0s autopkgtest [17:00:04]: starting date and time: 2024-03-16 17:00:04+0000 0s autopkgtest [17:00:04]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [17:00:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zm9i5s4c/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:hdf5,src:curl,src:libpsl,src:mpich,src:openmpi,src:openssl,src:orthanc-python,src:pmix --apt-upgrade kineticstools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=hdf5/1.10.10+repack-3.1ubuntu3 curl/8.5.0-2ubuntu7 libpsl/0.21.2-1.1 mpich/4.2.0-5build1 openmpi/4.1.6-6ubuntu1 openssl/3.0.13-0ubuntu1 orthanc-python/4.1+ds-2build3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-21.secgroup --name adt-noble-arm64-kineticstools-20240316-170004-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-arm64-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/ 96s autopkgtest [17:01:40]: testbed dpkg architecture: arm64 96s autopkgtest [17:01:40]: testbed apt version: 2.7.12 96s autopkgtest [17:01:40]: @@@@@@@@@@@@@@@@@@@@ test bed setup 97s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 97s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [474 kB] 97s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3673 kB] 98s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [51.4 kB] 98s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 98s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [646 kB] 98s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 98s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.6 kB] 98s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 98s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [3994 kB] 98s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 98s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [55.6 kB] 98s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 100s Fetched 9063 kB in 2s (4391 kB/s) 100s Reading package lists... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Calculating upgrade... 104s The following packages will be REMOVED: 104s libssl3 104s The following NEW packages will be installed: 104s libssl3t64 104s The following packages have been kept back: 104s curl 104s The following packages will be upgraded: 104s openssl ubuntu-minimal ubuntu-standard 105s 3 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 105s Need to get 2775 kB of archives. 105s After this operation, 72.7 kB of additional disk space will be used. 105s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu1 [983 kB] 105s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu1 [1770 kB] 105s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-minimal arm64 1.536 [10.7 kB] 105s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-standard arm64 1.536 [10.7 kB] 106s Fetched 2775 kB in 1s (3778 kB/s) 106s (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 ... 74758 files and directories currently installed.) 106s Preparing to unpack .../openssl_3.0.13-0ubuntu1_arm64.deb ... 106s Unpacking openssl (3.0.13-0ubuntu1) over (3.0.10-1ubuntu4) ... 106s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 106s wget depends on libssl3 (>= 3.0.0). 106s u-boot-tools depends on libssl3 (>= 3.0.0). 106s tnftp depends on libssl3 (>= 3.0.0). 106s tcpdump depends on libssl3 (>= 3.0.0). 106s systemd-resolved depends on libssl3 (>= 3.0.0). 106s systemd depends on libssl3 (>= 3.0.0). 106s sudo depends on libssl3 (>= 3.0.0). 106s sbsigntool depends on libssl3 (>= 3.0.0). 106s rsync depends on libssl3 (>= 3.0.0). 106s python3-cryptography depends on libssl3 (>= 3.0.0). 106s openssh-server depends on libssl3 (>= 3.0.10). 106s openssh-client depends on libssl3 (>= 3.0.10). 106s mtd-utils depends on libssl3 (>= 3.0.0). 106s mokutil depends on libssl3 (>= 3.0.0). 106s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 106s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 106s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 106s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 106s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 106s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 106s libnvme1 depends on libssl3 (>= 3.0.0). 106s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 106s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 106s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 106s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 106s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 106s kmod depends on libssl3 (>= 3.0.0). 106s dhcpcd-base depends on libssl3 (>= 3.0.0). 106s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 106s 106s (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 ... 74758 files and directories currently installed.) 106s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 106s Selecting previously unselected package libssl3t64:arm64. 106s (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 ... 74747 files and directories currently installed.) 106s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu1_arm64.deb ... 106s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu1) ... 106s Preparing to unpack .../ubuntu-minimal_1.536_arm64.deb ... 106s Unpacking ubuntu-minimal (1.536) over (1.535) ... 106s Preparing to unpack .../ubuntu-standard_1.536_arm64.deb ... 106s Unpacking ubuntu-standard (1.536) over (1.535) ... 106s Setting up ubuntu-minimal (1.536) ... 106s Setting up libssl3t64:arm64 (3.0.13-0ubuntu1) ... 106s Setting up ubuntu-standard (1.536) ... 106s Setting up openssl (3.0.13-0ubuntu1) ... 106s Processing triggers for man-db (2.12.0-3) ... 107s Processing triggers for libc-bin (2.39-0ubuntu2) ... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 110s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 118s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 118s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 118s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 118s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease 120s Reading package lists... 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade... 122s The following packages have been kept back: 122s curl 122s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 126s autopkgtest [17:02:10]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 127s autopkgtest [17:02:11]: @@@@@@@@@@@@@@@@@@@@ apt-source kineticstools 132s Get:1 http://ftpmaster.internal/ubuntu noble/universe kineticstools 0.6.1+git20220223.1326a4d+dfsg-2build2 (dsc) [2730 B] 132s Get:2 http://ftpmaster.internal/ubuntu noble/universe kineticstools 0.6.1+git20220223.1326a4d+dfsg-2build2 (tar) [21.8 MB] 132s Get:3 http://ftpmaster.internal/ubuntu noble/universe kineticstools 0.6.1+git20220223.1326a4d+dfsg-2build2 (diff) [10.4 kB] 132s gpgv: Signature made Fri Jan 19 19:47:07 2024 UTC 132s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./kineticstools_0.6.1+git20220223.1326a4d+dfsg-2build2.dsc: no acceptable signature found 133s autopkgtest [17:02:17]: testing package kineticstools version 0.6.1+git20220223.1326a4d+dfsg-2build2 134s autopkgtest [17:02:18]: build not needed 135s autopkgtest [17:02:19]: test command1: preparing testbed 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 138s Starting 2 pkgProblemResolver with broken count: 0 138s Done 139s The following additional packages will be installed: 139s curl fontconfig-config fonts-dejavu-core fonts-dejavu-extra 139s fonts-dejavu-mono fonts-urw-base35 hdf5-tools kineticstools 139s kineticstools-data libaec0 libbigwig0 libblas3 libcairo2 libcurl4t64 139s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 139s libharfbuzz0b libhdf5-103-1t64 libhts3 libhtscodecs2 libimagequant0 libjbig0 139s libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 139s libopenjp2-7 libpixman-1-0 libpsl5t64 libpython3.11 libpython3.11-minimal 139s libpython3.11-stdlib libpython3.12 libraqm0 libsharpyuv0 libsz2 libtiff6 139s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 139s python3-avro python3-biopython python3-cairo python3-cram python3-decorator 139s python3-freetype python3-iniconfig python3-iso8601 python3-kineticstools 139s python3-numpy python3-packaging python3-pbcommand python3-pbcore python3-pil 139s python3-pluggy python3-pybigwig python3-pysam python3-pytest 139s python3-reportlab python3-rlpycairo python3-scipy python3.11 139s python3.11-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 139s xfonts-utils xml-core 139s Suggested packages: 139s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 139s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 139s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 139s python3-rdflib python3-psycopg2 raxml samtools t-coffee wise gcc gfortran 139s python3-dev python-pbcore-doc python-pil-doc pdf-viewer 139s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 139s python-scipy-doc python3.11-venv python3.11-doc binfmt-support sgml-base-doc 139s debhelper 139s Recommended packages: 139s python-biopython-doc ncbi-blast+ python3-h5py python3-olefile g++ 139s | c++-compiler 139s The following packages will be REMOVED: 139s libcurl4 libpsl5 139s The following NEW packages will be installed: 139s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra 139s fonts-dejavu-mono fonts-urw-base35 hdf5-tools kineticstools 139s kineticstools-data libaec0 libbigwig0 libblas3 libcairo2 libcurl4t64 139s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 139s libharfbuzz0b libhdf5-103-1t64 libhts3 libhtscodecs2 libimagequant0 libjbig0 139s libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 139s libopenjp2-7 libpixman-1-0 libpsl5t64 libpython3.11 libpython3.11-minimal 139s libpython3.11-stdlib libpython3.12 libraqm0 libsharpyuv0 libsz2 libtiff6 139s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 139s python3-avro python3-biopython python3-cairo python3-cram python3-decorator 139s python3-freetype python3-iniconfig python3-iso8601 python3-kineticstools 139s python3-numpy python3-packaging python3-pbcommand python3-pbcore python3-pil 139s python3-pluggy python3-pybigwig python3-pysam python3-pytest 139s python3-reportlab python3-rlpycairo python3-scipy python3.11 139s python3.11-minimal sgml-base w3c-sgml-lib x11-common xfonts-encodings 139s xfonts-utils xml-core 139s The following packages will be upgraded: 139s curl 139s 1 upgraded, 78 newly installed, 2 to remove and 0 not upgraded. 139s Need to get 89.4 MB/89.4 MB of archives. 139s After this operation, 309 MB of additional disk space will be used. 139s Get:1 /tmp/autopkgtest.7WAqoS/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [748 B] 139s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1 [57.4 kB] 139s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 curl arm64 8.5.0-2ubuntu7 [222 kB] 139s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl4t64 arm64 8.5.0-2ubuntu7 [332 kB] 139s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 140s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 140s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 140s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 140s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 140s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 140s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 140s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 140s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 140s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 140s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 140s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 140s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 140s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 140s Get:19 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 140s Get:20 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 140s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu3 [1192 kB] 140s Get:22 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 hdf5-tools arm64 1.10.10+repack-3.1ubuntu3 [315 kB] 140s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 140s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 140s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 140s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 140s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 python3-iso8601 all 1.0.2-1 [15.8 kB] 140s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-avro all 1.11.1+dfsg-2 [71.6 kB] 140s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbcommand all 2.1.1+git20220616.3f2e6c2-2 [91.4 kB] 140s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 140s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 140s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 140s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 140s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 140s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 140s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 140s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 140s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 140s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 140s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 140s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 140s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 140s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 140s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 140s Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 140s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 140s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 140s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 140s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 140s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 140s Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 140s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 140s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 140s Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 140s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 140s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 140s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 141s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 141s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 141s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 141s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 141s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 141s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 141s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pbcore all 2.1.2+dfsg-5 [2836 kB] 141s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 libbigwig0 arm64 0.4.7+dfsg-3 [29.1 kB] 141s Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11 arm64 3.11.8-1 [2164 kB] 141s Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12 arm64 3.12.2-1 [2291 kB] 141s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybigwig arm64 0.3.22+dfsg-1build1 [53.2 kB] 141s Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 141s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 141s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 142s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 kineticstools-data all 0.6.1+git20220223.1326a4d+dfsg-2build2 [21.7 MB] 142s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kineticstools arm64 0.6.1+git20220223.1326a4d+dfsg-2build2 [47.0 kB] 142s Get:74 http://ftpmaster.internal/ubuntu noble/universe arm64 kineticstools all 0.6.1+git20220223.1326a4d+dfsg-2build2 [12.9 kB] 142s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cram all 0.7-5 [17.9 kB] 142s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 142s Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 142s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 142s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 144s Fetched 89.4 MB in 3s (27.3 MB/s) 144s dpkg: libpsl5:arm64: dependency problems, but removing anyway as you requested: 144s wget depends on libpsl5 (>= 0.16.0). 144s libcurl4:arm64 depends on libpsl5 (>= 0.16.0). 144s libcurl3-gnutls:arm64 depends on libpsl5 (>= 0.16.0). 144s 144s (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 ... 74760 files and directories currently installed.) 144s Removing libpsl5:arm64 (0.21.2-1build1) ... 144s Selecting previously unselected package libpsl5t64:arm64. 144s (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 ... 74755 files and directories currently installed.) 144s Preparing to unpack .../libpsl5t64_0.21.2-1.1_arm64.deb ... 144s Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... 144s Preparing to unpack .../curl_8.5.0-2ubuntu7_arm64.deb ... 144s Unpacking curl (8.5.0-2ubuntu7) over (8.5.0-2ubuntu2) ... 144s (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 ... 74761 files and directories currently installed.) 144s Removing libcurl4:arm64 (8.5.0-2ubuntu2) ... 145s Selecting previously unselected package libcurl4t64:arm64. 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 ... 74756 files and directories currently installed.) 145s Preparing to unpack .../00-libcurl4t64_8.5.0-2ubuntu7_arm64.deb ... 145s Unpacking libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 145s Selecting previously unselected package libpython3.11-minimal:arm64. 145s Preparing to unpack .../01-libpython3.11-minimal_3.11.8-1_arm64.deb ... 145s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 145s Selecting previously unselected package python3.11-minimal. 145s Preparing to unpack .../02-python3.11-minimal_3.11.8-1_arm64.deb ... 145s Unpacking python3.11-minimal (3.11.8-1) ... 145s Selecting previously unselected package sgml-base. 145s Preparing to unpack .../03-sgml-base_1.31_all.deb ... 145s Unpacking sgml-base (1.31) ... 145s Selecting previously unselected package libpython3.11-stdlib:arm64. 145s Preparing to unpack .../04-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 145s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 145s Selecting previously unselected package python3.11. 145s Preparing to unpack .../05-python3.11_3.11.8-1_arm64.deb ... 145s Unpacking python3.11 (3.11.8-1) ... 145s Selecting previously unselected package fonts-dejavu-mono. 145s Preparing to unpack .../06-fonts-dejavu-mono_2.37-8_all.deb ... 145s Unpacking fonts-dejavu-mono (2.37-8) ... 145s Selecting previously unselected package fonts-dejavu-core. 146s Preparing to unpack .../07-fonts-dejavu-core_2.37-8_all.deb ... 146s Unpacking fonts-dejavu-core (2.37-8) ... 146s Selecting previously unselected package libfontenc1:arm64. 146s Preparing to unpack .../08-libfontenc1_1%3a1.1.8-1_arm64.deb ... 146s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 146s Selecting previously unselected package x11-common. 146s Preparing to unpack .../09-x11-common_1%3a7.7+23ubuntu2_all.deb ... 146s Unpacking x11-common (1:7.7+23ubuntu2) ... 146s Selecting previously unselected package xfonts-encodings. 146s Preparing to unpack .../10-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 146s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 146s Selecting previously unselected package xfonts-utils. 146s Preparing to unpack .../11-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 146s Unpacking xfonts-utils (1:7.7+6build2) ... 146s Selecting previously unselected package fonts-urw-base35. 146s Preparing to unpack .../12-fonts-urw-base35_20200910-8_all.deb ... 146s Unpacking fonts-urw-base35 (20200910-8) ... 146s Selecting previously unselected package fontconfig-config. 146s Preparing to unpack .../13-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 146s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 146s Selecting previously unselected package fonts-dejavu-extra. 146s Preparing to unpack .../14-fonts-dejavu-extra_2.37-8_all.deb ... 146s Unpacking fonts-dejavu-extra (2.37-8) ... 146s Selecting previously unselected package libaec0:arm64. 146s Preparing to unpack .../15-libaec0_1.1.2-1_arm64.deb ... 146s Unpacking libaec0:arm64 (1.1.2-1) ... 147s Selecting previously unselected package libsz2:arm64. 147s Preparing to unpack .../16-libsz2_1.1.2-1_arm64.deb ... 147s Unpacking libsz2:arm64 (1.1.2-1) ... 147s Selecting previously unselected package libhdf5-103-1t64:arm64. 147s Preparing to unpack .../17-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu3_arm64.deb ... 147s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu3) ... 147s Selecting previously unselected package hdf5-tools. 147s Preparing to unpack .../18-hdf5-tools_1.10.10+repack-3.1ubuntu3_arm64.deb ... 147s Unpacking hdf5-tools (1.10.10+repack-3.1ubuntu3) ... 147s Selecting previously unselected package libblas3:arm64. 147s Preparing to unpack .../19-libblas3_3.12.0-3_arm64.deb ... 147s Unpacking libblas3:arm64 (3.12.0-3) ... 147s Selecting previously unselected package libgfortran5:arm64. 147s Preparing to unpack .../20-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 147s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 147s Selecting previously unselected package liblapack3:arm64. 147s Preparing to unpack .../21-liblapack3_3.12.0-3_arm64.deb ... 147s Unpacking liblapack3:arm64 (3.12.0-3) ... 147s Selecting previously unselected package python3-numpy. 147s Preparing to unpack .../22-python3-numpy_1%3a1.24.2-2_arm64.deb ... 147s Unpacking python3-numpy (1:1.24.2-2) ... 147s Selecting previously unselected package python3-iso8601. 147s Preparing to unpack .../23-python3-iso8601_1.0.2-1_all.deb ... 147s Unpacking python3-iso8601 (1.0.2-1) ... 147s Selecting previously unselected package python3-avro. 147s Preparing to unpack .../24-python3-avro_1.11.1+dfsg-2_all.deb ... 147s Unpacking python3-avro (1.11.1+dfsg-2) ... 147s Selecting previously unselected package python3-pbcommand. 147s Preparing to unpack .../25-python3-pbcommand_2.1.1+git20220616.3f2e6c2-2_all.deb ... 147s Unpacking python3-pbcommand (2.1.1+git20220616.3f2e6c2-2) ... 147s Selecting previously unselected package libgomp1:arm64. 147s Preparing to unpack .../26-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 147s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 147s Selecting previously unselected package libimagequant0:arm64. 147s Preparing to unpack .../27-libimagequant0_2.18.0-1_arm64.deb ... 147s Unpacking libimagequant0:arm64 (2.18.0-1) ... 147s Selecting previously unselected package libjpeg-turbo8:arm64. 147s Preparing to unpack .../28-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 147s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 147s Selecting previously unselected package libjpeg8:arm64. 147s Preparing to unpack .../29-libjpeg8_8c-2ubuntu11_arm64.deb ... 147s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 147s Selecting previously unselected package liblcms2-2:arm64. 147s Preparing to unpack .../30-liblcms2-2_2.14-2_arm64.deb ... 147s Unpacking liblcms2-2:arm64 (2.14-2) ... 147s Selecting previously unselected package libopenjp2-7:arm64. 148s Preparing to unpack .../31-libopenjp2-7_2.5.0-2_arm64.deb ... 148s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 148s Selecting previously unselected package libgraphite2-3:arm64. 148s Preparing to unpack .../32-libgraphite2-3_1.3.14-2_arm64.deb ... 148s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 148s Selecting previously unselected package libharfbuzz0b:arm64. 148s Preparing to unpack .../33-libharfbuzz0b_8.3.0-2_arm64.deb ... 148s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 148s Selecting previously unselected package libraqm0:arm64. 148s Preparing to unpack .../34-libraqm0_0.10.1-1_arm64.deb ... 148s Unpacking libraqm0:arm64 (0.10.1-1) ... 148s Selecting previously unselected package libdeflate0:arm64. 148s Preparing to unpack .../35-libdeflate0_1.19-1_arm64.deb ... 148s Unpacking libdeflate0:arm64 (1.19-1) ... 148s Selecting previously unselected package libjbig0:arm64. 148s Preparing to unpack .../36-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 148s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 148s Selecting previously unselected package liblerc4:arm64. 148s Preparing to unpack .../37-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 148s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 148s Selecting previously unselected package libsharpyuv0:arm64. 148s Preparing to unpack .../38-libsharpyuv0_1.3.2-0.4_arm64.deb ... 148s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 148s Selecting previously unselected package libwebp7:arm64. 148s Preparing to unpack .../39-libwebp7_1.3.2-0.4_arm64.deb ... 148s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 148s Selecting previously unselected package libtiff6:arm64. 148s Preparing to unpack .../40-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 148s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 148s Selecting previously unselected package libwebpdemux2:arm64. 148s Preparing to unpack .../41-libwebpdemux2_1.3.2-0.4_arm64.deb ... 148s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 149s Selecting previously unselected package libwebpmux3:arm64. 149s Preparing to unpack .../42-libwebpmux3_1.3.2-0.4_arm64.deb ... 149s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 149s Selecting previously unselected package python3-pil:arm64. 149s Preparing to unpack .../43-python3-pil_10.2.0-1_arm64.deb ... 149s Unpacking python3-pil:arm64 (10.2.0-1) ... 149s Selecting previously unselected package libfontconfig1:arm64. 149s Preparing to unpack .../44-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 149s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 149s Selecting previously unselected package libpixman-1-0:arm64. 149s Preparing to unpack .../45-libpixman-1-0_0.42.2-1_arm64.deb ... 149s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 149s Selecting previously unselected package libxcb-render0:arm64. 149s Preparing to unpack .../46-libxcb-render0_1.15-1_arm64.deb ... 149s Unpacking libxcb-render0:arm64 (1.15-1) ... 149s Selecting previously unselected package libxcb-shm0:arm64. 149s Preparing to unpack .../47-libxcb-shm0_1.15-1_arm64.deb ... 149s Unpacking libxcb-shm0:arm64 (1.15-1) ... 149s Selecting previously unselected package libxrender1:arm64. 149s Preparing to unpack .../48-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 149s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 149s Selecting previously unselected package libcairo2:arm64. 149s Preparing to unpack .../49-libcairo2_1.18.0-1_arm64.deb ... 149s Unpacking libcairo2:arm64 (1.18.0-1) ... 149s Selecting previously unselected package python3-cairo. 149s Preparing to unpack .../50-python3-cairo_1.25.1-2_arm64.deb ... 149s Unpacking python3-cairo (1.25.1-2) ... 149s Selecting previously unselected package python3-freetype. 150s Preparing to unpack .../51-python3-freetype_2.4.0-1_all.deb ... 150s Unpacking python3-freetype (2.4.0-1) ... 150s Selecting previously unselected package python3-rlpycairo. 150s Preparing to unpack .../52-python3-rlpycairo_0.3.0-3_all.deb ... 150s Unpacking python3-rlpycairo (0.3.0-3) ... 150s Selecting previously unselected package python3-reportlab. 150s Preparing to unpack .../53-python3-reportlab_4.1.0-1_all.deb ... 150s Unpacking python3-reportlab (4.1.0-1) ... 150s Selecting previously unselected package xml-core. 150s Preparing to unpack .../54-xml-core_0.19_all.deb ... 150s Unpacking xml-core (0.19) ... 150s Selecting previously unselected package w3c-sgml-lib. 150s Preparing to unpack .../55-w3c-sgml-lib_1.3-3_all.deb ... 150s Unpacking w3c-sgml-lib (1.3-3) ... 151s Selecting previously unselected package python3-biopython. 151s Preparing to unpack .../56-python3-biopython_1.81+dfsg-3_arm64.deb ... 151s Unpacking python3-biopython (1.81+dfsg-3) ... 151s Selecting previously unselected package libhtscodecs2:arm64. 151s Preparing to unpack .../57-libhtscodecs2_1.6.0-1_arm64.deb ... 151s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 151s Selecting previously unselected package libhts3:arm64. 152s Preparing to unpack .../58-libhts3_1.18+ds-1_arm64.deb ... 152s Unpacking libhts3:arm64 (1.18+ds-1) ... 152s Selecting previously unselected package python3-pysam. 152s Preparing to unpack .../59-python3-pysam_0.22.0+ds-1_arm64.deb ... 152s Unpacking python3-pysam (0.22.0+ds-1) ... 152s Selecting previously unselected package python3-pbcore. 153s Preparing to unpack .../60-python3-pbcore_2.1.2+dfsg-5_all.deb ... 153s Unpacking python3-pbcore (2.1.2+dfsg-5) ... 153s Selecting previously unselected package libbigwig0:arm64. 153s Preparing to unpack .../61-libbigwig0_0.4.7+dfsg-3_arm64.deb ... 153s Unpacking libbigwig0:arm64 (0.4.7+dfsg-3) ... 153s Selecting previously unselected package libpython3.11:arm64. 153s Preparing to unpack .../62-libpython3.11_3.11.8-1_arm64.deb ... 153s Unpacking libpython3.11:arm64 (3.11.8-1) ... 153s Selecting previously unselected package libpython3.12:arm64. 153s Preparing to unpack .../63-libpython3.12_3.12.2-1_arm64.deb ... 153s Unpacking libpython3.12:arm64 (3.12.2-1) ... 154s Selecting previously unselected package python3-pybigwig. 154s Preparing to unpack .../64-python3-pybigwig_0.3.22+dfsg-1build1_arm64.deb ... 154s Unpacking python3-pybigwig (0.3.22+dfsg-1build1) ... 155s Selecting previously unselected package python3-decorator. 155s Preparing to unpack .../65-python3-decorator_5.1.1-5_all.deb ... 155s Unpacking python3-decorator (5.1.1-5) ... 155s Selecting previously unselected package liblbfgsb0:arm64. 157s Preparing to unpack .../66-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 157s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 157s Selecting previously unselected package python3-scipy. 158s Preparing to unpack .../67-python3-scipy_1.11.4-6_arm64.deb ... 158s Unpacking python3-scipy (1.11.4-6) ... 160s Selecting previously unselected package kineticstools-data. 160s Preparing to unpack .../68-kineticstools-data_0.6.1+git20220223.1326a4d+dfsg-2build2_all.deb ... 160s Unpacking kineticstools-data (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 160s Selecting previously unselected package python3-kineticstools. 161s Preparing to unpack .../69-python3-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2build2_arm64.deb ... 161s Unpacking python3-kineticstools (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 161s Selecting previously unselected package kineticstools. 161s Preparing to unpack .../70-kineticstools_0.6.1+git20220223.1326a4d+dfsg-2build2_all.deb ... 161s Unpacking kineticstools (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 161s Selecting previously unselected package python3-cram. 161s Preparing to unpack .../71-python3-cram_0.7-5_all.deb ... 161s Unpacking python3-cram (0.7-5) ... 161s Selecting previously unselected package python3-iniconfig. 161s Preparing to unpack .../72-python3-iniconfig_1.1.1-2_all.deb ... 161s Unpacking python3-iniconfig (1.1.1-2) ... 161s Selecting previously unselected package python3-packaging. 161s Preparing to unpack .../73-python3-packaging_23.2-1_all.deb ... 161s Unpacking python3-packaging (23.2-1) ... 161s Selecting previously unselected package python3-pluggy. 161s Preparing to unpack .../74-python3-pluggy_1.4.0-1_all.deb ... 161s Unpacking python3-pluggy (1.4.0-1) ... 161s Selecting previously unselected package python3-pytest. 162s Preparing to unpack .../75-python3-pytest_7.4.4-1_all.deb ... 162s Unpacking python3-pytest (7.4.4-1) ... 162s Selecting previously unselected package autopkgtest-satdep. 162s Preparing to unpack .../76-1-autopkgtest-satdep.deb ... 162s Unpacking autopkgtest-satdep (0) ... 162s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 162s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 162s Setting up liblcms2-2:arm64 (2.14-2) ... 162s Setting up python3-iniconfig (1.1.1-2) ... 163s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 163s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 163s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 163s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 163s Setting up libxcb-render0:arm64 (1.15-1) ... 163s Setting up x11-common (1:7.7+23ubuntu2) ... 164s Setting up libpsl5t64:arm64 (0.21.2-1.1) ... 164s Setting up libdeflate0:arm64 (1.19-1) ... 164s Setting up libxcb-shm0:arm64 (1.15-1) ... 164s Setting up libbigwig0:arm64 (0.4.7+dfsg-3) ... 164s Setting up kineticstools-data (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 164s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 164s Setting up python3-freetype (2.4.0-1) ... 164s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 164s Setting up libaec0:arm64 (1.1.2-1) ... 164s Setting up python3-decorator (5.1.1-5) ... 164s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 164s Setting up libblas3:arm64 (3.12.0-3) ... 165s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 165s Setting up python3-packaging (23.2-1) ... 165s Setting up python3-iso8601 (1.0.2-1) ... 165s Setting up python3-avro (1.11.1+dfsg-2) ... 165s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 165s Setting up libimagequant0:arm64 (2.18.0-1) ... 165s Setting up fonts-dejavu-mono (2.37-8) ... 165s Setting up fonts-dejavu-core (2.37-8) ... 165s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 166s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 166s Setting up python3-pluggy (1.4.0-1) ... 166s Setting up libwebp7:arm64 (1.3.2-0.4) ... 166s Setting up fonts-dejavu-extra (2.37-8) ... 166s Setting up python3-cram (0.7-5) ... 166s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 166s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 166s Setting up sgml-base (1.31) ... 166s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 166s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 166s Setting up libpython3.12:arm64 (3.12.2-1) ... 166s Setting up libsz2:arm64 (1.1.2-1) ... 166s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 166s Setting up python3.11-minimal (3.11.8-1) ... 167s Setting up liblapack3:arm64 (3.12.0-3) ... 167s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 167s Setting up libhts3:arm64 (1.18+ds-1) ... 167s Setting up python3-pysam (0.22.0+ds-1) ... 167s Setting up libcurl4t64:arm64 (8.5.0-2ubuntu7) ... 167s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 167s Setting up python3-pytest (7.4.4-1) ... 168s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 168s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 168s Setting up xfonts-utils (1:7.7+6build2) ... 168s Setting up libraqm0:arm64 (0.10.1-1) ... 168s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 168s Setting up xml-core (0.19) ... 168s Setting up curl (8.5.0-2ubuntu7) ... 168s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 168s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu3) ... 168s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 168s Setting up python3.11 (3.11.8-1) ... 169s Setting up libpython3.11:arm64 (3.11.8-1) ... 169s Setting up fonts-urw-base35 (20200910-8) ... 170s Setting up libcairo2:arm64 (1.18.0-1) ... 170s Setting up hdf5-tools (1.10.10+repack-3.1ubuntu3) ... 170s Setting up python3-pil:arm64 (10.2.0-1) ... 170s Setting up python3-numpy (1:1.24.2-2) ... 172s Setting up python3-pybigwig (0.3.22+dfsg-1build1) ... 173s Setting up python3-scipy (1.11.4-6) ... 176s Setting up python3-cairo (1.25.1-2) ... 176s Setting up python3-rlpycairo (0.3.0-3) ... 177s Setting up python3-pbcommand (2.1.1+git20220616.3f2e6c2-2) ... 177s Setting up python3-reportlab (4.1.0-1) ... 178s Processing triggers for libc-bin (2.39-0ubuntu2) ... 179s Processing triggers for systemd (255.2-3ubuntu2) ... 179s Processing triggers for man-db (2.12.0-3) ... 180s Processing triggers for sgml-base (1.31) ... 180s Setting up w3c-sgml-lib (1.3-3) ... 207s Setting up python3-biopython (1.81+dfsg-3) ... 209s Setting up python3-pbcore (2.1.2+dfsg-5) ... 209s Setting up python3-kineticstools (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 209s Setting up kineticstools (0.6.1+git20220223.1326a4d+dfsg-2build2) ... 209s Setting up autopkgtest-satdep (0) ... 216s (Reading database ... 81241 files and directories currently installed.) 216s Removing autopkgtest-satdep (0) ... 217s autopkgtest [17:03:41]: test command1: cp -r Makefile test $AUTOPKGTEST_TMP/ && cd $AUTOPKGTEST_TMP && ln -s /usr/share/kineticstools kineticsTools && make -k py-tests cram-tests 217s autopkgtest [17:03:41]: test command1: [----------------------- 217s # pytest --cov=kineticsTools # does not quite work since we run in test/ dir. 217s cd test/; pytest-3 -s -v -p no:warnings --durations=20 --junitxml=../nosetests.xml test_*.py 217s ============================= test session starts ============================== 217s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 217s cachedir: .pytest_cache 217s rootdir: /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test 218s collecting ... /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_ReferenceUtils.py:17: PytestUnknownMarkWarning: Unknown pytest.mark.internal_data - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.internal_data 218s /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_gather_bigwig.py:50: PytestUnknownMarkWarning: Unknown pytest.mark.pybigwig - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.pybigwig 218s /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_integration.py:29: PytestUnknownMarkWarning: Unknown pytest.mark.internal_data - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.internal_data 218s /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_ipdModel.py:13: PytestUnknownMarkWarning: Unknown pytest.mark.internal_data - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.internal_data 218s /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_outputs.py:21: PytestUnknownMarkWarning: Unknown pytest.mark.internal_data - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.internal_data 218s /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/test/test_summarize_modifications.py:12: PytestUnknownMarkWarning: Unknown pytest.mark.internal_data - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 218s @pytest.mark.internal_data 218s collected 19 items 218s 218s test_ReferenceUtils.py::TestReferenceUtils::test_bam SKIPPED (need a...) 218s test_ReferenceUtils.py::TestReferenceUtils::test_dataset SKIPPED (ne...) 218s test_ReferenceUtils.py::TestReferenceUtils::test_parseReferenceWindow SKIPPED 218s test_ReferenceUtils.py::TestReferenceUtils::test_createReferenceWindows SKIPPED 218s test_ReferenceUtils.py::TestReferenceUtils::test_enumerateChunks SKIPPED 218s test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig PASSED 219s test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli PASSED 224s test_integration.py::TestKineticsTools::test_help PASSED 224s test_integration.py::TestKineticsTools::test_ecoli_first_50k SKIPPED 224s test_ipdModel.py::TestIpdModel::test_refLength SKIPPED (need access ...) 224s test_ipdModel.py::TestIpdModel::test_snippetFunc SKIPPED (need acces...) 224s test_ipdModel.py::TestIpdModel::test_getReferenceWindow SKIPPED (nee...) 224s test_loader.py::test_basic PASSED 224s test_loader.py::test_path PASSED 224s test_loader.py::test_path_with_prefixed_chem PASSED 224s test_loader.py::test_getResourcePathSpec PASSED 224s test_outputs.py::TestOutputs::test_csv_output SKIPPED (need access t...) 224s test_outputs.py::TestOutputs::test_bigwig SKIPPED (missing bw_file, ...) 224s test_summarize_modifications.py::TestSummarizeModifications::test_integration SKIPPED 224s 224s -- generated xml file: /tmp/autopkgtest.7WAqoS/autopkgtest_tmp/nosetests.xml --- 224s ============================= slowest 20 durations ============================= 224s 5.19s call test_integration.py::TestKineticsTools::test_help 224s 0.52s call test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig_cli 224s 0.17s setup test_gather_bigwig.py::TestGatherBigwig::test_gather_bigwig 224s 224s (17 durations < 0.005s hidden. Use -vv to show these durations.) 224s ======================== 7 passed, 12 skipped in 6.94s ========================= 225s cram3 --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v detection_bam` 228s test/cram/version.t: passed 228s # Ran 1 tests, 0 skipped, 0 failed. 229s autopkgtest [17:03:53]: test command1: -----------------------] 229s autopkgtest [17:03:53]: test command1: - - - - - - - - - - results - - - - - - - - - - 229s command1 PASS 230s autopkgtest [17:03:54]: @@@@@@@@@@@@@@@@@@@@ summary 230s command1 PASS 234s Creating nova instance adt-noble-arm64-kineticstools-20240316-170004-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240314.img (UUID 7faf5f09-d335-4346-a441-4eab2f9c04fe)...