0s autopkgtest [17:32:42]: starting date and time: 2024-03-24 17:32:42+0000 0s autopkgtest [17:32:42]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [17:32:42]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.qmfwvzvd/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:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade mirtop --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 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-2@bos02-arm64-10.secgroup --name adt-noble-arm64-mirtop-20240324-173242-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/ 312s autopkgtest [17:37:54]: testbed dpkg architecture: arm64 313s autopkgtest [17:37:55]: testbed apt version: 2.7.12 313s autopkgtest [17:37:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 315s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 316s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 317s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 319s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 319s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 319s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [708 kB] 319s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 320s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 320s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 320s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 321s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 321s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 321s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 338s Fetched 9850 kB in 10s (983 kB/s) 340s Reading package lists... 362s Reading package lists... 364s Building dependency tree... 364s Reading state information... 369s Calculating upgrade... 372s The following packages will be REMOVED: 372s libssl3 372s The following NEW packages will be installed: 372s libssl3t64 372s The following packages have been kept back: 372s curl 372s The following packages will be upgraded: 372s openssl 373s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 373s Need to get 2777 kB of archives. 373s After this operation, 139 kB of additional disk space will be used. 373s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 374s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 378s Fetched 2777 kB in 1s (2489 kB/s) 378s (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.) 378s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 378s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 380s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 380s wget depends on libssl3 (>= 3.0.0). 380s u-boot-tools depends on libssl3 (>= 3.0.0). 380s tnftp depends on libssl3 (>= 3.0.0). 380s tcpdump depends on libssl3 (>= 3.0.0). 380s systemd-resolved depends on libssl3 (>= 3.0.0). 380s systemd depends on libssl3 (>= 3.0.0). 380s sudo depends on libssl3 (>= 3.0.0). 380s sbsigntool depends on libssl3 (>= 3.0.0). 380s rsync depends on libssl3 (>= 3.0.0). 380s python3-cryptography depends on libssl3 (>= 3.0.0). 380s openssh-server depends on libssl3 (>= 3.0.10). 380s openssh-client depends on libssl3 (>= 3.0.10). 380s mtd-utils depends on libssl3 (>= 3.0.0). 380s mokutil depends on libssl3 (>= 3.0.0). 380s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 380s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 380s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 380s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 380s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 380s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 380s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 380s libnvme1 depends on libssl3 (>= 3.0.0). 380s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 380s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 380s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 380s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 380s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 380s kmod depends on libssl3 (>= 3.0.0). 380s dhcpcd-base depends on libssl3 (>= 3.0.0). 380s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 380s 381s (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.) 381s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 381s Selecting previously unselected package libssl3t64:arm64. 381s (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.) 381s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 381s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 382s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 382s Setting up openssl (3.0.13-0ubuntu2) ... 382s Processing triggers for man-db (2.12.0-3) ... 389s Processing triggers for libc-bin (2.39-0ubuntu6) ... 389s Reading package lists... 390s Building dependency tree... 390s Reading state information... 394s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 399s sh: Attempting to set up Debian/Ubuntu apt sources automatically 399s Reading package lists...sh: Distribution appears to be Ubuntu 406s 406s Building dependency tree... 406s Reading state information... 413s eatmydata is already the newest version (131-1). 413s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 413s Reading package lists... 413s Building dependency tree... 413s Reading state information... 420s dbus is already the newest version (1.14.10-4ubuntu1). 420s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 420s Reading package lists... 420s Building dependency tree... 420s Reading state information... 437s rng-tools-debian is already the newest version (2.4). 437s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 437s Reading package lists... 437s Building dependency tree... 437s Reading state information... 437s The following packages will be REMOVED: 437s cloud-init* python3-configobj* python3-debconf* 437s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 437s After this operation, 3256 kB disk space will be freed. 437s (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.) 437s Removing cloud-init (24.1.2-0ubuntu1) ... 448s Removing python3-configobj (5.0.8-3) ... 448s Removing python3-debconf (1.5.86) ... 448s Processing triggers for man-db (2.12.0-3) ... 449s (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.) 449s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 459s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 459s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 459s invoke-rc.d: policy-rc.d denied execution of try-restart. 465s Reading package lists... 465s Building dependency tree... 465s Reading state information... 470s linux-generic is already the newest version (6.8.0-11.11+1). 470s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 470s Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 470s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 470s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 493s Fetched 255 kB in 4s (63.4 kB/s) 494s Reading package lists... 495s Reading package lists... 497s Building dependency tree... 497s Reading state information... 502s Calculating upgrade... 504s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 505s Reading package lists... 505s Building dependency tree... 505s Reading state information... 509s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 510s autopkgtest [17:41:12]: rebooting testbed after setup commands that affected boot 739s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 772s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 802s autopkgtest [17:46:04]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 810s autopkgtest [17:46:12]: @@@@@@@@@@@@@@@@@@@@ apt-source mirtop 823s Get:1 http://ftpmaster.internal/ubuntu noble/universe mirtop 0.4.25-5 (dsc) [1697 B] 823s Get:2 http://ftpmaster.internal/ubuntu noble/universe mirtop 0.4.25-5 (tar) [720 kB] 823s Get:3 http://ftpmaster.internal/ubuntu noble/universe mirtop 0.4.25-5 (diff) [10.7 kB] 827s gpgv: Signature made Sun Feb 4 10:03:14 2024 UTC 827s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 827s gpgv: Can't check signature: No public key 828s dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.25-5.dsc: no acceptable signature found 830s autopkgtest [17:46:32]: testing package mirtop version 0.4.25-5 831s autopkgtest [17:46:33]: build not needed 833s autopkgtest [17:46:35]: test run-unit-test: preparing testbed 847s Reading package lists... 849s Building dependency tree... 849s Reading state information... 862s Starting pkgProblemResolver with broken count: 0 862s Starting 2 pkgProblemResolver with broken count: 0 862s Done 862s The following additional packages will be installed: 862s bedtools fontconfig-config fonts-dejavu-core fonts-dejavu-extra 862s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 862s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 862s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 862s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 862s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 862s libxcb-shm0 libxrender1 mirtop python3-all python3-biopython python3-cairo 862s python3-dateutil python3-freetype python3-iniconfig python3-mirtop 862s python3-numpy python3-packaging python3-pandas python3-pandas-lib 862s python3-pil python3-pluggy python3-pybedtools python3-pysam python3-pytest 862s python3-reportlab python3-rlpycairo samtools seqan-apps sgml-base 862s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 862s Suggested packages: 862s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 862s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 862s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 862s python3-rdflib python3-psycopg2 python3-scipy raxml t-coffee wise gcc 862s gfortran python3-dev python-pandas-doc python3-statsmodels python-pil-doc 862s python-pybedtools-doc pdf-viewer python3-egenix-mxtexttools 862s python-reportlab-doc rl-accel rl-renderpm cwltool cwltool | cwl-runner 862s sgml-base-doc debhelper 862s Recommended packages: 862s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 862s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 862s python3-html5lib python3-lxml python3-tables python3-olefile 862s The following NEW packages will be installed: 862s autopkgtest-satdep bedtools fontconfig-config fonts-dejavu-core 862s fonts-dejavu-extra fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 862s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 862s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 862s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 862s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 862s libxcb-shm0 libxrender1 mirtop python3-all python3-biopython python3-cairo 862s python3-dateutil python3-freetype python3-iniconfig python3-mirtop 862s python3-numpy python3-packaging python3-pandas python3-pandas-lib 862s python3-pil python3-pluggy python3-pybedtools python3-pysam python3-pytest 862s python3-reportlab python3-rlpycairo samtools seqan-apps sgml-base 862s w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 862s 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. 862s Need to get 70.0 MB/70.0 MB of archives. 862s After this operation, 284 MB of additional disk space will be used. 862s Get:1 /tmp/autopkgtest.0tP67d/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 862s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 862s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 bedtools arm64 2.31.1+dfsg-2 [636 kB] 862s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 865s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 866s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 866s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 866s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 870s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 870s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 875s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 875s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 875s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 875s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 875s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 875s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 875s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 875s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 875s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 875s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 875s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 875s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 875s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 875s Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 875s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 875s Get:26 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 875s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 875s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 875s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 875s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 875s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 875s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 875s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 875s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 875s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 875s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 875s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 875s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 875s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 875s Get:40 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 876s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 876s Get:42 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybedtools arm64 0.9.1-1 [12.3 MB] 883s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 883s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 884s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 884s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 884s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 884s Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 885s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 885s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 885s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 885s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 885s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 885s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 888s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mirtop all 0.4.25-5 [61.5 kB] 888s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 mirtop all 0.4.25-5 [13.3 kB] 888s Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 888s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 888s Get:59 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 888s Get:60 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 888s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 888s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 888s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 seqan-apps arm64 2.4.0+dfsg-16 [11.8 MB] 894s Fetched 70.0 MB in 28s (2458 kB/s) 894s Selecting previously unselected package sgml-base. 895s (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.) 895s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 895s Unpacking sgml-base (1.31) ... 896s Selecting previously unselected package bedtools. 896s Preparing to unpack .../01-bedtools_2.31.1+dfsg-2_arm64.deb ... 896s Unpacking bedtools (2.31.1+dfsg-2) ... 896s Selecting previously unselected package fonts-dejavu-mono. 896s Preparing to unpack .../02-fonts-dejavu-mono_2.37-8_all.deb ... 896s Unpacking fonts-dejavu-mono (2.37-8) ... 897s Selecting previously unselected package fonts-dejavu-core. 897s Preparing to unpack .../03-fonts-dejavu-core_2.37-8_all.deb ... 897s Unpacking fonts-dejavu-core (2.37-8) ... 898s Selecting previously unselected package libfontenc1:arm64. 898s Preparing to unpack .../04-libfontenc1_1%3a1.1.8-1_arm64.deb ... 898s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 898s Selecting previously unselected package x11-common. 898s Preparing to unpack .../05-x11-common_1%3a7.7+23ubuntu2_all.deb ... 898s Unpacking x11-common (1:7.7+23ubuntu2) ... 899s Selecting previously unselected package xfonts-encodings. 899s Preparing to unpack .../06-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 899s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 899s Selecting previously unselected package xfonts-utils. 899s Preparing to unpack .../07-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 899s Unpacking xfonts-utils (1:7.7+6build2) ... 899s Selecting previously unselected package fonts-urw-base35. 899s Preparing to unpack .../08-fonts-urw-base35_20200910-8_all.deb ... 900s Unpacking fonts-urw-base35 (20200910-8) ... 902s Selecting previously unselected package fontconfig-config. 902s Preparing to unpack .../09-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 903s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 903s Selecting previously unselected package fonts-dejavu-extra. 903s Preparing to unpack .../10-fonts-dejavu-extra_2.37-8_all.deb ... 903s Unpacking fonts-dejavu-extra (2.37-8) ... 904s Selecting previously unselected package libblas3:arm64. 904s Preparing to unpack .../11-libblas3_3.12.0-3_arm64.deb ... 904s Unpacking libblas3:arm64 (3.12.0-3) ... 904s Selecting previously unselected package libfontconfig1:arm64. 904s Preparing to unpack .../12-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 904s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 905s Selecting previously unselected package libpixman-1-0:arm64. 905s Preparing to unpack .../13-libpixman-1-0_0.42.2-1_arm64.deb ... 905s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 905s Selecting previously unselected package libxcb-render0:arm64. 905s Preparing to unpack .../14-libxcb-render0_1.15-1_arm64.deb ... 905s Unpacking libxcb-render0:arm64 (1.15-1) ... 905s Selecting previously unselected package libxcb-shm0:arm64. 905s Preparing to unpack .../15-libxcb-shm0_1.15-1_arm64.deb ... 905s Unpacking libxcb-shm0:arm64 (1.15-1) ... 905s Selecting previously unselected package libxrender1:arm64. 905s Preparing to unpack .../16-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 905s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 905s Selecting previously unselected package libcairo2:arm64. 905s Preparing to unpack .../17-libcairo2_1.18.0-1_arm64.deb ... 905s Unpacking libcairo2:arm64 (1.18.0-1) ... 906s Selecting previously unselected package libdeflate0:arm64. 906s Preparing to unpack .../18-libdeflate0_1.19-1_arm64.deb ... 906s Unpacking libdeflate0:arm64 (1.19-1) ... 906s Selecting previously unselected package libgfortran5:arm64. 906s Preparing to unpack .../19-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 906s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 906s Selecting previously unselected package libgomp1:arm64. 906s Preparing to unpack .../20-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 906s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 907s Selecting previously unselected package libgraphite2-3:arm64. 907s Preparing to unpack .../21-libgraphite2-3_1.3.14-2_arm64.deb ... 907s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 907s Selecting previously unselected package libharfbuzz0b:arm64. 907s Preparing to unpack .../22-libharfbuzz0b_8.3.0-2_arm64.deb ... 907s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 907s Selecting previously unselected package libhtscodecs2:arm64. 907s Preparing to unpack .../23-libhtscodecs2_1.6.0-1_arm64.deb ... 907s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 907s Selecting previously unselected package libhts3:arm64. 907s Preparing to unpack .../24-libhts3_1.18+ds-1_arm64.deb ... 907s Unpacking libhts3:arm64 (1.18+ds-1) ... 908s Selecting previously unselected package libimagequant0:arm64. 908s Preparing to unpack .../25-libimagequant0_2.18.0-1_arm64.deb ... 908s Unpacking libimagequant0:arm64 (2.18.0-1) ... 908s Selecting previously unselected package libjpeg-turbo8:arm64. 908s Preparing to unpack .../26-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 908s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 912s Selecting previously unselected package libjpeg8:arm64. 912s Preparing to unpack .../27-libjpeg8_8c-2ubuntu11_arm64.deb ... 912s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 912s Selecting previously unselected package liblapack3:arm64. 912s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ... 912s Unpacking liblapack3:arm64 (3.12.0-3) ... 912s Selecting previously unselected package liblcms2-2:arm64. 912s Preparing to unpack .../29-liblcms2-2_2.14-2_arm64.deb ... 912s Unpacking liblcms2-2:arm64 (2.14-2) ... 912s Selecting previously unselected package liblerc4:arm64. 912s Preparing to unpack .../30-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 912s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 912s Selecting previously unselected package libraqm0:arm64. 912s Preparing to unpack .../31-libraqm0_0.10.1-1_arm64.deb ... 912s Unpacking libraqm0:arm64 (0.10.1-1) ... 912s Selecting previously unselected package libsharpyuv0:arm64. 912s Preparing to unpack .../32-libsharpyuv0_1.3.2-0.4_arm64.deb ... 912s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 912s Selecting previously unselected package libjbig0:arm64. 912s Preparing to unpack .../33-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 912s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 912s Selecting previously unselected package libwebp7:arm64. 912s Preparing to unpack .../34-libwebp7_1.3.2-0.4_arm64.deb ... 912s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 912s Selecting previously unselected package libtiff6:arm64. 912s Preparing to unpack .../35-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 912s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 912s Selecting previously unselected package libwebpdemux2:arm64. 912s Preparing to unpack .../36-libwebpdemux2_1.3.2-0.4_arm64.deb ... 912s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 912s Selecting previously unselected package libwebpmux3:arm64. 912s Preparing to unpack .../37-libwebpmux3_1.3.2-0.4_arm64.deb ... 912s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 912s Selecting previously unselected package python3-pysam. 912s Preparing to unpack .../38-python3-pysam_0.22.0+ds-1_arm64.deb ... 912s Unpacking python3-pysam (0.22.0+ds-1) ... 914s Selecting previously unselected package python3-numpy. 914s Preparing to unpack .../39-python3-numpy_1%3a1.24.2-2_arm64.deb ... 914s Unpacking python3-numpy (1:1.24.2-2) ... 917s Selecting previously unselected package python3-pybedtools. 918s Preparing to unpack .../40-python3-pybedtools_0.9.1-1_arm64.deb ... 918s Unpacking python3-pybedtools (0.9.1-1) ... 923s Selecting previously unselected package python3-dateutil. 923s Preparing to unpack .../41-python3-dateutil_2.8.2-3_all.deb ... 923s Unpacking python3-dateutil (2.8.2-3) ... 923s Selecting previously unselected package python3-pandas-lib:arm64. 923s Preparing to unpack .../42-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 923s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 933s Selecting previously unselected package python3-pandas. 933s Preparing to unpack .../43-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 933s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 936s Selecting previously unselected package libopenjp2-7:arm64. 936s Preparing to unpack .../44-libopenjp2-7_2.5.0-2_arm64.deb ... 936s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 937s Selecting previously unselected package python3-pil:arm64. 937s Preparing to unpack .../45-python3-pil_10.2.0-1_arm64.deb ... 937s Unpacking python3-pil:arm64 (10.2.0-1) ... 937s Selecting previously unselected package python3-cairo. 937s Preparing to unpack .../46-python3-cairo_1.25.1-2_arm64.deb ... 937s Unpacking python3-cairo (1.25.1-2) ... 937s Selecting previously unselected package python3-freetype. 937s Preparing to unpack .../47-python3-freetype_2.4.0-1_all.deb ... 937s Unpacking python3-freetype (2.4.0-1) ... 937s Selecting previously unselected package python3-rlpycairo. 937s Preparing to unpack .../48-python3-rlpycairo_0.3.0-3_all.deb ... 937s Unpacking python3-rlpycairo (0.3.0-3) ... 937s Selecting previously unselected package python3-reportlab. 937s Preparing to unpack .../49-python3-reportlab_4.1.0-1_all.deb ... 937s Unpacking python3-reportlab (4.1.0-1) ... 939s Selecting previously unselected package xml-core. 939s Preparing to unpack .../50-xml-core_0.19_all.deb ... 939s Unpacking xml-core (0.19) ... 939s Selecting previously unselected package w3c-sgml-lib. 939s Preparing to unpack .../51-w3c-sgml-lib_1.3-3_all.deb ... 939s Unpacking w3c-sgml-lib (1.3-3) ... 940s Selecting previously unselected package python3-biopython. 940s Preparing to unpack .../52-python3-biopython_1.81+dfsg-3_arm64.deb ... 940s Unpacking python3-biopython (1.81+dfsg-3) ... 947s Selecting previously unselected package python3-mirtop. 947s Preparing to unpack .../53-python3-mirtop_0.4.25-5_all.deb ... 947s Unpacking python3-mirtop (0.4.25-5) ... 947s Selecting previously unselected package mirtop. 947s Preparing to unpack .../54-mirtop_0.4.25-5_all.deb ... 947s Unpacking mirtop (0.4.25-5) ... 947s Selecting previously unselected package python3-all. 947s Preparing to unpack .../55-python3-all_3.12.1-0ubuntu2_arm64.deb ... 947s Unpacking python3-all (3.12.1-0ubuntu2) ... 947s Selecting previously unselected package python3-iniconfig. 947s Preparing to unpack .../56-python3-iniconfig_1.1.1-2_all.deb ... 947s Unpacking python3-iniconfig (1.1.1-2) ... 947s Selecting previously unselected package python3-packaging. 947s Preparing to unpack .../57-python3-packaging_23.2-1_all.deb ... 947s Unpacking python3-packaging (23.2-1) ... 947s Selecting previously unselected package python3-pluggy. 947s Preparing to unpack .../58-python3-pluggy_1.4.0-1_all.deb ... 947s Unpacking python3-pluggy (1.4.0-1) ... 947s Selecting previously unselected package python3-pytest. 947s Preparing to unpack .../59-python3-pytest_7.4.4-1_all.deb ... 947s Unpacking python3-pytest (7.4.4-1) ... 947s Selecting previously unselected package samtools. 947s Preparing to unpack .../60-samtools_1.19.2-1_arm64.deb ... 947s Unpacking samtools (1.19.2-1) ... 947s Selecting previously unselected package seqan-apps. 947s Preparing to unpack .../61-seqan-apps_2.4.0+dfsg-16_arm64.deb ... 947s Unpacking seqan-apps (2.4.0+dfsg-16) ... 953s Selecting previously unselected package autopkgtest-satdep. 953s Preparing to unpack .../62-1-autopkgtest-satdep.deb ... 953s Unpacking autopkgtest-satdep (0) ... 954s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 954s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 954s Setting up liblcms2-2:arm64 (2.14-2) ... 954s Setting up python3-iniconfig (1.1.1-2) ... 955s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 955s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 955s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 955s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 955s Setting up libxcb-render0:arm64 (1.15-1) ... 955s Setting up x11-common (1:7.7+23ubuntu2) ... 960s Setting up libdeflate0:arm64 (1.19-1) ... 960s Setting up python3-all (3.12.1-0ubuntu2) ... 960s Setting up libxcb-shm0:arm64 (1.15-1) ... 960s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 960s Setting up python3-freetype (2.4.0-1) ... 963s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 963s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 963s Setting up libblas3:arm64 (3.12.0-3) ... 963s 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 964s Setting up python3-packaging (23.2-1) ... 966s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 966s Setting up libimagequant0:arm64 (2.18.0-1) ... 966s Setting up seqan-apps (2.4.0+dfsg-16) ... 966s Setting up fonts-dejavu-mono (2.37-8) ... 966s Setting up fonts-dejavu-core (2.37-8) ... 966s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 966s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 966s Setting up python3-pluggy (1.4.0-1) ... 967s Setting up libwebp7:arm64 (1.3.2-0.4) ... 967s Setting up fonts-dejavu-extra (2.37-8) ... 967s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 967s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 967s Setting up python3-dateutil (2.8.2-3) ... 968s Setting up sgml-base (1.31) ... 969s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 969s Setting up bedtools (2.31.1+dfsg-2) ... 969s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 969s Setting up liblapack3:arm64 (3.12.0-3) ... 969s 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 969s Setting up libhts3:arm64 (1.18+ds-1) ... 969s Setting up python3-pysam (0.22.0+ds-1) ... 970s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 971s Setting up python3-pytest (7.4.4-1) ... 974s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 974s Setting up xfonts-utils (1:7.7+6build2) ... 974s Setting up samtools (1.19.2-1) ... 974s Setting up libraqm0:arm64 (0.10.1-1) ... 974s Setting up python3-numpy (1:1.24.2-2) ... 992s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 992s Setting up xml-core (0.19) ... 994s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 994s Setting up python3-pybedtools (0.9.1-1) ... 996s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 997s Setting up fonts-urw-base35 (20200910-8) ... 998s Setting up libcairo2:arm64 (1.18.0-1) ... 998s Setting up python3-pil:arm64 (10.2.0-1) ... 1002s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 1035s Setting up python3-cairo (1.25.1-2) ... 1036s Setting up python3-rlpycairo (0.3.0-3) ... 1037s Setting up python3-reportlab (4.1.0-1) ... 1041s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1042s Processing triggers for man-db (2.12.0-3) ... 1049s Processing triggers for sgml-base (1.31) ... 1049s Setting up w3c-sgml-lib (1.3-3) ... 1281s Setting up python3-biopython (1.81+dfsg-3) ... 1294s Setting up python3-mirtop (0.4.25-5) ... 1297s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 1297s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 1297s Setting up mirtop (0.4.25-5) ... 1297s Setting up autopkgtest-satdep (0) ... 1328s (Reading database ... 81639 files and directories currently installed.) 1328s Removing autopkgtest-satdep (0) ... 1331s autopkgtest [17:54:53]: test run-unit-test: [----------------------- 1332s Testing with python3.12 in /tmp/autopkgtest.0tP67d/autopkgtest_tmp: 1335s ============================= test session starts ============================== 1335s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 1335s cachedir: .pytest_cache 1335s rootdir: /tmp/autopkgtest.0tP67d/autopkgtest_tmp 1336s collecting ... collected 69 items 1336s 1346s test/test_automated_analysis.py::AutomatedAnalysisTest::test_count PASSED [ 1%] 1354s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_fasta PASSED [ 2%] 1363s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_seqbuster PASSED [ 4%] 1368s test/test_automated_analysis.py::AutomatedAnalysisTest::test_export_vcf PASSED [ 5%] 1373s test/test_automated_analysis.py::AutomatedAnalysisTest::test_merge_bam PASSED [ 7%] 1373s test/test_automated_analysis.py::AutomatedAnalysisTest::test_simulate PASSED [ 8%] 1387s test/test_automated_analysis.py::AutomatedAnalysisTest::test_spikeins_cmd PASSED [ 10%] 1395s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_1_cmd PASSED [ 11%] 1403s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_create_2_cmd PASSED [ 13%] 1410s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectColumns_cmd PASSED [ 14%] 1417s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectCount_cmd PASSED [ 15%] 1423s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectFilter_cmd PASSED [ 17%] 1430s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectLimit_cmd PASSED [ 18%] 1436s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectMirna_cmd PASSED [ 20%] 1442s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectTextOut_cmd PASSED [ 21%] 1450s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_SelectiVariant_cmd PASSED [ 23%] 1458s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_descSummary_cmd PASSED [ 24%] 1462s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showColumns_cmd PASSED [ 26%] 1467s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showSchema_cmd PASSED [ 27%] 1474s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_showTables_cmd PASSED [ 28%] 1479s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirsFile_cmd PASSED [ 30%] 1484s test/test_automated_analysis.py::AutomatedAnalysisTest::test_sql_query_statIsomirs_cmd PASSED [ 31%] 1490s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam PASSED [ 33%] 1496s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_bam_chunk PASSED [ 34%] 1501s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam PASSED [ 36%] 1505s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_genomic_bam_low_memory PASSED [ 37%] 1511s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_isomirsea PASSED [ 39%] 1518s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_manatee PASSED [ 40%] 1524s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_optimir PASSED [ 42%] 1530s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_seqbuster PASSED [ 43%] 1535s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_seqbuster_low_memory PASSED [ 44%] 1543s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_annotation_srnabench PASSED [ 46%] 1549s test/test_automated_analysis.py::AutomatedAnalysisTest::test_srnaseq_stats PASSED [ 47%] 1554s test/test_automated_analysis.py::AutomatedAnalysisTest::test_update_cmd PASSED [ 49%] 1561s test/test_automated_analysis.py::AutomatedAnalysisTest::test_validate_cmd PASSED [ 50%] 1565s test/test_functions.py::FunctionsTest::test_alignment PASSED [ 52%] 1566s test/test_functions.py::FunctionsTest::test_alignment_genomic PASSED [ 53%] 1566s test/test_functions.py::FunctionsTest::test_cigar PASSED [ 55%] 1566s test/test_functions.py::FunctionsTest::test_class PASSED [ 56%] 1566s test/test_functions.py::FunctionsTest::test_code PASSED [ 57%] 1566s test/test_functions.py::FunctionsTest::test_code_convert PASSED [ 59%] 1566s test/test_functions.py::FunctionsTest::test_collapse PASSED [ 60%] 1567s test/test_functions.py::FunctionsTest::test_counts PASSED [ 62%] 1567s test/test_functions.py::FunctionsTest::test_database PASSED [ 63%] 1567s test/test_functions.py::FunctionsTest::test_error69 PASSED [ 65%] 1567s test/test_functions.py::FunctionsTest::test_export_fasta PASSED [ 66%] 1568s test/test_functions.py::FunctionsTest::test_gff PASSED [ 68%] 1568s test/test_functions.py::FunctionsTest::test_is_sequence PASSED [ 69%] 1568s test/test_functions.py::FunctionsTest::test_issue64 PASSED [ 71%] 1568s test/test_functions.py::FunctionsTest::test_keep_name PASSED [ 72%] 1568s test/test_functions.py::FunctionsTest::test_locala PASSED [ 73%] 1568s test/test_functions.py::FunctionsTest::test_merge PASSED [ 75%] 1569s test/test_functions.py::FunctionsTest::test_optimir PASSED [ 76%] 1569s test/test_functions.py::FunctionsTest::test_prost PASSED [ 78%] 1569s test/test_functions.py::FunctionsTest::test_read_hairpin PASSED [ 79%] 1569s test/test_functions.py::FunctionsTest::test_read_hairpin_mirgenedb PASSED [ 81%] 1569s test/test_functions.py::FunctionsTest::test_read_line PASSED [ 82%] 1569s test/test_functions.py::FunctionsTest::test_read_mir2chr PASSED [ 84%] 1569s test/test_functions.py::FunctionsTest::test_read_mir2genomic PASSED [ 85%] 1569s test/test_functions.py::FunctionsTest::test_reverse PASSED [ 86%] 1572s test/test_functions.py::FunctionsTest::test_seqbuster PASSED [ 88%] 1573s test/test_functions.py::FunctionsTest::test_spikeins PASSED [ 89%] 1575s test/test_functions.py::FunctionsTest::test_sql PASSED [ 91%] 1575s test/test_functions.py::FunctionsTest::test_srnabench PASSED [ 92%] 1577s test/test_functions.py::FunctionsTest::test_stats PASSED [ 94%] 1577s test/test_functions.py::FunctionsTest::test_string_variant PASSED [ 95%] 1577s test/test_functions.py::FunctionsTest::test_update PASSED [ 97%] 1578s test/test_functions.py::FunctionsTest::test_validator PASSED [ 98%] 1578s test/test_functions.py::FunctionsTest::test_variant PASSED [100%] 1578s 1578s =============================== warnings summary =============================== 1578s test/test_functions.py::FunctionsTest::test_alignment 1578s /usr/lib/python3/dist-packages/mirtop/libs/config.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 1578s import pkg_resources 1578s 1578s test/test_functions.py::FunctionsTest::test_alignment 1578s /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. 1578s warnings.warn( 1578s 1578s test/test_functions.py::FunctionsTest::test_collapse 1578s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 1578s return self.run(*args, **kwds) 1578s 1578s test/test_functions.py::FunctionsTest::test_counts 1578s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 1578s return self.run(*args, **kwds) 1578s 1578s test/test_functions.py::FunctionsTest::test_gff 1578s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 1578s return self.run(*args, **kwds) 1578s 1578s test/test_functions.py::FunctionsTest::test_read_hairpin 1578s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 1578s return self.run(*args, **kwds) 1578s 1578s test/test_functions.py::FunctionsTest::test_sql 1578s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 1578s return self.run(*args, **kwds) 1578s 1578s test/test_functions.py::FunctionsTest::test_stats 1578s /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). 1578s EPOCH = datetime.datetime.utcfromtimestamp(0) 1578s 1578s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 1578s ================== 69 passed, 8 warnings in 242.90s (0:04:02) ================== 1580s autopkgtest [17:59:02]: test run-unit-test: -----------------------] 1581s autopkgtest [17:59:03]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1581s run-unit-test PASS 1581s autopkgtest [17:59:03]: test autodep8-python3: preparing testbed 2054s autopkgtest [18:06:55]: testbed dpkg architecture: arm64 2054s autopkgtest [18:06:56]: testbed apt version: 2.7.12 2054s autopkgtest [18:06:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 2060s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 2063s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 2064s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 2064s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 2068s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 2068s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 2072s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 2072s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 2072s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 2072s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 2074s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 2074s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 2074s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 2146s Fetched 9851 kB in 36s (272 kB/s) 2152s Reading package lists... 2190s Reading package lists... 2190s Building dependency tree... 2190s Reading state information... 2199s Calculating upgrade... 2199s The following packages will be REMOVED: 2199s libssl3 2199s The following NEW packages will be installed: 2199s libssl3t64 2199s The following packages have been kept back: 2199s curl 2199s The following packages will be upgraded: 2199s openssl 2199s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 2199s Need to get 2777 kB of archives. 2199s After this operation, 139 kB of additional disk space will be used. 2199s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 2200s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 2210s Fetched 2777 kB in 2s (1363 kB/s) 2210s (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.) 2210s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 2210s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 2217s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 2217s wget depends on libssl3 (>= 3.0.0). 2217s u-boot-tools depends on libssl3 (>= 3.0.0). 2217s tnftp depends on libssl3 (>= 3.0.0). 2217s tcpdump depends on libssl3 (>= 3.0.0). 2217s systemd-resolved depends on libssl3 (>= 3.0.0). 2217s systemd depends on libssl3 (>= 3.0.0). 2217s sudo depends on libssl3 (>= 3.0.0). 2217s sbsigntool depends on libssl3 (>= 3.0.0). 2217s rsync depends on libssl3 (>= 3.0.0). 2217s python3-cryptography depends on libssl3 (>= 3.0.0). 2217s openssh-server depends on libssl3 (>= 3.0.10). 2217s openssh-client depends on libssl3 (>= 3.0.10). 2217s mtd-utils depends on libssl3 (>= 3.0.0). 2217s mokutil depends on libssl3 (>= 3.0.0). 2217s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 2217s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 2217s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 2217s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 2217s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 2217s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 2217s libpython3.11-minimal:arm64 depends on libssl3 (>= 3.0.0). 2217s libnvme1 depends on libssl3 (>= 3.0.0). 2217s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 2217s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 2217s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 2217s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 2217s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 2217s kmod depends on libssl3 (>= 3.0.0). 2217s dhcpcd-base depends on libssl3 (>= 3.0.0). 2217s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 2217s 2217s (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.) 2217s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 2217s Selecting previously unselected package libssl3t64:arm64. 2217s (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.) 2217s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 2217s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 2219s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 2219s Setting up openssl (3.0.13-0ubuntu2) ... 2219s Processing triggers for man-db (2.12.0-3) ... 2231s Processing triggers for libc-bin (2.39-0ubuntu6) ... 2233s Reading package lists... 2237s Building dependency tree... 2237s Reading state information... 2243s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 2254s sh: Attempting to set up Debian/Ubuntu apt sources automatically 2262s sh: Distribution appears to be Ubuntu 2276s Reading package lists... 2279s Building dependency tree... 2279s Reading state information... 2285s eatmydata is already the newest version (131-1). 2286s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2286s Reading package lists... 2287s Building dependency tree... 2287s Reading state information... 2303s dbus is already the newest version (1.14.10-4ubuntu1). 2303s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2303s Reading package lists... 2303s Building dependency tree... 2303s Reading state information... 2303s rng-tools-debian is already the newest version (2.4). 2303s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2303s Reading package lists... 2305s Building dependency tree... 2305s Reading state information... 2311s The following packages will be REMOVED: 2311s cloud-init* python3-configobj* python3-debconf* 2316s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 2316s After this operation, 3256 kB disk space will be freed. 2317s (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.) 2318s Removing cloud-init (24.1.2-0ubuntu1) ... 2331s Removing python3-configobj (5.0.8-3) ... 2342s Removing python3-debconf (1.5.86) ... 2342s Processing triggers for man-db (2.12.0-3) ... 2342s (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.) 2342s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 2364s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 2364s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 2365s invoke-rc.d: policy-rc.d denied execution of try-restart. 2369s Reading package lists... 2382s Building dependency tree... 2382s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 2382s Reading state information... 2382s linux-generic is already the newest version (6.8.0-11.11+1). 2382s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2382s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 2382s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 2445s Reading package lists... 2446s Reading package lists... 2448s Building dependency tree... 2448s Reading state information... 2455s Calculating upgrade... 2457s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2458s Reading package lists... 2460s Building dependency tree... 2460s Reading state information... 2468s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2470s autopkgtest [18:13:52]: rebooting testbed after setup commands that affected boot 2666s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 2697s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 2730s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 2763s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 2796s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 2848s Reading package lists... 2851s Building dependency tree... 2851s Reading state information... 2854s Starting pkgProblemResolver with broken count: 0 2855s Starting 2 pkgProblemResolver with broken count: 0 2855s Done 2860s The following additional packages will be installed: 2860s fontconfig-config fonts-dejavu-core fonts-dejavu-extra fonts-dejavu-mono 2860s fonts-urw-base35 libblas3 libcairo2 libdeflate0 libfontconfig1 libfontenc1 2860s libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 2860s libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 2860s liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 libsharpyuv0 libtiff6 libwebp7 2860s libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxrender1 python3-all 2860s python3-biopython python3-cairo python3-dateutil python3-freetype 2860s python3-mirtop python3-numpy python3-pandas python3-pandas-lib python3-pil 2860s python3-pybedtools python3-pysam python3-reportlab python3-rlpycairo 2860s sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 2860s Suggested packages: 2860s fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre liblcms2-utils 2860s python3-tk bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 2860s phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf 2860s python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise 2860s gcc gfortran python3-dev python3-pytest python-pandas-doc 2860s python3-statsmodels python-pil-doc python-pybedtools-doc pdf-viewer 2860s python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm 2860s sgml-base-doc debhelper 2860s Recommended packages: 2860s python-biopython-doc ncbi-blast+ python3-scipy python3-matplotlib 2860s python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 2860s python3-html5lib python3-lxml python3-tables python3-olefile 2861s The following NEW packages will be installed: 2861s autopkgtest-satdep fontconfig-config fonts-dejavu-core fonts-dejavu-extra 2861s fonts-dejavu-mono fonts-urw-base35 libblas3 libcairo2 libdeflate0 2861s libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgraphite2-3 2861s libharfbuzz0b libhts3 libhtscodecs2 libimagequant0 libjbig0 libjpeg-turbo8 2861s libjpeg8 liblapack3 liblcms2-2 liblerc4 libopenjp2-7 libpixman-1-0 libraqm0 2861s libsharpyuv0 libtiff6 libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 2861s libxcb-shm0 libxrender1 python3-all python3-biopython python3-cairo 2861s python3-dateutil python3-freetype python3-mirtop python3-numpy 2861s python3-pandas python3-pandas-lib python3-pil python3-pybedtools 2861s python3-pysam python3-reportlab python3-rlpycairo sgml-base w3c-sgml-lib 2861s x11-common xfonts-encodings xfonts-utils xml-core 2861s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 2861s Need to get 56.7 MB/56.7 MB of archives. 2861s After this operation, 218 MB of additional disk space will be used. 2861s Get:1 /tmp/autopkgtest.0tP67d/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 2861s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 2862s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 2864s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 2873s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libfontenc1 arm64 1:1.1.8-1 [13.9 kB] 2873s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 2873s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 2873s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 xfonts-utils arm64 1:7.7+6build2 [93.6 kB] 2873s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-urw-base35 all 20200910-8 [11.0 MB] 2873s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 2873s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-extra all 2.37-8 [1947 kB] 2874s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 2874s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 2874s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] 2874s Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] 2874s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] 2874s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 2875s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libcairo2 arm64 1.18.0-1 [550 kB] 2875s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 2875s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 2875s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 2875s Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 2875s Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 2875s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 2875s Get:25 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 2875s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 2875s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 2875s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 2875s Get:29 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 2876s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 2876s Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 2876s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 2876s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 2876s Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 2876s Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 2876s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 2876s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 2876s Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 2876s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 python3-all arm64 3.12.1-0ubuntu2 [906 B] 2876s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 2878s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 2878s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 2878s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 python3-cairo arm64 1.25.1-2 [153 kB] 2878s Get:44 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-freetype all 2.4.0-1 [83.1 kB] 2878s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-rlpycairo all 0.3.0-3 [9130 B] 2878s Get:46 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-reportlab all 4.1.0-1 [683 kB] 2878s Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 2878s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 w3c-sgml-lib all 1.3-3 [280 kB] 2878s Get:49 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-biopython arm64 1.81+dfsg-3 [1664 kB] 2879s Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 2879s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] 2880s Get:52 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pybedtools arm64 0.9.1-1 [12.3 MB] 2885s Get:53 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 2887s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 2888s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mirtop all 0.4.25-5 [61.5 kB] 2895s Fetched 56.7 MB in 27s (2081 kB/s) 2895s Selecting previously unselected package sgml-base. 2899s (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.) 2899s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 2899s Unpacking sgml-base (1.31) ... 2899s Selecting previously unselected package fonts-dejavu-mono. 2899s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 2899s Unpacking fonts-dejavu-mono (2.37-8) ... 2899s Selecting previously unselected package fonts-dejavu-core. 2899s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 2900s Unpacking fonts-dejavu-core (2.37-8) ... 2900s Selecting previously unselected package libfontenc1:arm64. 2900s Preparing to unpack .../03-libfontenc1_1%3a1.1.8-1_arm64.deb ... 2900s Unpacking libfontenc1:arm64 (1:1.1.8-1) ... 2901s Selecting previously unselected package x11-common. 2901s Preparing to unpack .../04-x11-common_1%3a7.7+23ubuntu2_all.deb ... 2901s Unpacking x11-common (1:7.7+23ubuntu2) ... 2901s Selecting previously unselected package xfonts-encodings. 2902s Preparing to unpack .../05-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 2902s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 2902s Selecting previously unselected package xfonts-utils. 2902s Preparing to unpack .../06-xfonts-utils_1%3a7.7+6build2_arm64.deb ... 2902s Unpacking xfonts-utils (1:7.7+6build2) ... 2903s Selecting previously unselected package fonts-urw-base35. 2903s Preparing to unpack .../07-fonts-urw-base35_20200910-8_all.deb ... 2905s Unpacking fonts-urw-base35 (20200910-8) ... 2908s Selecting previously unselected package fontconfig-config. 2908s Preparing to unpack .../08-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 2912s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 2912s Selecting previously unselected package fonts-dejavu-extra. 2912s Preparing to unpack .../09-fonts-dejavu-extra_2.37-8_all.deb ... 2912s Unpacking fonts-dejavu-extra (2.37-8) ... 2914s Selecting previously unselected package libblas3:arm64. 2914s Preparing to unpack .../10-libblas3_3.12.0-3_arm64.deb ... 2914s Unpacking libblas3:arm64 (3.12.0-3) ... 2914s Selecting previously unselected package libfontconfig1:arm64. 2914s Preparing to unpack .../11-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 2914s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 2915s Selecting previously unselected package libpixman-1-0:arm64. 2915s Preparing to unpack .../12-libpixman-1-0_0.42.2-1_arm64.deb ... 2915s Unpacking libpixman-1-0:arm64 (0.42.2-1) ... 2915s Selecting previously unselected package libxcb-render0:arm64. 2915s Preparing to unpack .../13-libxcb-render0_1.15-1_arm64.deb ... 2915s Unpacking libxcb-render0:arm64 (1.15-1) ... 2916s Selecting previously unselected package libxcb-shm0:arm64. 2916s Preparing to unpack .../14-libxcb-shm0_1.15-1_arm64.deb ... 2916s Unpacking libxcb-shm0:arm64 (1.15-1) ... 2916s Selecting previously unselected package libxrender1:arm64. 2916s Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 2916s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 2917s Selecting previously unselected package libcairo2:arm64. 2917s Preparing to unpack .../16-libcairo2_1.18.0-1_arm64.deb ... 2917s Unpacking libcairo2:arm64 (1.18.0-1) ... 2917s Selecting previously unselected package libdeflate0:arm64. 2918s Preparing to unpack .../17-libdeflate0_1.19-1_arm64.deb ... 2918s Unpacking libdeflate0:arm64 (1.19-1) ... 2918s Selecting previously unselected package libgfortran5:arm64. 2918s Preparing to unpack .../18-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 2918s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 2919s Selecting previously unselected package libgomp1:arm64. 2920s Preparing to unpack .../19-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 2920s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 2921s Selecting previously unselected package libgraphite2-3:arm64. 2921s Preparing to unpack .../20-libgraphite2-3_1.3.14-2_arm64.deb ... 2921s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 2921s Selecting previously unselected package libharfbuzz0b:arm64. 2922s Preparing to unpack .../21-libharfbuzz0b_8.3.0-2_arm64.deb ... 2922s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 2922s Selecting previously unselected package libhtscodecs2:arm64. 2922s Preparing to unpack .../22-libhtscodecs2_1.6.0-1_arm64.deb ... 2922s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 2923s Selecting previously unselected package libhts3:arm64. 2923s Preparing to unpack .../23-libhts3_1.18+ds-1_arm64.deb ... 2923s Unpacking libhts3:arm64 (1.18+ds-1) ... 2924s Selecting previously unselected package libimagequant0:arm64. 2924s Preparing to unpack .../24-libimagequant0_2.18.0-1_arm64.deb ... 2924s Unpacking libimagequant0:arm64 (2.18.0-1) ... 2924s Selecting previously unselected package libjpeg-turbo8:arm64. 2925s Preparing to unpack .../25-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 2925s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 2925s Selecting previously unselected package libjpeg8:arm64. 2925s Preparing to unpack .../26-libjpeg8_8c-2ubuntu11_arm64.deb ... 2925s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 2926s Selecting previously unselected package liblapack3:arm64. 2926s Preparing to unpack .../27-liblapack3_3.12.0-3_arm64.deb ... 2926s Unpacking liblapack3:arm64 (3.12.0-3) ... 2930s Selecting previously unselected package liblcms2-2:arm64. 2930s Preparing to unpack .../28-liblcms2-2_2.14-2_arm64.deb ... 2930s Unpacking liblcms2-2:arm64 (2.14-2) ... 2930s Selecting previously unselected package liblerc4:arm64. 2930s Preparing to unpack .../29-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 2930s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 2931s Selecting previously unselected package libraqm0:arm64. 2931s Preparing to unpack .../30-libraqm0_0.10.1-1_arm64.deb ... 2931s Unpacking libraqm0:arm64 (0.10.1-1) ... 2931s Selecting previously unselected package libsharpyuv0:arm64. 2932s Preparing to unpack .../31-libsharpyuv0_1.3.2-0.4_arm64.deb ... 2932s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 2932s Selecting previously unselected package libjbig0:arm64. 2932s Preparing to unpack .../32-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 2932s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 2933s Selecting previously unselected package libwebp7:arm64. 2933s Preparing to unpack .../33-libwebp7_1.3.2-0.4_arm64.deb ... 2933s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 2934s Selecting previously unselected package libtiff6:arm64. 2935s Preparing to unpack .../34-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 2935s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 2935s Selecting previously unselected package libwebpdemux2:arm64. 2935s Preparing to unpack .../35-libwebpdemux2_1.3.2-0.4_arm64.deb ... 2935s Unpacking libwebpdemux2:arm64 (1.3.2-0.4) ... 2935s Selecting previously unselected package libwebpmux3:arm64. 2936s Preparing to unpack .../36-libwebpmux3_1.3.2-0.4_arm64.deb ... 2936s Unpacking libwebpmux3:arm64 (1.3.2-0.4) ... 2936s Selecting previously unselected package python3-all. 2936s Preparing to unpack .../37-python3-all_3.12.1-0ubuntu2_arm64.deb ... 2936s Unpacking python3-all (3.12.1-0ubuntu2) ... 2936s Selecting previously unselected package python3-numpy. 2937s Preparing to unpack .../38-python3-numpy_1%3a1.24.2-2_arm64.deb ... 2937s Unpacking python3-numpy (1:1.24.2-2) ... 2944s Selecting previously unselected package libopenjp2-7:arm64. 2944s Preparing to unpack .../39-libopenjp2-7_2.5.0-2_arm64.deb ... 2944s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 2945s Selecting previously unselected package python3-pil:arm64. 2945s Preparing to unpack .../40-python3-pil_10.2.0-1_arm64.deb ... 2945s Unpacking python3-pil:arm64 (10.2.0-1) ... 2946s Selecting previously unselected package python3-cairo. 2946s Preparing to unpack .../41-python3-cairo_1.25.1-2_arm64.deb ... 2946s Unpacking python3-cairo (1.25.1-2) ... 2947s Selecting previously unselected package python3-freetype. 2947s Preparing to unpack .../42-python3-freetype_2.4.0-1_all.deb ... 2947s Unpacking python3-freetype (2.4.0-1) ... 2947s Selecting previously unselected package python3-rlpycairo. 2948s Preparing to unpack .../43-python3-rlpycairo_0.3.0-3_all.deb ... 2948s Unpacking python3-rlpycairo (0.3.0-3) ... 2948s Selecting previously unselected package python3-reportlab. 2948s Preparing to unpack .../44-python3-reportlab_4.1.0-1_all.deb ... 2948s Unpacking python3-reportlab (4.1.0-1) ... 2950s Selecting previously unselected package xml-core. 2950s Preparing to unpack .../45-xml-core_0.19_all.deb ... 2950s Unpacking xml-core (0.19) ... 2951s Selecting previously unselected package w3c-sgml-lib. 2951s Preparing to unpack .../46-w3c-sgml-lib_1.3-3_all.deb ... 2951s Unpacking w3c-sgml-lib (1.3-3) ... 2953s Selecting previously unselected package python3-biopython. 2953s Preparing to unpack .../47-python3-biopython_1.81+dfsg-3_arm64.deb ... 2953s Unpacking python3-biopython (1.81+dfsg-3) ... 2958s Selecting previously unselected package python3-dateutil. 2958s Preparing to unpack .../48-python3-dateutil_2.8.2-3_all.deb ... 2958s Unpacking python3-dateutil (2.8.2-3) ... 2959s Selecting previously unselected package python3-pysam. 2959s Preparing to unpack .../49-python3-pysam_0.22.0+ds-1_arm64.deb ... 2959s Unpacking python3-pysam (0.22.0+ds-1) ... 2964s Selecting previously unselected package python3-pybedtools. 2964s Preparing to unpack .../50-python3-pybedtools_0.9.1-1_arm64.deb ... 2964s Unpacking python3-pybedtools (0.9.1-1) ... 2967s Selecting previously unselected package python3-pandas-lib:arm64. 2967s Preparing to unpack .../51-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 2967s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 2976s Selecting previously unselected package python3-pandas. 2976s Preparing to unpack .../52-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 2976s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 2985s Selecting previously unselected package python3-mirtop. 2985s Preparing to unpack .../53-python3-mirtop_0.4.25-5_all.deb ... 2985s Unpacking python3-mirtop (0.4.25-5) ... 2986s Selecting previously unselected package autopkgtest-satdep. 2986s Preparing to unpack .../54-2-autopkgtest-satdep.deb ... 2986s Unpacking autopkgtest-satdep (0) ... 2987s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 2987s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 2987s Setting up liblcms2-2:arm64 (2.14-2) ... 2987s Setting up libpixman-1-0:arm64 (0.42.2-1) ... 2987s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 2987s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 2987s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 2987s Setting up libxcb-render0:arm64 (1.15-1) ... 2987s Setting up x11-common (1:7.7+23ubuntu2) ... 2998s Setting up libdeflate0:arm64 (1.19-1) ... 2998s Setting up python3-all (3.12.1-0ubuntu2) ... 2998s Setting up libxcb-shm0:arm64 (1.15-1) ... 2998s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 2998s Setting up python3-freetype (2.4.0-1) ... 3003s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 3003s Setting up libfontenc1:arm64 (1:1.1.8-1) ... 3003s Setting up libblas3:arm64 (3.12.0-3) ... 3003s 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 3003s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 3003s Setting up libimagequant0:arm64 (2.18.0-1) ... 3003s Setting up fonts-dejavu-mono (2.37-8) ... 3003s Setting up fonts-dejavu-core (2.37-8) ... 3003s Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 3004s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 3004s Setting up libwebp7:arm64 (1.3.2-0.4) ... 3004s Setting up fonts-dejavu-extra (2.37-8) ... 3004s Setting up libopenjp2-7:arm64 (2.5.0-2) ... 3004s Setting up libharfbuzz0b:arm64 (8.3.0-2) ... 3004s Setting up python3-dateutil (2.8.2-3) ... 3009s Setting up sgml-base (1.31) ... 3010s Setting up libwebpmux3:arm64 (1.3.2-0.4) ... 3010s Setting up libjpeg8:arm64 (8c-2ubuntu11) ... 3010s Setting up liblapack3:arm64 (3.12.0-3) ... 3010s 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 3010s Setting up libhts3:arm64 (1.18+ds-1) ... 3010s Setting up python3-pysam (0.22.0+ds-1) ... 3013s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 3020s Setting up libwebpdemux2:arm64 (1.3.2-0.4) ... 3020s Setting up xfonts-utils (1:7.7+6build2) ... 3020s Setting up libraqm0:arm64 (0.10.1-1) ... 3020s Setting up python3-numpy (1:1.24.2-2) ... 3062s Setting up libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 3063s Setting up xml-core (0.19) ... 3068s Setting up libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 3068s Setting up python3-pybedtools (0.9.1-1) ... 3073s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 3073s Setting up fonts-urw-base35 (20200910-8) ... 3077s Setting up libcairo2:arm64 (1.18.0-1) ... 3077s Setting up python3-pil:arm64 (10.2.0-1) ... 3084s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 3186s Setting up python3-cairo (1.25.1-2) ... 3189s Setting up python3-rlpycairo (0.3.0-3) ... 3192s Setting up python3-reportlab (4.1.0-1) ... 3207s Processing triggers for libc-bin (2.39-0ubuntu6) ... 3208s Processing triggers for man-db (2.12.0-3) ... 3224s Processing triggers for sgml-base (1.31) ... 3224s Setting up w3c-sgml-lib (1.3-3) ... 3968s Setting up python3-biopython (1.81+dfsg-3) ... 3997s Setting up python3-mirtop (0.4.25-5) ... 4002s /usr/lib/python3/dist-packages/mirtop/sql/sql.py:478: SyntaxWarning: invalid escape sequence '\(' 4002s print("Usage: mirtop sql --create --gff --db \(Default: mirtop.db\)") 4002s Setting up autopkgtest-satdep (0) ... 4042s (Reading database ... 81104 files and directories currently installed.) 4042s Removing autopkgtest-satdep (0) ... 4055s autopkgtest [18:40:17]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import mirtop; print(mirtop)" ; done 4055s autopkgtest [18:40:17]: test autodep8-python3: [----------------------- 4057s Testing with python3.12: 4060s 4061s autopkgtest [18:40:23]: test autodep8-python3: -----------------------] 4063s autodep8-python3 PASS (superficial) 4063s autopkgtest [18:40:25]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 4065s autopkgtest [18:40:27]: @@@@@@@@@@@@@@@@@@@@ summary 4065s run-unit-test PASS 4065s autodep8-python3 PASS (superficial) 4092s Creating nova instance adt-noble-arm64-mirtop-20240324-173242-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)... 4092s Creating nova instance adt-noble-arm64-mirtop-20240324-173242-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 86f9118c-691d-4fd3-ac71-bf5396ee0d8a)...