0s autopkgtest [04:29:02]: starting date and time: 2024-03-23 04:29:02+0000 0s autopkgtest [04:29:02]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [04:29:02]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ej4kzn95/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 optimir --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-2@bos02-s390x-20.secgroup --name adt-noble-s390x-optimir-20240323-042902-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 103s autopkgtest [04:30:45]: testbed dpkg architecture: s390x 103s autopkgtest [04:30:45]: testbed apt version: 2.7.12 103s autopkgtest [04:30:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 104s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [495 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 105s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4001 kB] 105s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [661 kB] 105s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 105s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 105s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 105s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4154 kB] 105s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 105s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [47.5 kB] 105s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 107s Fetched 9552 kB in 2s (3907 kB/s) 108s Reading package lists... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s Calculating upgrade... 111s The following packages will be upgraded: 111s 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 (166 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) ... 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Unknown architecture, assuming PC-style ttyS0 112s sh: Attempting to set up Debian/Ubuntu apt sources automatically 112s sh: Distribution appears to be Ubuntu 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s eatmydata is already the newest version (131-1). 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s dbus is already the newest version (1.14.10-4ubuntu1). 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... 114s rng-tools-debian is already the newest version (2.4). 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 The following packages will be REMOVED: 115s cloud-init* python3-configobj* python3-debconf* 115s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 115s After this operation, 3256 kB disk space will be freed. 115s (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.) 115s Removing cloud-init (24.1.2-0ubuntu1) ... 115s Removing python3-configobj (5.0.8-3) ... 115s Removing python3-debconf (1.5.86) ... 115s Processing triggers for man-db (2.12.0-3) ... 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 ... 51781 files and directories currently installed.) 116s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 116s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 116s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 116s invoke-rc.d: policy-rc.d denied execution of try-restart. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s linux-generic is already the newest version (6.8.0-11.11+1). 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 117s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 119s Reading package lists... 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Calculating upgrade... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [04:31:02]: rebooting testbed after setup commands that affected boot 134s autopkgtest [04:31:16]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 137s autopkgtest [04:31:19]: @@@@@@@@@@@@@@@@@@@@ apt-source optimir 139s Get:1 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (dsc) [1984 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (tar) [1748 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble/universe optimir 1.2-1 (diff) [3476 B] 139s gpgv: Signature made Fri Mar 18 14:54:34 2022 UTC 139s gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 139s gpgv: issuer "daissi@debian.org" 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./optimir_1.2-1.dsc: no acceptable signature found 139s autopkgtest [04:31:21]: testing package optimir version 1.2-1 139s autopkgtest [04:31:21]: build not needed 140s autopkgtest [04:31:22]: test run-unit-test: preparing testbed 145s Reading package lists... 145s Building dependency tree... 145s Reading state information... 145s Starting pkgProblemResolver with broken count: 1 145s Starting 2 pkgProblemResolver with broken count: 1 145s Investigating (0) optimir:s390x < none -> 1.2-1 @un puN Ib > 145s Broken optimir:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 145s Considering python3-biopython:s390x 1 as a solution to optimir:s390x 0 145s Re-Instated libblas3:s390x 145s Re-Instated libgfortran5:s390x 145s Re-Instated liblapack3:s390x 145s Re-Instated python3-numpy:s390x 145s Re-Instated libfreetype6:s390x 145s Re-Instated libgomp1:s390x 145s Re-Instated libimagequant0:s390x 145s Re-Instated libjpeg-turbo8:s390x 145s Re-Instated libjpeg8:s390x 145s Re-Instated liblcms2-2:s390x 145s Re-Instated libopenjp2-7:s390x 145s Re-Instated libgraphite2-3:s390x 145s Re-Instated libharfbuzz0b:s390x 145s Re-Instated libraqm0:s390x 145s Re-Instated libdeflate0:s390x 145s Re-Instated libjbig0:s390x 145s Re-Instated libsharpyuv0:s390x 145s Re-Instated libwebp7:s390x 145s Re-Instated libtiff6:s390x 145s Re-Instated libwebpdemux2:s390x 145s Re-Instated libwebpmux3:s390x 145s Re-Instated python3-pil:s390x 145s Re-Instated fonts-dejavu-mono:s390x 145s Re-Instated fonts-dejavu-core:s390x 145s Re-Instated fontconfig-config:s390x 145s Re-Instated libfontconfig1:s390x 145s Re-Instated libpixman-1-0:s390x 145s Re-Instated libxcb-render0:s390x 145s Re-Instated libxcb-shm0:s390x 145s Re-Instated libxrender1:s390x 145s Re-Instated libcairo2:s390x 145s Re-Instated python3-cairo:s390x 145s Re-Instated python3-freetype:s390x 145s Re-Instated python3-rlpycairo:s390x 145s Re-Instated fonts-dejavu-extra:s390x 145s Re-Instated libfontenc1:s390x 145s Re-Instated x11-common:s390x 145s Re-Instated xfonts-encodings:s390x 145s Re-Instated xfonts-utils:s390x 145s Re-Instated fonts-urw-base35:s390x 145s Re-Instated python3-reportlab:s390x 145s Re-Instated sgml-base:s390x 145s Re-Instated xml-core:s390x 145s Re-Instated w3c-sgml-lib:s390x 145s Re-Instated python3-biopython:s390x 145s Broken optimir:s390x Depends on python3-pysam:s390x < none @un H > 145s Broken optimir:s390x Depends on bowtie2:s390x < none @un H > 145s Broken optimir:s390x Depends on cutadapt:s390x < none | 4.4-1build1 @un uH > 145s Considering cutadapt:s390x 1 as a solution to optimir:s390x 0 145s Re-Instated pigz:s390x 145s Re-Instated python3-xopen:s390x 145s Re-Instated python3-dnaio:s390x 145s Re-Instated python3-cutadapt:s390x 145s Re-Instated cutadapt:s390x 145s Broken optimir:s390x Depends on samtools:s390x < none | 1.19.2-1 @un uH > 145s Considering samtools:s390x 1 as a solution to optimir:s390x 0 145s Re-Instated libhtscodecs2:s390x 145s Re-Instated libhts3:s390x 145s Re-Instated samtools:s390x 145s Done 145s Some packages could not be installed. This may mean that you have 145s requested an impossible situation or if you are using the unstable 145s distribution that some required packages have not yet been created 145s or been moved out of Incoming. 145s The following information may help to resolve the situation: 145s 145s The following packages have unmet dependencies: 145s optimir : Depends: python3-pysam but it is not installable 145s Depends: bowtie2 but it is not installable 145s E: Unable to correct problems, you have held broken packages. 145s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Starting pkgProblemResolver with broken count: 1 146s Starting 2 pkgProblemResolver with broken count: 1 146s Investigating (0) optimir:s390x < none -> 1.2-1 @un puN Ib > 146s Broken optimir:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 146s Considering python3-biopython:s390x 1 as a solution to optimir:s390x 0 146s Re-Instated libblas3:s390x 146s Re-Instated libgfortran5:s390x 146s Re-Instated liblapack3:s390x 146s Re-Instated python3-numpy:s390x 146s Re-Instated libfreetype6:s390x 146s Re-Instated libgomp1:s390x 146s Re-Instated libimagequant0:s390x 146s Re-Instated libjpeg-turbo8:s390x 146s Re-Instated libjpeg8:s390x 146s Re-Instated liblcms2-2:s390x 146s Re-Instated libopenjp2-7:s390x 146s Re-Instated libgraphite2-3:s390x 146s Re-Instated libharfbuzz0b:s390x 146s Re-Instated libraqm0:s390x 146s Re-Instated libdeflate0:s390x 146s Re-Instated libjbig0:s390x 146s Re-Instated libsharpyuv0:s390x 146s Re-Instated libwebp7:s390x 146s Re-Instated libtiff6:s390x 146s Re-Instated libwebpdemux2:s390x 146s Re-Instated libwebpmux3:s390x 146s Re-Instated python3-pil:s390x 146s Re-Instated fonts-dejavu-mono:s390x 146s Re-Instated fonts-dejavu-core:s390x 146s Re-Instated fontconfig-config:s390x 146s Re-Instated libfontconfig1:s390x 146s Re-Instated libpixman-1-0:s390x 146s Re-Instated libxcb-render0:s390x 146s Re-Instated libxcb-shm0:s390x 146s Re-Instated libxrender1:s390x 146s Re-Instated libcairo2:s390x 146s Re-Instated python3-cairo:s390x 146s Re-Instated python3-freetype:s390x 146s Re-Instated python3-rlpycairo:s390x 146s Re-Instated fonts-dejavu-extra:s390x 146s Re-Instated libfontenc1:s390x 146s Re-Instated x11-common:s390x 146s Re-Instated xfonts-encodings:s390x 146s Re-Instated xfonts-utils:s390x 146s Re-Instated fonts-urw-base35:s390x 146s Re-Instated python3-reportlab:s390x 146s Re-Instated sgml-base:s390x 146s Re-Instated xml-core:s390x 146s Re-Instated w3c-sgml-lib:s390x 146s Re-Instated python3-biopython:s390x 146s Broken optimir:s390x Depends on python3-pysam:s390x < none @un H > 146s Broken optimir:s390x Depends on bowtie2:s390x < none @un H > 146s Broken optimir:s390x Depends on cutadapt:s390x < none | 4.4-1build1 @un uH > 146s Considering cutadapt:s390x 1 as a solution to optimir:s390x 0 146s Re-Instated pigz:s390x 146s Re-Instated python3-xopen:s390x 146s Re-Instated python3-dnaio:s390x 146s Re-Instated python3-cutadapt:s390x 146s Re-Instated cutadapt:s390x 146s Broken optimir:s390x Depends on samtools:s390x < none | 1.19.2-1 @un uH > 146s Considering samtools:s390x 1 as a solution to optimir:s390x 0 146s Re-Instated libhtscodecs2:s390x 146s Re-Instated libhts3:s390x 146s Re-Instated samtools:s390x 146s Done 146s Some packages could not be installed. This may mean that you have 146s requested an impossible situation or if you are using the unstable 146s distribution that some required packages have not yet been created 146s or been moved out of Incoming. 146s The following information may help to resolve the situation: 146s 146s The following packages have unmet dependencies: 146s optimir : Depends: python3-pysam but it is not installable 146s Depends: bowtie2 but it is not installable 146s E: Unable to correct problems, you have held broken packages. 146s autopkgtest: WARNING: Test dependencies are unsatisfiable - calling apt install on test deps directly for further data about failing dependencies in test logs 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Starting pkgProblemResolver with broken count: 1 147s Starting 2 pkgProblemResolver with broken count: 1 147s Investigating (0) optimir:s390x < none -> 1.2-1 @un puN Ib > 147s Broken optimir:s390x Depends on python3-biopython:s390x < none | 1.81+dfsg-3 @un uH > 147s Considering python3-biopython:s390x 1 as a solution to optimir:s390x 9999 147s Re-Instated libblas3:s390x 147s Re-Instated libgfortran5:s390x 147s Re-Instated liblapack3:s390x 147s Re-Instated python3-numpy:s390x 147s Re-Instated libfreetype6:s390x 147s Re-Instated libgomp1:s390x 147s Re-Instated libimagequant0:s390x 147s Re-Instated libjpeg-turbo8:s390x 147s Re-Instated libjpeg8:s390x 147s Re-Instated liblcms2-2:s390x 147s Re-Instated libopenjp2-7:s390x 147s Re-Instated libgraphite2-3:s390x 147s Re-Instated libharfbuzz0b:s390x 147s Re-Instated libraqm0:s390x 147s Re-Instated libdeflate0:s390x 147s Re-Instated libjbig0:s390x 147s Re-Instated libsharpyuv0:s390x 147s Re-Instated libwebp7:s390x 147s Re-Instated libtiff6:s390x 147s Re-Instated libwebpdemux2:s390x 147s Re-Instated libwebpmux3:s390x 147s Re-Instated python3-pil:s390x 147s Re-Instated fonts-dejavu-mono:s390x 147s Re-Instated fonts-dejavu-core:s390x 147s Re-Instated fontconfig-config:s390x 147s Re-Instated libfontconfig1:s390x 147s Re-Instated libpixman-1-0:s390x 147s Re-Instated libxcb-render0:s390x 147s Re-Instated libxcb-shm0:s390x 147s Re-Instated libxrender1:s390x 147s Re-Instated libcairo2:s390x 147s Re-Instated python3-cairo:s390x 147s Re-Instated python3-freetype:s390x 147s Re-Instated python3-rlpycairo:s390x 147s Re-Instated fonts-dejavu-extra:s390x 147s Re-Instated libfontenc1:s390x 147s Re-Instated x11-common:s390x 147s Re-Instated xfonts-encodings:s390x 147s Re-Instated xfonts-utils:s390x 147s Re-Instated fonts-urw-base35:s390x 147s Re-Instated python3-reportlab:s390x 147s Re-Instated sgml-base:s390x 147s Re-Instated xml-core:s390x 147s Re-Instated w3c-sgml-lib:s390x 147s Re-Instated python3-biopython:s390x 147s Broken optimir:s390x Depends on python3-pysam:s390x < none @un H > 147s Broken optimir:s390x Depends on bowtie2:s390x < none @un H > 147s Broken optimir:s390x Depends on cutadapt:s390x < none | 4.4-1build1 @un uH > 147s Considering cutadapt:s390x 1 as a solution to optimir:s390x 9999 147s Re-Instated pigz:s390x 147s Re-Instated python3-xopen:s390x 147s Re-Instated python3-dnaio:s390x 147s Re-Instated python3-cutadapt:s390x 147s Re-Instated cutadapt:s390x 147s Broken optimir:s390x Depends on samtools:s390x < none | 1.19.2-1 @un uH > 147s Considering samtools:s390x 1 as a solution to optimir:s390x 9999 147s Re-Instated libhtscodecs2:s390x 147s Re-Instated libhts3:s390x 147s Re-Instated samtools:s390x 147s Done 147s Some packages could not be installed. This may mean that you have 147s requested an impossible situation or if you are using the unstable 147s distribution that some required packages have not yet been created 147s or been moved out of Incoming. 147s The following information may help to resolve the situation: 147s 147s The following packages have unmet dependencies: 147s optimir : Depends: python3-pysam but it is not installable 147s Depends: bowtie2 but it is not installable 147s E: Unable to correct problems, you have held broken packages. 147s run-unit-test FAIL badpkg 147s blame: optimir 147s 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. 147s autopkgtest [04:31:29]: @@@@@@@@@@@@@@@@@@@@ summary 147s run-unit-test FAIL badpkg 147s blame: optimir 147s 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. 158s Creating nova instance adt-noble-s390x-optimir-20240323-042902-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...