @un uH >
168s   Considering pybuild-plugin-autopkgtest:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated autotools-dev:s390x
168s   Re-Instated m4:s390x
168s   Re-Instated autoconf:s390x
168s   Re-Instated automake:s390x
168s   Re-Instated autopoint:s390x
168s   Re-Instated libdebhelper-perl:s390x
168s   Re-Instated libisl23:s390x
168s   Re-Instated libmpc3:s390x
168s   Re-Instated cpp-14-s390x-linux-gnu:s390x
168s   Re-Instated cpp-14:s390x
168s   Re-Instated cpp-s390x-linux-gnu:s390x
168s   Re-Instated cpp:s390x
168s   Re-Instated libcc1-0:s390x
168s   Re-Instated libitm1:s390x
168s   Re-Instated libasan8:s390x
168s   Re-Instated libubsan1:s390x
168s   Re-Instated libgcc-14-dev:s390x
168s   Re-Instated gcc-14-s390x-linux-gnu:s390x
168s   Re-Instated gcc-14:s390x
168s   Re-Instated gcc-s390x-linux-gnu:s390x
168s   Re-Instated gcc:s390x
168s   Re-Instated libtool:s390x
168s   Re-Instated dh-autoreconf:s390x
168s   Re-Instated libarchive-zip-perl:s390x
168s   Re-Instated libfile-stripnondeterminism-perl:s390x
168s   Re-Instated dh-strip-nondeterminism:s390x
168s   Re-Instated debugedit:s390x
168s   Re-Instated dwz:s390x
168s   Re-Instated gettext:s390x
168s   Re-Instated intltool-debian:s390x
168s   Re-Instated po-debconf:s390x
168s   Re-Instated debhelper:s390x
168s   Re-Instated dh-python:s390x
168s   Re-Instated pybuild-plugin-autopkgtest:s390x
168s Broken autopkgtest-satdep:s390x Depends on python3-all:s390x < none | 3.12.7-1 @un uH >
168s   Considering python3-all:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated libpython3.13-minimal:s390x
168s   Re-Instated python3.13-minimal:s390x
168s   Re-Instated libpython3.13-stdlib:s390x
168s   Re-Instated python3.13:s390x
168s   Re-Instated python3-all:s390x
168s Broken autopkgtest-satdep:s390x Depends on pybuild-plugin-pyproject:s390x < none | 6.20241024 @un uH >
168s   Considering pybuild-plugin-pyproject:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated python3-pyproject-hooks:s390x
168s   Re-Instated python3-toml:s390x
168s   Re-Instated python3-wheel:s390x
168s   Re-Instated python3-build:s390x
168s   Re-Instated python3-installer:s390x
168s   Re-Instated pybuild-plugin-pyproject:s390x
168s Broken autopkgtest-satdep:s390x Depends on python3-pytest:s390x < none | 8.3.3-1 @un uH >
168s   Considering python3-pytest:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated python3-iniconfig:s390x
168s   Re-Instated python3-pluggy:s390x
168s   Re-Instated python3-pytest:s390x
168s Broken autopkgtest-satdep:s390x Depends on python3-pysam:s390x < none @un H >
168s Broken autopkgtest-satdep:s390x Depends on r-bioc-dnacopy:s390x < none | 1.78.0-1 @un uH >
168s   Considering r-bioc-dnacopy:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated zip:s390x
168s   Re-Instated unzip:s390x
168s   Re-Instated libpaper1:s390x
168s   Re-Instated libpaper-utils:s390x
168s   Re-Instated xdg-utils:s390x
168s   Re-Instated fontconfig:s390x
168s   Re-Instated libthai-data:s390x
168s   Re-Instated libdatrie1:s390x
168s   Re-Instated libthai0:s390x
168s   Re-Instated libpango-1.0-0:s390x
168s   Re-Instated libpangoft2-1.0-0:s390x
168s   Re-Instated libpangocairo-1.0-0:s390x
168s   Re-Instated libice6:s390x
168s   Re-Instated libsm6:s390x
168s   Re-Instated libxt6t64:s390x
168s   Re-Instated r-base-core:s390x
168s   Re-Instated r-bioc-biocgenerics:s390x
168s   Re-Instated r-bioc-dnacopy:s390x
168s Broken autopkgtest-satdep:s390x Depends on poppler-utils:s390x < none | 24.08.0-3 @un uH >
168s   Considering poppler-utils:s390x 1 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated libgpgmepp6t64:s390x
168s   Re-Instated libpoppler140:s390x
168s   Re-Instated poppler-utils:s390x
168s Broken autopkgtest-satdep:s390x Depends on build-essential:s390x < none | 12.10ubuntu1 @un umH >
168s   Considering build-essential:s390x 2 as a solution to autopkgtest-satdep:s390x 9998
168s   Re-Instated libstdc++-14-dev:s390x
168s   Re-Instated g++-14-s390x-linux-gnu:s390x
168s   Re-Instated g++-14:s390x
168s   Re-Instated g++-s390x-linux-gnu:s390x
168s   Re-Instated g++:s390x
168s   Re-Instated build-essential:s390x
168s Done
168s Some packages could not be installed. This may mean that you have
168s requested an impossible situation or if you are using the unstable
168s distribution that some required packages have not yet been created
168s or been moved out of Incoming.
168s The following information may help to resolve the situation:
168s 
168s The following packages have unmet dependencies:
168s  autopkgtest-satdep : Depends: cnvkit but it is not going to be installed
168s                       Depends: python3-pysam but it is not installable
168s E: Unable to correct problems, you have held broken packages.
168s autopkgtest: WARNING: Test dependencies are unsatisfiable - calling apt install on test deps directly for further data about failing dependencies in test logs
169s pybuild-autopkgtest  SKIP installation fails and skip-not-installable set
169s autopkgtest [10:40:28]: @@@@@@@@@@@@@@@@@@@@ summary
169s run-unit-test        SKIP installation fails and skip-not-installable set
169s pybuild-autopkgtest  SKIP installation fails and skip-not-installable set
189s nova [W] Using flock in prodstack6-s390x
189s Creating nova instance adt-plucky-s390x-cnvkit-20241113-103738-juju-7f2275-prod-proposed-migration-environment-15-e888ad8c-508a-4da6-a362-b8fe10396024 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...