0s autopkgtest [17:07:16]: starting date and time: 2024-03-24 17:07:16+0000 0s autopkgtest [17:07:16]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:07:16]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9t_fbpsd/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,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade python-cooler --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python-pysam/0.22.0+ds-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-arm64-19.secgroup --name adt-noble-arm64-python-cooler-20240324-170716-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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/ 318s autopkgtest [17:12:34]: testbed dpkg architecture: arm64 319s autopkgtest [17:12:35]: testbed apt version: 2.7.12 319s autopkgtest [17:12:35]: @@@@@@@@@@@@@@@@@@@@ test bed setup 322s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 324s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 325s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 325s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 327s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 327s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 327s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 327s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 327s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 327s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 328s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 328s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 328s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 353s Fetched 9850 kB in 15s (654 kB/s) 355s Reading package lists... 373s Reading package lists... 375s Building dependency tree... 375s Reading state information... 379s Calculating upgrade... 381s The following packages will be REMOVED: 381s libssl3 381s The following NEW packages will be installed: 381s libssl3t64 381s The following packages have been kept back: 381s curl 381s The following packages will be upgraded: 381s openssl 382s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 382s Need to get 2777 kB of archives. 382s After this operation, 139 kB of additional disk space will be used. 382s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 382s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 387s Fetched 2777 kB in 1s (2207 kB/s) 389s (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 ... 75911 files and directories currently installed.) 389s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 389s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 391s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 391s wget depends on libssl3 (>= 3.0.0). 391s u-boot-tools depends on libssl3 (>= 3.0.0). 391s tnftp depends on libssl3 (>= 3.0.0). 391s tcpdump depends on libssl3 (>= 3.0.0). 391s systemd-resolved depends on libssl3 (>= 3.0.0). 391s systemd depends on libssl3 (>= 3.0.0). 391s sudo depends on libssl3 (>= 3.0.0). 391s sbsigntool depends on libssl3 (>= 3.0.0). 391s rsync depends on libssl3 (>= 3.0.0). 391s python3-cryptography depends on libssl3 (>= 3.0.0). 391s openssh-server depends on libssl3 (>= 3.0.10). 391s openssh-client depends on libssl3 (>= 3.0.10). 391s mtd-utils depends on libssl3 (>= 3.0.0). 391s mokutil depends on libssl3 (>= 3.0.0). 391s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 391s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 391s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 391s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 391s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 391s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 391s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 391s libnvme1 depends on libssl3 (>= 3.0.0). 391s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 391s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 391s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 391s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 391s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 391s kmod depends on libssl3 (>= 3.0.0). 391s dhcpcd-base depends on libssl3 (>= 3.0.0). 391s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 391s 392s (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 ... 75911 files and directories currently installed.) 392s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 392s Selecting previously unselected package libssl3t64:arm64. 392s (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 ... 75900 files and directories currently installed.) 392s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 392s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 393s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 393s Setting up openssl (3.0.13-0ubuntu2) ... 393s Processing triggers for man-db (2.12.0-3) ... 398s Processing triggers for libc-bin (2.39-0ubuntu6) ... 404s Reading package lists... 407s Building dependency tree... 407s Reading state information... 412s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 418s sh: Attempting to set up Debian/Ubuntu apt sources automatically 418s sh: Distribution appears to be Ubuntu 428s Reading package lists... 431s Building dependency tree... 431s Reading state information... 436s eatmydata is already the newest version (131-1). 436s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 436s Reading package lists... 438s Building dependency tree... 438s Reading state information... 443s dbus is already the newest version (1.14.10-4ubuntu1). 443s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 444s Reading package lists... 445s Building dependency tree... 445s Reading state information... 448s rng-tools-debian is already the newest version (2.4). 448s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 448s Reading package lists... 450s Building dependency tree... 450s Reading state information... 454s The following packages will be REMOVED: 454s cloud-init* python3-configobj* python3-debconf* 456s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 456s After this operation, 3256 kB disk space will be freed. 457s (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 ... 75913 files and directories currently installed.) 457s Removing cloud-init (24.1.2-0ubuntu1) ... 461s Removing python3-configobj (5.0.8-3) ... 461s Removing python3-debconf (1.5.86) ... 462s Processing triggers for man-db (2.12.0-3) ... 464s (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 ... 75524 files and directories currently installed.) 464s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 471s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 471s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 471s invoke-rc.d: policy-rc.d denied execution of try-restart. 472s Reading package lists... 473s Building dependency tree... 473s Reading state information... 477s linux-generic is already the newest version (6.8.0-11.11+1). 477s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 479s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 479s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 479s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 507s Reading package lists... 507s Reading package lists... 509s Building dependency tree... 509s Reading state information... 513s Calculating upgrade... 517s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 517s Reading package lists... 519s Building dependency tree... 519s Reading state information... 522s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 524s autopkgtest [17:16:00]: rebooting testbed after setup commands that affected boot 695s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 728s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 745s autopkgtest [17:19:41]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 752s autopkgtest [17:19:48]: @@@@@@@@@@@@@@@@@@@@ apt-source python-cooler 767s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-cooler 0.9.3-1 (dsc) [2825 B] 767s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-cooler 0.9.3-1 (tar) [11.4 MB] 767s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-cooler 0.9.3-1 (diff) [7460 B] 770s gpgv: Signature made Sun Feb 4 19:13:06 2024 UTC 770s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 770s gpgv: issuer "tillea@rki.de" 770s gpgv: Can't check signature: No public key 770s dpkg-source: warning: cannot verify inline signature for ./python-cooler_0.9.3-1.dsc: no acceptable signature found 774s autopkgtest [17:20:10]: testing package python-cooler version 0.9.3-1 775s autopkgtest [17:20:11]: build not needed 783s autopkgtest [17:20:19]: test run-unit-test: preparing testbed 789s Reading package lists... 791s Building dependency tree... 791s Reading state information... 794s Starting pkgProblemResolver with broken count: 0 796s Starting 2 pkgProblemResolver with broken count: 0 796s Done 801s The following additional packages will be installed: 801s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 801s fonts-urw-base35 libaec0 libblas3 libcairo2 libdeflate0 libfontconfig1 801s libfontenc1 libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1 801s libhdf5-hl-100 libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 801s libjpeg8 liblapack3 liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libopenjp2-7 801s libpixman-1-0 libraqm0 libsharpyuv0 libsz2 libtiff6 libwebp7 libwebpdemux2 801s libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-asciitree 801s python3-biopython python3-cairo python3-click python3-cloudpickle 801s python3-colorama python3-cooler python3-cooler-examples python3-cytoolz 801s python3-dask python3-dateutil python3-decorator python3-dill 801s python3-freetype python3-fsspec python3-h5py python3-h5py-serial 801s python3-importlib-metadata python3-iniconfig python3-locket python3-mock 801s python3-more-itertools python3-multiprocess python3-numpy python3-packaging 801s python3-pairix python3-pandas python3-pandas-lib python3-partd python3-pil 801s python3-pluggy python3-pyfaidx python3-pysam python3-pytest 801s python3-reportlab python3-rlpycairo python3-scipy python3-simplejson 801s python3-toolz python3-zipp sgml-base w3c-sgml-lib x11-common 801s xfonts-encodings xfonts-utils xml-core 801s Suggested packages: 801s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 801s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 801s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 801s python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python3-pip 801s ipython python-dask-doc python3-blosc python3-boto python3-distributed 801s python3-graphviz python3-psutil python3-skimage python3-sklearn 801s python3-sqlalchemy python3-tables python3-objgraph python-fsspec-doc 801s python-h5py-doc python-mock-doc gcc gfortran python3-dev python-pandas-doc 801s python3-statsmodels python-pil-doc pdf-viewer python3-egenix-mxtexttools 801s python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python-toolz-doc 801s sgml-base-doc debhelper 801s Recommended packages: 801s python-biopython-doc ncbi-blast+ git python3-distributed python3-dropbox 801s python3-fusepy python3-libarchive-c python3-paramiko python3-pygit2 801s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 801s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 801s python3-blosc python3-zmq python3-olefile g++ | c++-compiler 801s The following NEW packages will be installed: 801s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra 801s fonts-dejavu-mono fonts-urw-base35 libaec0 libblas3 libcairo2 libdeflate0 801s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 801s libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 801s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblbfgsb0 801s liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 801s libsz2 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 801s libxcb-shm0 libxrender1 python3-asciitree python3-biopython python3-cairo 801s python3-click python3-cloudpickle python3-colorama python3-cooler 801s python3-cooler-examples python3-cytoolz python3-dask python3-dateutil 801s python3-decorator python3-dill python3-freetype python3-fsspec python3-h5py 801s python3-h5py-serial python3-importlib-metadata python3-iniconfig 801s python3-locket python3-mock python3-more-itertools python3-multiprocess 801s python3-numpy python3-packaging python3-pairix python3-pandas 801s python3-pandas-lib python3-partd python3-pil python3-pluggy python3-pyfaidx 801s python3-pysam python3-pytest python3-reportlab python3-rlpycairo 801s python3-scipy python3-simplejson python3-toolz python3-zipp sgml-base 801s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 802s 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. 802s Need to get 77.8 MB/77.8 MB of archives. 802s After this operation, 331 MB of additional disk space will be used. 802s Get:1 /tmp/autopkgtest.4B7jg4/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [732 B] 802s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 802s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 802s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 803s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 803s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 803s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 803s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 803s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 804s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 804s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 805s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 805s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 805s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 805s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 805s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 805s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 805s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 805s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 805s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 805s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 805s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 805s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 805s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 805s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 805s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 805s Get:27 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 805s Get:28 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 805s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 805s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 805s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 805s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 805s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 805s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 805s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 805s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 805s Get:37 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 806s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 806s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 806s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 806s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 806s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 806s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 806s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 806s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-asciitree all 0.3.3-4 [5644 B] 806s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 807s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 807s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 807s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 807s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 807s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 807s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 807s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 807s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 807s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 807s Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 807s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 python3-more-itertools all 10.2.0-1 [52.9 kB] 807s Get:58 http://ftpmaster.internal/ubuntu noble/main arm64 python3-zipp all 1.0.0-6 [6090 B] 807s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 python3-importlib-metadata all 4.12.0-1 [17.8 kB] 807s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 python3-click all 8.1.6-1 [79.0 kB] 807s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cloudpickle all 3.0.0-1 [21.4 kB] 808s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-toolz all 0.12.0-2 [52.7 kB] 808s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cytoolz arm64 0.12.2-1 [580 kB] 808s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 808s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 808s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dill all 0.3.8-1 [83.0 kB] 808s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-multiprocess all 0.70.16-2 [105 kB] 808s Get:68 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 808s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 809s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 809s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pyfaidx all 0.8.1.1-1 [29.6 kB] 809s Get:72 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 809s Get:73 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 811s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 python3-simplejson arm64 3.19.2-1build1 [61.4 kB] 812s Get:75 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 812s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pairix arm64 0.3.7-7 [48.0 kB] 812s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cooler arm64 0.9.3-1 [78.7 kB] 812s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cooler-examples all 0.9.3-1 [9226 kB] 813s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fsspec all 2023.10.0-1 [111 kB] 813s Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 813s Get:81 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-locket all 1.0.0-2 [5872 B] 813s Get:82 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-partd all 1.4.1-1 [17.7 kB] 813s Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-dask all 2023.12.1+dfsg-2 [1124 kB] 813s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 813s Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 813s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 813s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mock all 5.1.0-1 [64.1 kB] 818s Fetched 77.8 MB in 12s (6655 kB/s) 818s Selecting previously unselected package sgml-base. 820s (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 ... 75469 files and directories currently installed.) 820s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 820s Unpacking sgml-base (1.31) ... 820s Selecting previously unselected package fonts-dejavu-mono. 820s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 820s Unpacking fonts-dejavu-mono (2.37-8) ... 821s Selecting previously unselected package fonts-dejavu-core. 821s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 821s Unpacking fonts-dejavu-core (2.37-8) ... 822s Selecting previously unselected package libfontenc1:arm64. 822s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_arm64.deb ... 822s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 822s Selecting previously unselected package x11-common. 822s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu2_all.deb ... 822s Unpacking x11-common (1:7.7+23ubuntu2) ... 822s Selecting previously unselected package xfonts-encodings. 822s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 822s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 823s Selecting previously unselected package xfonts-utils. 823s Preparing to unpack .../06-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 823s Unpacking xfonts-utils (1:7.7+6build2) ... 823s Selecting previously unselected package fonts-urw-base35. 823s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 824s Unpacking fonts-urw-base35 (20200910-8) ... 825s Selecting previously unselected package fontconfig-config. 825s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 827s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 828s Selecting previously unselected package fonts-dejavu-extra. 828s Preparing to unpack .../09-fonts-dejavu-extra_2.37-8_all.deb ... 828s Unpacking fonts-dejavu-extra (2.37-8) ... 828s Selecting previously unselected package libaec0:arm64. 828s Preparing to unpack .../10-libaec0_1.1.2-1_arm64.deb ... 828s Unpacking libaec0:arm64 (1.1.2-1) ... 828s Selecting previously unselected package libblas3:arm64. 829s Preparing to unpack .../11-libblas3_3.12.0-3_arm64.deb ... 829s Unpacking libblas3:arm64 (3.12.0-3) ... 829s Selecting previously unselected package libfontconfig1:arm64. 829s Preparing to unpack .../12-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 829s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 829s Selecting previously unselected package libpixman-1-0:arm64. 829s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_arm64.deb ... 829s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 830s Selecting previously unselected package libxcb-render0:arm64. 830s Preparing to unpack .../14-libxcb-render0_1.15-1_arm64.deb ... 830s Unpacking libxcb-render0:arm64 (1.15-1) ... 830s Selecting previously unselected package libxcb-shm0:arm64. 830s Preparing to unpack .../15-libxcb-shm0_1.15-1_arm64.deb ... 830s Unpacking libxcb-shm0:arm64 (1.15-1) ... 830s Selecting previously unselected package libxrender1:arm64. 830s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 830s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 830s Selecting previously unselected package libcairo2:arm64. 830s Preparing to unpack .../17-libcairo2_1.18.0-1_arm64.deb ... 830s Unpacking libcairo2:arm64 (1.18.0-1) ... 830s Selecting previously unselected package libdeflate0:arm64. 830s Preparing to unpack .../18-libdeflate0_1.19-1_arm64.deb ... 830s Unpacking libdeflate0:arm64 (1.19-1) ... 830s Selecting previously unselected package libgfortran5:arm64. 831s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 831s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 831s Selecting previously unselected package libgomp1:arm64. 831s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 831s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 831s Selecting previously unselected package libgraphite2-3:arm64. 831s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_arm64.deb ... 831s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 831s Selecting previously unselected package libharfbuzz0b:arm64. 831s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_arm64.deb ... 831s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 831s Selecting previously unselected package libsz2:arm64. 831s Preparing to unpack .../23-libsz2_1.1.2-1_arm64.deb ... 831s Unpacking libsz2:arm64 (1.1.2-1) ... 831s Selecting previously unselected package libhdf5-103-1:arm64. 831s Preparing to unpack .../24-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 831s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 832s Selecting previously unselected package libhdf5-hl-100:arm64. 832s Preparing to unpack .../25-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 832s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 832s Selecting previously unselected package libhtscodecs2:arm64. 832s Preparing to unpack .../26-libhtscodecs2_1.6.0-1_arm64.deb ... 832s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 832s Selecting previously unselected package libhts3:arm64. 832s Preparing to unpack .../27-libhts3_1.18+ds-1_arm64.deb ... 832s Unpacking libhts3:arm64 (1.18+ds-1) ... 832s Selecting previously unselected package libimagequant0:arm64. 833s Preparing to unpack .../28-libimagequant0_2.18.0-1_arm64.deb ... 833s Unpacking libimagequant0:arm64 (2.18.0-1) ... 833s Selecting previously unselected package libjpeg-turbo8:arm64. 833s Preparing to unpack .../29-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 833s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 833s Selecting previously unselected package libjpeg8:arm64. 833s Preparing to unpack .../30-libjpeg8_8c-2ubuntu11_arm64.deb ... 833s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 833s Selecting previously unselected package liblapack3:arm64. 834s Preparing to unpack .../31-liblapack3_3.12.0-3_arm64.deb ... 834s Unpacking liblapack3:arm64 (3.12.0-3) ... 834s Selecting previously unselected package liblbfgsb0:arm64. 834s Preparing to unpack .../32-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 834s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 835s Selecting previously unselected package liblcms2-2:arm64. 835s Preparing to unpack .../33-liblcms2-2_2.14-2_arm64.deb ... 835s Unpacking liblcms2-2:arm64 (2.14-2) ... 835s Selecting previously unselected package liblerc4:arm64. 835s Preparing to unpack .../34-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 835s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 836s Selecting previously unselected package liblzf1:arm64. 836s Preparing to unpack .../35-liblzf1_3.6-4_arm64.deb ... 836s Unpacking liblzf1:arm64 (3.6-4) ... 836s Selecting previously unselected package libraqm0:arm64. 836s Preparing to unpack .../36-libraqm0_0.10.1-1_arm64.deb ... 836s Unpacking libraqm0:arm64 (0.10.1-1) ... 836s Selecting previously unselected package libsharpyuv0:arm64. 836s Preparing to unpack .../37-libsharpyuv0_1.3.2-0.4_arm64.deb ... 836s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 836s Selecting previously unselected package libjbig0:arm64. 836s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 836s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 836s Selecting previously unselected package libwebp7:arm64. 836s Preparing to unpack .../39-libwebp7_1.3.2-0.4_arm64.deb ... 837s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 837s Selecting previously unselected package libtiff6:arm64. 837s Preparing to unpack .../40-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 837s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 837s Selecting previously unselected package libwebpdemux2:arm64. 837s Preparing to unpack .../41-libwebpdemux2_1.3.2-0.4_arm64.deb ... 837s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 839s Selecting previously unselected package libwebpmux3:arm64. 839s Preparing to unpack .../42-libwebpmux3_1.3.2-0.4_arm64.deb ... 839s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 839s Selecting previously unselected package python3-asciitree. 839s Preparing to unpack .../43-python3-asciitree_0.3.3-4_all.deb ... 839s Unpacking python3-asciitree (0.3.3-4) ... 839s Selecting previously unselected package python3-numpy. 839s Preparing to unpack .../44-python3-numpy_1%3a1.24.2-2_arm64.deb ... 839s Unpacking python3-numpy (1:1.24.2-2) ... 843s Selecting previously unselected package libopenjp2-7:arm64. 843s Preparing to unpack .../45-libopenjp2-7_2.5.0-2_arm64.deb ... 843s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 843s Selecting previously unselected package python3-pil:arm64. 843s Preparing to unpack .../46-python3-pil_10.2.0-1_arm64.deb ... 843s Unpacking python3-pil:arm64 (10.2.0-1) ... 844s Selecting previously unselected package python3-cairo. 844s Preparing to unpack .../47-python3-cairo_1.25.1-2_arm64.deb ... 844s Unpacking python3-cairo (1.25.1-2) ... 844s Selecting previously unselected package python3-freetype. 844s Preparing to unpack .../48-python3-freetype_2.4.0-1_all.deb ... 844s Unpacking python3-freetype (2.4.0-1) ... 845s Selecting previously unselected package python3-rlpycairo. 845s Preparing to unpack .../49-python3-rlpycairo_0.3.0-3_all.deb ... 845s Unpacking python3-rlpycairo (0.3.0-3) ... 845s Selecting previously unselected package python3-reportlab. 845s Preparing to unpack .../50-python3-reportlab_4.1.0-1_all.deb ... 845s Unpacking python3-reportlab (4.1.0-1) ... 846s Selecting previously unselected package xml-core. 846s Preparing to unpack .../51-xml-core_0.19_all.deb ... 846s Unpacking xml-core (0.19) ... 846s Selecting previously unselected package w3c-sgml-lib. 846s Preparing to unpack .../52-w3c-sgml-lib_1.3-3_all.deb ... 846s Unpacking w3c-sgml-lib (1.3-3) ... 847s Selecting previously unselected package python3-biopython. 848s Preparing to unpack .../53-python3-biopython_1.81+dfsg-3_arm64.deb ... 848s Unpacking python3-biopython (1.81+dfsg-3) ... 851s Selecting previously unselected package python3-colorama. 851s Preparing to unpack .../54-python3-colorama_0.4.6-4_all.deb ... 851s Unpacking python3-colorama (0.4.6-4) ... 852s Selecting previously unselected package python3-more-itertools. 852s Preparing to unpack .../55-python3-more-itertools_10.2.0-1_all.deb ... 852s Unpacking python3-more-itertools (10.2.0-1) ... 852s Selecting previously unselected package python3-zipp. 852s Preparing to unpack .../56-python3-zipp_1.0.0-6_all.deb ... 852s Unpacking python3-zipp (1.0.0-6) ... 852s Selecting previously unselected package python3-importlib-metadata. 852s Preparing to unpack .../57-python3-importlib-metadata_4.12.0-1_all.deb ... 852s Unpacking python3-importlib-metadata (4.12.0-1) ... 852s Selecting previously unselected package python3-click. 852s Preparing to unpack .../58-python3-click_8.1.6-1_all.deb ... 852s Unpacking python3-click (8.1.6-1) ... 852s Selecting previously unselected package python3-cloudpickle. 852s Preparing to unpack .../59-python3-cloudpickle_3.0.0-1_all.deb ... 852s Unpacking python3-cloudpickle (3.0.0-1) ... 852s Selecting previously unselected package python3-toolz. 852s Preparing to unpack .../60-python3-toolz_0.12.0-2_all.deb ... 852s Unpacking python3-toolz (0.12.0-2) ... 853s Selecting previously unselected package python3-cytoolz. 853s Preparing to unpack .../61-python3-cytoolz_0.12.2-1_arm64.deb ... 853s Unpacking python3-cytoolz (0.12.2-1) ... 853s Selecting previously unselected package python3-h5py-serial. 853s Preparing to unpack .../62-python3-h5py-serial_3.10.0-1ubuntu1_arm64.deb ... 853s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 854s Selecting previously unselected package python3-h5py. 854s Preparing to unpack .../63-python3-h5py_3.10.0-1ubuntu1_all.deb ... 854s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 854s Selecting previously unselected package python3-dill. 854s Preparing to unpack .../64-python3-dill_0.3.8-1_all.deb ... 854s Unpacking python3-dill (0.3.8-1) ... 855s Selecting previously unselected package python3-multiprocess. 855s Preparing to unpack .../65-python3-multiprocess_0.70.16-2_all.deb ... 855s Unpacking python3-multiprocess (0.70.16-2) ... 855s Selecting previously unselected package python3-dateutil. 855s Preparing to unpack .../66-python3-dateutil_2.8.2-3_all.deb ... 855s Unpacking python3-dateutil (2.8.2-3) ... 855s Selecting previously unselected package python3-pandas-lib:arm64. 855s Preparing to unpack .../67-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 855s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 858s Selecting previously unselected package python3-pandas. 858s Preparing to unpack .../68-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 858s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 863s Selecting previously unselected package python3-pyfaidx. 863s Preparing to unpack .../69-python3-pyfaidx_0.8.1.1-1_all.deb ... 863s Unpacking python3-pyfaidx (0.8.1.1-1) ... 863s Selecting previously unselected package python3-decorator. 863s Preparing to unpack .../70-python3-decorator_5.1.1-5_all.deb ... 863s Unpacking python3-decorator (5.1.1-5) ... 863s Selecting previously unselected package python3-scipy. 863s Preparing to unpack .../71-python3-scipy_1.11.4-6_arm64.deb ... 863s Unpacking python3-scipy (1.11.4-6) ... 872s Selecting previously unselected package python3-simplejson. 872s Preparing to unpack .../72-python3-simplejson_3.19.2-1build1_arm64.deb ... 872s Unpacking python3-simplejson (3.19.2-1build1) ... 872s Selecting previously unselected package python3-pysam. 872s Preparing to unpack .../73-python3-pysam_0.22.0+ds-1_arm64.deb ... 872s Unpacking python3-pysam (0.22.0+ds-1) ... 875s Selecting previously unselected package python3-pairix:arm64. 875s Preparing to unpack .../74-python3-pairix_0.3.7-7_arm64.deb ... 875s Unpacking python3-pairix:arm64 (0.3.7-7) ... 876s Selecting previously unselected package python3-cooler. 876s Preparing to unpack .../75-python3-cooler_0.9.3-1_arm64.deb ... 876s Unpacking python3-cooler (0.9.3-1) ... 877s Selecting previously unselected package python3-cooler-examples. 877s Preparing to unpack .../76-python3-cooler-examples_0.9.3-1_all.deb ... 877s Unpacking python3-cooler-examples (0.9.3-1) ... 877s Selecting previously unselected package python3-fsspec. 877s Preparing to unpack .../77-python3-fsspec_2023.10.0-1_all.deb ... 877s Unpacking python3-fsspec (2023.10.0-1) ... 878s Selecting previously unselected package python3-packaging. 878s Preparing to 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unselected package python3-pytest. 880s Preparing to unpack .../84-python3-pytest_7.4.4-1_all.deb ... 880s Unpacking python3-pytest (7.4.4-1) ... 881s Selecting previously unselected package python3-mock. 881s Preparing to unpack .../85-python3-mock_5.1.0-1_all.deb ... 881s Unpacking python3-mock (5.1.0-1) ... 881s Selecting previously unselected package autopkgtest-satdep. 881s Preparing to unpack .../86-1-autopkgtest-satdep.deb ... 881s Unpacking autopkgtest-satdep (0) ... 881s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 881s Setting up python3-more-itertools (10.2.0-1) ... 882s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 882s Setting up liblcms2-2:arm64 (2.14-2) ... 882s Setting up python3-iniconfig (1.1.1-2) ... 883s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 883s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 883s Setting up python3-pairix:arm64 (0.3.7-7) ... 884s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 884s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 884s Setting up python3-colorama (0.4.6-4) ... 884s Setting up libxcb-render0:arm64 (1.15-1) ... 884s Setting up python3-fsspec (2023.10.0-1) ... 888s Setting up x11-common (1:7.7+23ubuntu2) ... 891s Setting up libdeflate0:arm64 (1.19-1) ... 891s Setting up libxcb-shm0:arm64 (1.15-1) ... 891s Setting up python3-zipp (1.0.0-6) ... 893s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 893s Setting up python3-click (8.1.6-1) ... 894s Setting up python3-freetype (2.4.0-1) ... 895s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 895s Setting up libaec0:arm64 (1.1.2-1) ... 895s Setting up python3-cloudpickle (3.0.0-1) ... 896s Setting up python3-mock (5.1.0-1) ... 897s Setting up python3-simplejson (3.19.2-1build1) ... 898s Setting up python3-decorator (5.1.1-5) ... 899s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 899s Setting up libblas3:arm64 (3.12.0-3) ... 900s 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 900s Setting up python3-packaging (23.2-1) ... 901s Setting up python3-dill (0.3.8-1) ... 903s Setting up liblzf1:arm64 (3.6-4) ... 903s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 903s Setting up libimagequant0:arm64 (2.18.0-1) ... 903s Setting up fonts-dejavu-mono (2.37-8) ... 903s Setting up fonts-dejavu-core (2.37-8) ... 903s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 903s Setting up python3-asciitree (0.3.3-4) ... 904s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 904s Setting up python3-pluggy (1.4.0-1) ... 905s Setting up python3-cooler-examples (0.9.3-1) ... 905s Setting up libwebp7:arm64 (1.3.2-0.4) ... 905s Setting up fonts-dejavu-extra (2.37-8) ... 905s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 905s Setting up python3-toolz (0.12.0-2) ... 906s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 906s Setting up python3-dateutil (2.8.2-3) ... 908s Setting up sgml-base (1.31) ... 909s Setting up python3-multiprocess (0.70.16-2) ... 914s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 914s Setting up python3-locket (1.0.0-2) ... 916s Setting up libsz2:arm64 (1.1.2-1) ... 916s Setting up python3-cytoolz (0.12.2-1) ... 917s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 917s Setting up python3-partd (1.4.1-1) ... 918s Setting up liblapack3:arm64 (3.12.0-3) ... 918s 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 918s Setting up libhts3:arm64 (1.18+ds-1) ... 918s Setting up python3-pysam (0.22.0+ds-1) ... 920s Setting up python3-importlib-metadata (4.12.0-1) ... 921s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 924s Setting up python3-pytest (7.4.4-1) ... 926s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 926s Setting up python3-dask (2023.12.1+dfsg-2) ... 937s Setting up xfonts-utils (1:7.7+6build2) ... 937s Setting up libraqm0:arm64 (0.10.1-1) ... 937s Setting up python3-numpy (1:1.24.2-2) ... 953s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 953s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 953s Setting up xml-core (0.19) ... 956s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 956s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 956s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 956s Setting up python3-pyfaidx (0.8.1.1-1) ... 957s Setting up python3-scipy (1.11.4-6) ... 978s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 978s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 980s Setting up fonts-urw-base35 (20200910-8) ... 982s Setting up libcairo2:arm64 (1.18.0-1) ... 982s Setting up python3-pil:arm64 (10.2.0-1) ... 985s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 1029s Setting up python3-h5py (3.10.0-1ubuntu1) ... 1030s Setting up python3-cairo (1.25.1-2) ... 1031s Setting up python3-rlpycairo (0.3.0-3) ... 1032s Setting up python3-reportlab (4.1.0-1) ... 1039s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1039s Processing triggers for man-db (2.12.0-3) ... 1045s Processing triggers for sgml-base (1.31) ... 1045s Setting up w3c-sgml-lib (1.3-3) ... 1290s Setting up python3-biopython (1.81+dfsg-3) ... 1300s Setting up python3-cooler (0.9.3-1) ... 1301s Setting up autopkgtest-satdep (0) ... 1327s (Reading database ... 83600 files and directories currently installed.) 1327s Removing autopkgtest-satdep (0) ... 1329s autopkgtest [17:29:25]: test run-unit-test: [----------------------- 1330s + cp -a /usr/share/doc/python3-cooler/tests.tar.xz /tmp/autopkgtest.4B7jg4/autopkgtest_tmp 1330s + cd /tmp/autopkgtest.4B7jg4/autopkgtest_tmp 1330s + tar xaf tests.tar.xz 1332s + pytest-3 1344s ============================= test session starts ============================== 1344s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 1344s rootdir: /tmp/autopkgtest.4B7jg4/autopkgtest_tmp 1344s collected 136 items 1344s 1345s tests/test_api.py .......... [ 7%] 1354s tests/test_balance.py .... [ 10%] 1356s tests/test_cli.py .s..s..... [ 17%] 1360s tests/test_cli_export.py ..s [ 19%] 1361s tests/test_cli_fileops.py .... [ 22%] 1396s tests/test_cli_ingest.py ........... [ 30%] 1412s tests/test_cli_ops.py .... [ 33%] 1412s tests/test_core.py ........... [ 41%] 1445s tests/test_create.py .s....... [ 48%] 1550s tests/test_create_ingest.py ............... [ 59%] 1552s tests/test_create_sanitize.py ........ [ 65%] 1553s tests/test_fileops.py ........s.. [ 73%] 1553s tests/test_parallel.py ... [ 75%] 1585s tests/test_reduce.py .......... [ 83%] 1589s tests/test_util.py .........s............. [100%] 1589s 1589s =============================== warnings summary =============================== 1589s ../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 1589s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 1589s EPOCH = datetime.datetime.utcfromtimestamp(0) 1589s 1589s tests/test_api.py::test_bintable_many_contigs 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_api.py:44: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) 1589s 1589s tests/test_api.py::test_bintable_many_contigs 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_api.py:47: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) 1589s 1589s tests/test_api.py::test_bintable_many_contigs 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_api.py:51: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert pd.api.types.is_categorical_dtype(chroms.dtype) 1589s 1589s tests/test_balance.py::test_balancing_other_options[/tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/data/toy.symm.upper.2.cool-0.01] 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s /usr/lib/python3/dist-packages/cooler/balance.py:112: RuntimeWarning: Mean of empty slice. 1589s scale = nzmarg.mean() 1589s 1589s tests/test_balance.py::test_balancing_other_options[/tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/data/toy.symm.upper.2.cool-0.01] 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s /usr/lib/python3/dist-packages/numpy/core/_methods.py:192: RuntimeWarning: invalid value encountered in scalar divide 1589s ret = ret.dtype.type(ret / rcount) 1589s 1589s tests/test_cli.py::test_makebins 1589s /usr/lib/python3/dist-packages/cooler/cli/makebins.py:55: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s bins["id"] = bins.groupby("chrom").cumcount() 1589s 1589s tests/test_cli_export.py: 1 warning 1589s tests/test_create.py: 1 warning 1589s tests/test_reduce.py: 15 warnings 1589s /usr/lib/python3/dist-packages/cooler/create/_create.py:555: UserWarning: Creating a non-symmetric matrix, but `triucheck` was set to True. Changing to False. 1589s warnings.warn( 1589s 1589s tests/test_cli_ingest.py: 14 warnings 1589s tests/test_cli_ops.py: 6 warnings 1589s tests/test_create_ingest.py: 31 warnings 1589s tests/test_create_sanitize.py: 18 warnings 1589s tests/test_reduce.py: 26 warnings 1589s tests/test_util.py: 2 warnings 1589s /usr/lib/python3/dist-packages/cooler/util.py:730: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s is_cat = pd.api.types.is_categorical_dtype(bins["chrom"]) 1589s 1589s tests/test_cli_ingest.py: 14 warnings 1589s tests/test_cli_ops.py: 6 warnings 1589s tests/test_create_ingest.py: 31 warnings 1589s tests/test_create_sanitize.py: 18 warnings 1589s tests/test_reduce.py: 26 warnings 1589s tests/test_util.py: 1 warning 1589s /usr/lib/python3/dist-packages/cooler/util.py:771: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s self._bins_grouped = bins.groupby("chrom", sort=False) 1589s 1589s tests/test_cli_ingest.py: 14 warnings 1589s tests/test_cli_ops.py: 6 warnings 1589s tests/test_create_ingest.py: 31 warnings 1589s tests/test_create_sanitize.py: 18 warnings 1589s tests/test_reduce.py: 26 warnings 1589s tests/test_util.py: 2 warnings 1589s /usr/lib/python3/dist-packages/cooler/util.py:395: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s for _chrom, group in bins.groupby("chrom"): 1589s 1589s tests/test_cli_ingest.py: 115 warnings 1589s tests/test_create_ingest.py: 56 warnings 1589s tests/test_create_sanitize.py: 9 warnings 1589s /usr/lib/python3/dist-packages/cooler/create/_ingest.py:133: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 1589s chromsizes1 = gs.chromsizes[chrom1_ids].values 1589s 1589s tests/test_cli_ingest.py: 115 warnings 1589s tests/test_create_ingest.py: 56 warnings 1589s tests/test_create_sanitize.py: 9 warnings 1589s /usr/lib/python3/dist-packages/cooler/create/_ingest.py:134: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 1589s chromsizes2 = gs.chromsizes[chrom2_ids].values 1589s 1589s tests/test_cli_ops.py: 6 warnings 1589s tests/test_reduce.py: 26 warnings 1589s /usr/lib/python3/dist-packages/cooler/reduce.py:548: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s return old_bins.groupby("chrom").apply(_each).reset_index(drop=True) 1589s 1589s tests/test_cli_ops.py::test_zoomify 1589s /usr/lib/python3/dist-packages/cooler/cli/zoomify.py:198: UserWarning: Map is already < 256 x 256. Provide resolutions explicitly if you want to coarsen more. 1589s warnings.warn( 1589s 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_cli_ops.py::test_zoomify 1589s tests/test_reduce.py::test_zoomify 1589s tests/test_reduce.py::test_zoomify 1589s tests/test_reduce.py::test_zoomify 1589s /usr/lib/python3/dist-packages/cooler/reduce.py:792: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s n_bins_longest_chrom[base_binsize] = clr.bins()[:].groupby("chrom").size().max() 1589s 1589s tests/test_cli_ops.py::test_balance 1589s tests/test_cli_ops.py::test_balance 1589s tests/test_cli_ops.py::test_balance 1589s /usr/lib/python3/dist-packages/cooler/balance.py:108: ConvergenceWarning: Iteration limit reached without convergence. 1589s warnings.warn( 1589s 1589s tests/test_cli_ops.py::test_balance 1589s /usr/lib/python3/dist-packages/cooler/cli/balance.py:183: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s bins_grouped = clr.bins()[:].groupby('chrom') 1589s 1589s tests/test_core.py: 6 warnings 1589s tests/test_create.py: 29 warnings 1589s /usr/lib/python3/dist-packages/cooler/core/_tableops.py:120: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s elif is_categorical_dtype(data): 1589s 1589s tests/test_core.py::test_put 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_core.py:94: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert pd.api.types.is_categorical_dtype(out['chrom_enum'].dtype) 1589s 1589s tests/test_core.py::test_put 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_core.py:104: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert not pd.api.types.is_categorical_dtype(out['chrom_string'].dtype) 1589s 1589s tests/test_create.py::test_rename_chroms 1589s tests/test_create.py::test_many_contigs 1589s /usr/lib/python3/dist-packages/cooler/create/_create.py:349: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s if is_categorical_dtype(bins["chrom"]): 1589s 1589s tests/test_create_ingest.py: 8 warnings 1589s tests/test_reduce.py: 6 warnings 1589s /usr/lib/python3/dist-packages/multiprocess/popen_fork.py:66: DeprecationWarning: This process (pid=4022) is multi-threaded, use of fork() may lead to deadlocks in the child. 1589s self.pid = os.fork() 1589s 1589s tests/test_reduce.py::test_merge2 1589s /usr/lib/python3/dist-packages/cooler/reduce.py:139: UserWarning: Some merge passes will use more than 3 pixels 1589s warnings.warn(f"Some merge passes will use more than {self.maxbuf} pixels") 1589s 1589s tests/test_util.py::test_bedslice 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_util.py:234: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. 1589s grouped = bins.groupby('chrom') 1589s 1589s tests/test_util.py::test_check_bins 1589s /tmp/autopkgtest.4B7jg4/autopkgtest_tmp/tests/test_util.py:312: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead 1589s assert pd.api.types.is_categorical_dtype(bins["chrom"]) 1589s 1589s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1589s =========== 130 passed, 6 skipped, 787 warnings in 253.21s (0:04:13) =========== 1592s autopkgtest [17:33:48]: test run-unit-test: -----------------------] 1593s autopkgtest [17:33:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1593s run-unit-test PASS 1595s autopkgtest [17:33:51]: @@@@@@@@@@@@@@@@@@@@ summary 1595s run-unit-test PASS 1613s Creating nova instance adt-noble-arm64-python-cooler-20240324-170716-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...