0s autopkgtest [04:22:46]: starting date and time: 2024-03-23 04:22:46+0000 0s autopkgtest [04:22:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [04:22:46]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w8ng2xf_/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:python-pysam --apt-upgrade insilicoseq --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-4.secgroup --name adt-noble-s390x-insilicoseq-20240323-042246-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 101s autopkgtest [04:24:27]: testbed dpkg architecture: s390x 101s autopkgtest [04:24:27]: testbed apt version: 2.7.12 101s autopkgtest [04:24:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 102s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 103s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4001 kB] 103s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 103s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 104s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 104s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [661 kB] 104s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 104s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 104s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 104s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4154 kB] 104s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 104s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.5 kB] 104s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 107s Fetched 9552 kB in 3s (2861 kB/s) 107s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 110s The following packages will be upgraded: 110s libbsd0 111s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 111s Need to get 46.7 kB of archives. 111s After this operation, 0 B of additional disk space will be used. 111s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 111s Fetched 46.7 kB in 0s (172 kB/s) 111s (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 ... 52170 files and directories currently installed.) 111s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 111s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 111s Setting up libbsd0:s390x (0.12.1-1) ... 111s Processing triggers for libc-bin (2.39-0ubuntu2) ... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Unknown architecture, assuming PC-style ttyS0 113s sh: Attempting to set up Debian/Ubuntu apt sources automatically 113s sh: Distribution appears to be Ubuntu 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s eatmydata is already the newest version (131-1). 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s dbus is already the newest version (1.14.10-4ubuntu1). 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s rng-tools-debian is already the newest version (2.4). 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s The following packages will be REMOVED: 116s cloud-init* python3-configobj* python3-debconf* 116s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 116s After this operation, 3256 kB disk space will be freed. 116s (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 ... 52170 files and directories currently installed.) 116s Removing cloud-init (24.1.2-0ubuntu1) ... 117s Removing python3-configobj (5.0.8-3) ... 117s Removing python3-debconf (1.5.86) ... 117s Processing triggers for man-db (2.12.0-3) ... 117s (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 ... 51781 files and directories currently installed.) 117s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 118s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 118s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 118s invoke-rc.d: policy-rc.d denied execution of try-restart. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 119s linux-generic is already the newest version (6.8.0-11.11+1). 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 119s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 119s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 121s Reading package lists... 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [04:24:48]: rebooting testbed after setup commands that affected boot 140s autopkgtest [04:25:06]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 143s autopkgtest [04:25:09]: @@@@@@@@@@@@@@@@@@@@ apt-source insilicoseq 146s Get:1 http://ftpmaster.internal/ubuntu noble/universe insilicoseq 2.0.0-1 (dsc) [2411 B] 146s Get:2 http://ftpmaster.internal/ubuntu noble/universe insilicoseq 2.0.0-1 (tar) [4591 kB] 146s Get:3 http://ftpmaster.internal/ubuntu noble/universe insilicoseq 2.0.0-1 (diff) [5272 B] 146s gpgv: Signature made Sun Feb 18 09:47:08 2024 UTC 146s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 146s gpgv: issuer "emollier@debian.org" 146s gpgv: Can't check signature: No public key 146s dpkg-source: warning: cannot verify inline signature for ./insilicoseq_2.0.0-1.dsc: no acceptable signature found 146s autopkgtest [04:25:12]: testing package insilicoseq version 2.0.0-1 146s autopkgtest [04:25:12]: build not needed 149s autopkgtest [04:25:15]: test run-unit-test: preparing testbed 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 154s Starting pkgProblemResolver with broken count: 1 154s Starting 2 pkgProblemResolver with broken count: 1 154s Investigating (0) insilicoseq:s390x < none -> 2.0.0-1 @un puN Ib > 154s Broken insilicoseq:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 154s Considering python3-biopython:s390x 1 as a solution to insilicoseq:s390x 0 154s Re-Instated libblas3:s390x 154s Re-Instated libgfortran5:s390x 154s Re-Instated liblapack3:s390x 154s Re-Instated python3-numpy:s390x 154s Re-Instated libfreetype6:s390x 154s Re-Instated libgomp1:s390x 154s Re-Instated libimagequant0:s390x 154s Re-Instated libjpeg-turbo8:s390x 154s Re-Instated libjpeg8:s390x 154s Re-Instated liblcms2-2:s390x 154s Re-Instated libopenjp2-7:s390x 154s Re-Instated libgraphite2-3:s390x 154s Re-Instated libharfbuzz0b:s390x 154s Re-Instated libraqm0:s390x 154s Re-Instated libdeflate0:s390x 154s Re-Instated libjbig0:s390x 154s Re-Instated libsharpyuv0:s390x 154s Re-Instated libwebp7:s390x 154s Re-Instated libtiff6:s390x 154s Re-Instated libwebpdemux2:s390x 154s Re-Instated libwebpmux3:s390x 154s Re-Instated python3-pil:s390x 154s Re-Instated fonts-dejavu-mono:s390x 154s Re-Instated fonts-dejavu-core:s390x 154s Re-Instated fontconfig-config:s390x 154s Re-Instated libfontconfig1:s390x 154s Re-Instated libpixman-1-0:s390x 154s Re-Instated libxcb-render0:s390x 154s Re-Instated libxcb-shm0:s390x 154s Re-Instated libxrender1:s390x 154s Re-Instated libcairo2:s390x 154s Re-Instated python3-cairo:s390x 154s Re-Instated python3-freetype:s390x 154s Re-Instated python3-rlpycairo:s390x 154s Re-Instated fonts-dejavu-extra:s390x 154s Re-Instated libfontenc1:s390x 154s Re-Instated x11-common:s390x 154s Re-Instated xfonts-encodings:s390x 154s Re-Instated xfonts-utils:s390x 154s Re-Instated fonts-urw-base35:s390x 154s Re-Instated python3-reportlab:s390x 154s Re-Instated sgml-base:s390x 154s Re-Instated xml-core:s390x 154s Re-Instated w3c-sgml-lib:s390x 154s Re-Instated python3-biopython:s390x 154s Broken insilicoseq:s390x Depends on python3-pysam:s390x < none @un H > 154s Broken insilicoseq:s390x Depends on python3-scipy:s390x < none | 1.11.4-6 @un uH > 154s Considering python3-scipy:s390x 1 as a solution to insilicoseq:s390x 0 154s Re-Instated python3-decorator:s390x 154s Re-Instated liblbfgsb0:s390x 154s Re-Instated python3-scipy:s390x 154s Done 154s Some packages could not be installed. This may mean that you have 154s requested an impossible situation or if you are using the unstable 154s distribution that some required packages have not yet been created 154s or been moved out of Incoming. 154s The following information may help to resolve the situation: 154s 154s The following packages have unmet dependencies: 154s insilicoseq : Depends: python3-pysam but it is not installable 155s E: Unable to correct problems, you have held broken packages. 155s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 156s Starting pkgProblemResolver with broken count: 1 156s Starting 2 pkgProblemResolver with broken count: 1 156s Investigating (0) insilicoseq:s390x < none -> 2.0.0-1 @un puN Ib > 156s Broken insilicoseq:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 156s Considering python3-biopython:s390x 1 as a solution to insilicoseq:s390x 0 156s Re-Instated libblas3:s390x 156s Re-Instated libgfortran5:s390x 156s Re-Instated liblapack3:s390x 156s Re-Instated python3-numpy:s390x 156s Re-Instated libfreetype6:s390x 156s Re-Instated libgomp1:s390x 156s Re-Instated libimagequant0:s390x 156s Re-Instated libjpeg-turbo8:s390x 156s Re-Instated libjpeg8:s390x 156s Re-Instated liblcms2-2:s390x 156s Re-Instated libopenjp2-7:s390x 156s Re-Instated libgraphite2-3:s390x 156s Re-Instated libharfbuzz0b:s390x 156s Re-Instated libraqm0:s390x 156s Re-Instated libdeflate0:s390x 156s Re-Instated libjbig0:s390x 156s Re-Instated libsharpyuv0:s390x 156s Re-Instated libwebp7:s390x 156s Re-Instated libtiff6:s390x 156s Re-Instated libwebpdemux2:s390x 156s Re-Instated libwebpmux3:s390x 156s Re-Instated python3-pil:s390x 156s Re-Instated fonts-dejavu-mono:s390x 156s Re-Instated fonts-dejavu-core:s390x 156s Re-Instated fontconfig-config:s390x 156s Re-Instated libfontconfig1:s390x 156s Re-Instated libpixman-1-0:s390x 156s Re-Instated libxcb-render0:s390x 156s Re-Instated libxcb-shm0:s390x 156s Re-Instated libxrender1:s390x 156s Re-Instated libcairo2:s390x 156s Re-Instated python3-cairo:s390x 156s Re-Instated python3-freetype:s390x 156s Re-Instated python3-rlpycairo:s390x 156s Re-Instated fonts-dejavu-extra:s390x 156s Re-Instated libfontenc1:s390x 156s Re-Instated x11-common:s390x 156s Re-Instated xfonts-encodings:s390x 156s Re-Instated xfonts-utils:s390x 156s Re-Instated fonts-urw-base35:s390x 156s Re-Instated python3-reportlab:s390x 156s Re-Instated sgml-base:s390x 156s Re-Instated xml-core:s390x 156s Re-Instated w3c-sgml-lib:s390x 156s Re-Instated python3-biopython:s390x 156s Broken insilicoseq:s390x Depends on python3-pysam:s390x < none @un H > 156s Broken insilicoseq:s390x Depends on python3-scipy:s390x < none | 1.11.4-6 @un uH > 156s Considering python3-scipy:s390x 1 as a solution to insilicoseq:s390x 0 156s Re-Instated python3-decorator:s390x 156s Re-Instated liblbfgsb0:s390x 156s Re-Instated python3-scipy:s390x 156s Done 156s Some packages could not be installed. This may mean that you have 156s requested an impossible situation or if you are using the unstable 156s distribution that some required packages have not yet been created 156s or been moved out of Incoming. 156s The following information may help to resolve the situation: 156s 156s The following packages have unmet dependencies: 156s insilicoseq : Depends: python3-pysam but it is not installable 156s E: Unable to correct problems, you have held broken packages. 156s autopkgtest: WARNING: Test dependencies are unsatisfiable - calling apt install on test deps directly for further data about failing dependencies in test logs 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Starting pkgProblemResolver with broken count: 1 157s Starting 2 pkgProblemResolver with broken count: 1 157s Investigating (0) insilicoseq:s390x < none -> 2.0.0-1 @un puN Ib > 157s Broken insilicoseq:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 157s Considering python3-biopython:s390x 1 as a solution to insilicoseq:s390x 9999 157s Re-Instated libblas3:s390x 157s Re-Instated libgfortran5:s390x 157s Re-Instated liblapack3:s390x 157s Re-Instated python3-numpy:s390x 157s Re-Instated libfreetype6:s390x 157s Re-Instated libgomp1:s390x 157s Re-Instated libimagequant0:s390x 157s Re-Instated libjpeg-turbo8:s390x 157s Re-Instated libjpeg8:s390x 157s Re-Instated liblcms2-2:s390x 157s Re-Instated libopenjp2-7:s390x 157s Re-Instated libgraphite2-3:s390x 157s Re-Instated libharfbuzz0b:s390x 157s Re-Instated libraqm0:s390x 157s Re-Instated libdeflate0:s390x 157s Re-Instated libjbig0:s390x 157s Re-Instated libsharpyuv0:s390x 157s Re-Instated libwebp7:s390x 157s Re-Instated libtiff6:s390x 157s Re-Instated libwebpdemux2:s390x 157s Re-Instated libwebpmux3:s390x 157s Re-Instated python3-pil:s390x 157s Re-Instated fonts-dejavu-mono:s390x 157s Re-Instated fonts-dejavu-core:s390x 157s Re-Instated fontconfig-config:s390x 157s Re-Instated libfontconfig1:s390x 157s Re-Instated libpixman-1-0:s390x 157s Re-Instated libxcb-render0:s390x 157s Re-Instated libxcb-shm0:s390x 157s Re-Instated libxrender1:s390x 157s Re-Instated libcairo2:s390x 157s Re-Instated python3-cairo:s390x 157s Re-Instated python3-freetype:s390x 157s Re-Instated python3-rlpycairo:s390x 157s Re-Instated fonts-dejavu-extra:s390x 157s Re-Instated libfontenc1:s390x 157s Re-Instated x11-common:s390x 157s Re-Instated xfonts-encodings:s390x 157s Re-Instated xfonts-utils:s390x 157s Re-Instated fonts-urw-base35:s390x 157s Re-Instated python3-reportlab:s390x 157s Re-Instated sgml-base:s390x 157s Re-Instated xml-core:s390x 157s Re-Instated w3c-sgml-lib:s390x 157s Re-Instated python3-biopython:s390x 157s Broken insilicoseq:s390x Depends on python3-pysam:s390x < none @un H > 157s Broken insilicoseq:s390x Depends on python3-scipy:s390x < none | 1.11.4-6 @un uH > 157s Considering python3-scipy:s390x 1 as a solution to insilicoseq:s390x 9999 157s Re-Instated python3-decorator:s390x 157s Re-Instated liblbfgsb0:s390x 157s Re-Instated python3-scipy:s390x 157s Done 157s Some packages could not be installed. This may mean that you have 157s requested an impossible situation or if you are using the unstable 157s distribution that some required packages have not yet been created 157s or been moved out of Incoming. 157s The following information may help to resolve the situation: 157s 157s The following packages have unmet dependencies: 157s insilicoseq : Depends: python3-pysam but it is not installable 157s E: Unable to correct problems, you have held broken packages. 157s run-unit-test FAIL badpkg 157s blame: insilicoseq 157s 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. 157s autopkgtest [04:25:23]: @@@@@@@@@@@@@@@@@@@@ summary 157s run-unit-test FAIL badpkg 157s blame: insilicoseq 157s 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. 168s Creating nova instance adt-noble-s390x-insilicoseq-20240323-042246-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...