0s autopkgtest [01:39:03]: starting date and time: 2025-03-16 01:39:03+0000 0s autopkgtest [01:39:03]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:39:03]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.me4fia1j/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:scikit-learn --apt-upgrade cnvkit --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-6.secgroup --name adt-plucky-i386-cnvkit-20250316-013902-juju-7f2275-prod-proposed-migration-environment-15-f810ddf9-1f1c-4889-88fb-59aa0d227647 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 44s autopkgtest [01:39:47]: testbed dpkg architecture: amd64 44s autopkgtest [01:39:47]: testbed apt version: 2.9.31ubuntu1 44s autopkgtest [01:39:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 44s autopkgtest [01:39:47]: testbed release detected to be: None 45s autopkgtest [01:39:48]: updating testbed package index (apt update) 45s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 45s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 45s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 45s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 45s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 45s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 45s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 45s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [84.0 kB] 45s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [66.6 kB] 45s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1844 B] 45s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 45s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [168 kB] 45s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [338 kB] 45s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [14.9 kB] 45s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9324 B] 45s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [18.0 kB] 45s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 45s Fetched 1252 kB in 0s (5721 kB/s) 46s Reading package lists... 46s + lsb_release --codename --short 46s + RELEASE=plucky 46s + cat 46s + [ plucky != trusty ] 46s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 46s Reading package lists... 47s Building dependency tree... 47s Reading state information... 47s Calculating upgrade... 47s Calculating upgrade... 47s The following package was automatically installed and is no longer required: 47s libnl-genl-3-200 47s Use 'sudo apt autoremove' to remove it. 47s The following NEW packages will be installed: 47s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 47s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 47s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 47s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 47s The following packages will be upgraded: 47s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 47s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 47s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 47s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 47s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 47s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 47s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 47s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 47s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 47s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 47s linux-headers-generic linux-headers-virtual linux-image-generic 47s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 47s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 47s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 47s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 47s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 47s python3.13-minimal rsync rsyslog strace xz-utils 47s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 807 MB of archives. 47s After this operation, 326 MB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 47s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 47s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 47s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 47s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 47s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 47s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 47s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 47s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 47s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 47s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 48s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 48s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 48s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 48s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 48s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 48s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 48s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 48s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 48s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 48s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 48s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 48s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 48s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 48s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 48s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 48s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 48s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 48s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 48s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 48s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 48s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 48s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 48s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 48s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 48s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 48s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 48s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 48s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 48s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 48s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 48s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 48s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 48s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 48s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 48s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 48s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 48s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 48s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 48s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 48s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 48s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 48s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 48s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 48s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 48s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 48s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 48s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 48s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 48s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 48s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 48s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 48s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 48s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 48s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 48s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 48s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 48s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 48s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 48s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 48s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 48s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 48s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 48s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 48s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 48s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 48s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 52s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 53s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 53s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 54s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 54s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 54s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 54s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 54s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 54s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 54s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 54s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 54s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 54s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 54s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 54s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 54s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 54s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 54s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 54s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 54s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 54s Preconfiguring packages ... 54s Fetched 807 MB in 7s (124 MB/s) 54s (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 ... 109138 files and directories currently installed.) 54s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 54s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 55s Setting up ncurses-bin (6.5+20250216-2) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 55s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 55s Setting up ncurses-base (6.5+20250216-2) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 55s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 55s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 55s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 55s Setting up liblz4-1:amd64 (1.10.0-4) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 55s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 55s Setting up liblzma5:amd64 (5.6.4-1) ... 55s (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 ... 109138 files and directories currently installed.) 55s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 55s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 56s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 56s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 56s Setting up apt (2.9.33) ... 56s (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 ... 109138 files and directories currently installed.) 56s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 56s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 56s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 56s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 57s Setting up python3-minimal (3.13.2-2) ... 57s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 72s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 72s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 72s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 72s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 72s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 72s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 72s Setting up media-types (13.0.0) ... 72s Installing new version of config file /etc/mime.types ... 72s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 72s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 72s Setting up pci.ids (0.0~2025.03.09-1) ... 72s Setting up apt-utils (2.9.33) ... 72s Setting up libdebuginfod-common (0.192-4) ... 72s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 72s Setting up bpftool (7.6.0+6.14.0-10.10) ... 72s Setting up libestr0:amd64 (0.1.11-2) ... 72s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 72s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 72s Setting up dosfstools (4.2-1.2) ... 72s Setting up rsyslog (8.2412.0-2ubuntu2) ... 72s info: The user `syslog' is already a member of `adm'. 73s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 73s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 73s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 73s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 73s Setting up linux-headers-generic (6.14.0-10.10) ... 73s Setting up libjemalloc2:amd64 (5.3.0-3) ... 73s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 73s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 73s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 74s Installing new version of config file /etc/apparmor.d/openvpn ... 75s Reloading AppArmor profiles 76s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 76s No schema files found: doing nothing. 76s Setting up libglib2.0-data (2.84.0-1) ... 76s Setting up libncurses6:amd64 (6.5+20250216-2) ... 76s Setting up strace (6.13+ds-1ubuntu1) ... 76s Setting up xz-utils (5.6.4-1) ... 76s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 76s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 78s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 78s Setting up libpci3:amd64 (1:3.13.0-2) ... 78s Setting up python-apt-common (2.9.9build1) ... 78s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 78s Setting up pnp.ids (0.393-3) ... 78s Setting up libnl-3-200:amd64 (3.7.0-1) ... 78s Setting up python3.13-minimal (3.13.2-2) ... 79s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 79s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 79s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 79s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 79s Setting up rsync (3.4.1+ds1-3) ... 80s rsync.service is a disabled or a static unit not running, not starting it. 80s Setting up python3.13-gdbm (3.13.2-2) ... 80s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 80s Setting up ncurses-term (6.5+20250216-2) ... 80s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 80s Setting up libpython3.13:amd64 (3.13.2-2) ... 80s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 80s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 80s Setting up linux-headers-virtual (6.14.0-10.10) ... 80s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 80s Setting up python3.13 (3.13.2-2) ... 80s Setting up htop (3.4.0-2) ... 80s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 82s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 82s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 82s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 82s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 82s Setting up libfwupd3:amd64 (2.0.6-4) ... 82s Setting up python3 (3.13.2-2) ... 83s Setting up python3-markupsafe (2.1.5-1build4) ... 83s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 85s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 85s Setting up hwdata (0.393-3) ... 85s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 85s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 85s Setting up linux-perf (6.14.0-10.10) ... 85s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 85s Setting up python3-gi (3.50.0-4build1) ... 85s Setting up pciutils (1:3.13.0-2) ... 85s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 85s Setting up curl (8.12.1-3ubuntu1) ... 85s Setting up linux-image-virtual (6.14.0-10.10) ... 85s Setting up linux-tools-common (6.14.0-10.10) ... 85s Setting up fwupd (2.0.6-4) ... 86s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 86s fwupd.service is a disabled or a static unit not running, not starting it. 86s Setting up python3-systemd (235-1build6) ... 86s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 86s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 86s Setting up linux-image-generic (6.14.0-10.10) ... 86s Setting up python3-dbus (1.3.2-5build5) ... 86s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 86s Setting up linux-generic (6.14.0-10.10) ... 86s Setting up python3-apt (2.9.9build1) ... 86s Setting up python3-yaml (6.0.2-1build2) ... 86s Setting up python3-lazr.uri (1.0.6-6) ... 86s Setting up binutils (2.44-3ubuntu1) ... 86s Setting up cloud-init-base (25.1-0ubuntu3) ... 88s Setting up linux-virtual (6.14.0-10.10) ... 88s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 88s Setting up cloud-init (25.1-0ubuntu3) ... 88s Processing triggers for systemd (257.3-1ubuntu3) ... 88s Processing triggers for man-db (2.13.0-1) ... 90s Processing triggers for dbus (1.16.2-1ubuntu1) ... 90s Processing triggers for libc-bin (2.41-1ubuntu1) ... 90s Processing triggers for initramfs-tools (0.146ubuntu1) ... 90s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 90s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 100s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 100s /etc/kernel/postinst.d/initramfs-tools: 100s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 100s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 110s /etc/kernel/postinst.d/zz-update-grub: 110s Sourcing file `/etc/default/grub' 110s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 110s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 110s Generating grub configuration file ... 110s Found linux image: /boot/vmlinuz-6.14.0-10-generic 110s Found initrd image: /boot/initrd.img-6.14.0-10-generic 110s Found linux image: /boot/vmlinuz-6.12.0-16-generic 110s Found initrd image: /boot/initrd.img-6.12.0-16-generic 110s Found linux image: /boot/vmlinuz-6.11.0-8-generic 110s Found initrd image: /boot/initrd.img-6.11.0-8-generic 111s Warning: os-prober will not be executed to detect other bootable partitions. 111s Systems on them will not be added to the GRUB boot configuration. 111s Check GRUB_DISABLE_OS_PROBER documentation entry. 111s Adding boot menu entry for UEFI Firmware Settings ... 111s done 111s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 111s + /usr/lib/apt/apt-helper analyze-pattern ?true 111s + uname -r 111s + sed s/\./\\./g 111s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 111s + apt list ?obsolete 111s + grep -v ^linux-.*6\.12\.0-16-generic.* 111s + tail -n+2 111s + cut -d/ -f1 112s + obsolete_pkgs=linux-headers-6.11.0-8-generic 112s linux-headers-6.11.0-8 112s linux-headers-6.12.0-16 112s linux-image-6.11.0-8-generic 112s linux-modules-6.11.0-8-generic 112s linux-tools-6.11.0-8-generic 112s linux-tools-6.11.0-8 112s linux-tools-6.12.0-16 112s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-headers-6.12.0-16 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 linux-tools-6.12.0-16 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Solving dependencies... 113s The following packages will be REMOVED: 113s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 113s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 113s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 113s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 113s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 113s linux-tools-6.12.0-16-generic* 113s 0 upgraded, 0 newly installed, 15 to remove and 0 not upgraded. 113s After this operation, 371 MB disk space will be freed. 113s (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 ... 148643 files and directories currently installed.) 113s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 113s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 113s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 113s Removing libpython3.12t64:amd64 (3.12.9-1) ... 113s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 113s Removing libnsl2:amd64 (1.3.0-3build3) ... 113s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 113s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 114s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 116s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 116s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 118s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 119s /etc/kernel/postrm.d/initramfs-tools: 119s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 119s /etc/kernel/postrm.d/zz-update-grub: 119s Sourcing file `/etc/default/grub' 119s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 119s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 119s Generating grub configuration file ... 119s Found linux image: /boot/vmlinuz-6.14.0-10-generic 119s Found initrd image: /boot/initrd.img-6.14.0-10-generic 119s Found linux image: /boot/vmlinuz-6.12.0-16-generic 119s Found initrd image: /boot/initrd.img-6.12.0-16-generic 119s Warning: os-prober will not be executed to detect other bootable partitions. 119s Systems on them will not be added to the GRUB boot configuration. 119s Check GRUB_DISABLE_OS_PROBER documentation entry. 119s Adding boot menu entry for UEFI Firmware Settings ... 119s done 120s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 120s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 120s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 120s Processing triggers for libc-bin (2.41-1ubuntu1) ... 120s (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 ... 84830 files and directories currently installed.) 120s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 120s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 120s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 120s + grep -q trusty /etc/lsb-release 120s + [ ! -d /usr/share/doc/unattended-upgrades ] 120s + [ ! -d /usr/share/doc/lxd ] 120s + [ ! -d /usr/share/doc/lxd-client ] 120s + [ ! -d /usr/share/doc/snapd ] 120s + type iptables 120s + cat 120s + chmod 755 /etc/rc.local 120s + . /etc/rc.local 120s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 120s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 120s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 120s + uname -m 120s + [ x86_64 = ppc64le ] 120s + [ -d /run/systemd/system ] 120s + systemd-detect-virt --quiet --vm 120s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 120s + cat 120s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 120s + echo COMPRESS=lz4 120s autopkgtest [01:41:03]: upgrading testbed (apt dist-upgrade and autopurge) 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 121s Starting 2 pkgProblemResolver with broken count: 0 121s Done 122s Entering ResolveByKeep 122s 122s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s Starting pkgProblemResolver with broken count: 0 123s Starting 2 pkgProblemResolver with broken count: 0 123s Done 123s Solving dependencies... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s autopkgtest [01:41:06]: rebooting testbed after setup commands that affected boot 144s autopkgtest [01:41:27]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 145s autopkgtest [01:41:28]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 146s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (dsc) [2483 B] 146s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (tar) [32.1 MB] 146s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (diff) [20.8 kB] 147s gpgv: Signature made Thu Feb 6 14:25:04 2025 UTC 147s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 147s gpgv: issuer "crusoe@debian.org" 147s gpgv: Can't check signature: No public key 147s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.12-1.dsc: no acceptable signature found 148s autopkgtest [01:41:31]: testing package cnvkit version 0.9.12-1 148s autopkgtest [01:41:31]: build not needed 155s autopkgtest [01:41:38]: test run-unit-test: preparing testbed 155s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s Starting pkgProblemResolver with broken count: 0 155s Starting 2 pkgProblemResolver with broken count: 0 155s Done 156s The following NEW packages will be installed: 156s blt cnvkit cython3 fontconfig fontconfig-config fonts-dejavu-core 156s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 156s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgpgmepp6t64 156s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 156s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 156s liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 156s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 156s libpoppler147 libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 156s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 156s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 156s poppler-utils python-matplotlib-data python3-biopython python3-brotli 156s python3-cairo python3-contourpy python3-cycler python3-dateutil 156s python3-decorator python3-fonttools python3-freetype python3-fs 156s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 156s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 156s python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib 156s python3-pil python3-pil.imagetk python3-platformdirs python3-pomegranate 156s python3-pyfaidx python3-pysam python3-pytz python3-reportlab 156s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 156s python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 156s python3-unicodedata2 python3.12-tk python3.13-tk r-base-core 156s r-bioc-biocgenerics r-bioc-dnacopy sgml-base tk8.6-blt2.5 unicode-data unzip 156s w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 156s 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 183 MB of archives. 156s After this operation, 760 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 156s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 156s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 156s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 156s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 156s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 156s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 156s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 156s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 156s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 156s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 156s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 156s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 156s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 156s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 156s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 156s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 156s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 156s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 156s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 156s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 156s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 156s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 156s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 156s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 156s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 156s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 156s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 156s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 156s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 156s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 156s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 156s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 156s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 156s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 156s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 156s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 156s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 156s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 156s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 156s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 156s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 156s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 156s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 156s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 156s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 156s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 156s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 156s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build2 [124 kB] 156s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 156s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 156s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 156s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 156s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 156s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 156s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 156s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 156s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 156s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 156s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 156s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 156s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 156s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 156s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 156s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 156s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 156s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 156s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 156s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 156s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 156s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 156s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 156s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 156s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 156s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 156s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 156s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 156s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 156s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 156s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 156s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 157s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 157s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 157s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8build1 [5332 kB] 157s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 157s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 157s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 157s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 157s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 157s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 157s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 157s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 157s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 157s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 157s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 157s Get:96 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 157s Get:97 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 157s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 157s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 157s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 157s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 157s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 157s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 157s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 157s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 157s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 157s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 157s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 157s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 157s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 157s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 157s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 157s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 157s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 157s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 157s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 157s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgmepp6t64 amd64 1.24.2-1ubuntu2 [126 kB] 157s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler147 amd64 25.03.0-2 [1295 kB] 157s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 25.03.0-2 [232 kB] 158s Preconfiguring packages ... 158s Fetched 183 MB in 2s (114 MB/s) 158s Selecting previously unselected package python3-numpy-dev:amd64. 158s (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 ... 84827 files and directories currently installed.) 158s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 158s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 158s Selecting previously unselected package libblas3:amd64. 158s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 158s Unpacking libblas3:amd64 (3.12.1-2) ... 158s Selecting previously unselected package libgfortran5:amd64. 158s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 158s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 158s Selecting previously unselected package liblapack3:amd64. 158s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 158s Unpacking liblapack3:amd64 (3.12.1-2) ... 158s Selecting previously unselected package python3-numpy. 158s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 158s Unpacking python3-numpy (1:2.2.3+ds-5) ... 159s Selecting previously unselected package sgml-base. 159s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 159s Unpacking sgml-base (1.31) ... 159s Selecting previously unselected package libtcl8.6:amd64. 159s Preparing to unpack .../006-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 159s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 159s Selecting previously unselected package fonts-dejavu-mono. 159s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-mono (2.37-8) ... 159s Selecting previously unselected package fonts-dejavu-core. 159s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... 159s Unpacking fonts-dejavu-core (2.37-8) ... 159s Selecting previously unselected package libfontenc1:amd64. 159s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 159s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 159s Selecting previously unselected package x11-common. 159s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 159s Unpacking x11-common (1:7.7+23ubuntu3) ... 159s Selecting previously unselected package xfonts-encodings. 159s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 159s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 159s Selecting previously unselected package xfonts-utils. 159s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_amd64.deb ... 159s Unpacking xfonts-utils (1:7.7+7) ... 159s Selecting previously unselected package fonts-urw-base35. 159s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ... 159s Unpacking fonts-urw-base35 (20200910-8) ... 159s Selecting previously unselected package fontconfig-config. 159s Preparing to unpack .../014-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 159s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 159s Selecting previously unselected package libfontconfig1:amd64. 159s Preparing to unpack .../015-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 159s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 159s Selecting previously unselected package libxrender1:amd64. 159s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 159s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 159s Selecting previously unselected package libxft2:amd64. 159s Preparing to unpack .../017-libxft2_2.3.6-1build1_amd64.deb ... 159s Unpacking libxft2:amd64 (2.3.6-1build1) ... 159s Selecting previously unselected package libxss1:amd64. 159s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_amd64.deb ... 159s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 159s Selecting previously unselected package libtk8.6:amd64. 159s Preparing to unpack .../019-libtk8.6_8.6.16-1_amd64.deb ... 159s Unpacking libtk8.6:amd64 (8.6.16-1) ... 159s Selecting previously unselected package tk8.6-blt2.5. 159s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 159s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 159s Selecting previously unselected package blt. 159s Preparing to unpack .../021-blt_2.5.3+dfsg-8_amd64.deb ... 159s Unpacking blt (2.5.3+dfsg-8) ... 159s Selecting previously unselected package python3.12-tk. 159s Preparing to unpack .../022-python3.12-tk_3.12.9-1_amd64.deb ... 159s Unpacking python3.12-tk (3.12.9-1) ... 159s Selecting previously unselected package python3.13-tk. 159s Preparing to unpack .../023-python3.13-tk_3.13.2-2_amd64.deb ... 159s Unpacking python3.13-tk (3.13.2-2) ... 160s Selecting previously unselected package python3-tk:amd64. 160s Preparing to unpack .../024-python3-tk_3.13.1-1_amd64.deb ... 160s Unpacking python3-tk:amd64 (3.13.1-1) ... 160s Selecting previously unselected package python3-pil.imagetk:amd64. 160s Preparing to unpack .../025-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 160s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 160s Selecting previously unselected package libgomp1:amd64. 160s Preparing to unpack .../026-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 160s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 160s Selecting previously unselected package libimagequant0:amd64. 160s Preparing to unpack .../027-libimagequant0_2.18.0-1build1_amd64.deb ... 160s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 160s Selecting previously unselected package libjpeg-turbo8:amd64. 160s Preparing to unpack .../028-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 160s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 160s Selecting previously unselected package libjpeg8:amd64. 160s Preparing to unpack .../029-libjpeg8_8c-2ubuntu11_amd64.deb ... 160s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 160s Selecting previously unselected package liblcms2-2:amd64. 160s Preparing to unpack .../030-liblcms2-2_2.16-2_amd64.deb ... 160s Unpacking liblcms2-2:amd64 (2.16-2) ... 160s Selecting previously unselected package libopenjp2-7:amd64. 160s Preparing to unpack .../031-libopenjp2-7_2.5.3-2_amd64.deb ... 160s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 160s Selecting previously unselected package libgraphite2-3:amd64. 160s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 160s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 160s Selecting previously unselected package libharfbuzz0b:amd64. 160s Preparing to unpack .../033-libharfbuzz0b_10.2.0-1_amd64.deb ... 160s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 160s Selecting previously unselected package libraqm0:amd64. 160s Preparing to unpack .../034-libraqm0_0.10.2-1_amd64.deb ... 160s Unpacking libraqm0:amd64 (0.10.2-1) ... 160s Selecting previously unselected package libdeflate0:amd64. 160s Preparing to unpack .../035-libdeflate0_1.23-1_amd64.deb ... 160s Unpacking libdeflate0:amd64 (1.23-1) ... 160s Selecting previously unselected package libjbig0:amd64. 160s Preparing to unpack .../036-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 160s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 160s Selecting previously unselected package liblerc4:amd64. 160s Preparing to unpack .../037-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 160s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 160s Selecting previously unselected package libsharpyuv0:amd64. 160s Preparing to unpack .../038-libsharpyuv0_1.5.0-0.1_amd64.deb ... 160s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 160s Selecting previously unselected package libwebp7:amd64. 160s Preparing to unpack .../039-libwebp7_1.5.0-0.1_amd64.deb ... 160s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 160s Selecting previously unselected package libtiff6:amd64. 160s Preparing to unpack .../040-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 160s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 160s Selecting previously unselected package libwebpdemux2:amd64. 160s Preparing to unpack .../041-libwebpdemux2_1.5.0-0.1_amd64.deb ... 160s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 160s Selecting previously unselected package libwebpmux3:amd64. 160s Preparing to unpack .../042-libwebpmux3_1.5.0-0.1_amd64.deb ... 160s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 160s Selecting previously unselected package python3-pil:amd64. 160s Preparing to unpack .../043-python3-pil_11.1.0-5build1_amd64.deb ... 160s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 160s Selecting previously unselected package libpixman-1-0:amd64. 160s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_amd64.deb ... 160s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 160s Selecting previously unselected package libxcb-render0:amd64. 160s Preparing to unpack .../045-libxcb-render0_1.17.0-2_amd64.deb ... 160s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 160s Selecting previously unselected package libxcb-shm0:amd64. 160s Preparing to unpack .../046-libxcb-shm0_1.17.0-2_amd64.deb ... 160s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 160s Selecting previously unselected package libcairo2:amd64. 160s Preparing to unpack .../047-libcairo2_1.18.2-2_amd64.deb ... 160s Unpacking libcairo2:amd64 (1.18.2-2) ... 160s Selecting previously unselected package python3-cairo. 160s Preparing to unpack .../048-python3-cairo_1.26.1-2build2_amd64.deb ... 160s Unpacking python3-cairo (1.26.1-2build2) ... 160s Selecting previously unselected package python3-freetype. 160s Preparing to unpack .../049-python3-freetype_2.5.1-1_all.deb ... 160s Unpacking python3-freetype (2.5.1-1) ... 160s Selecting previously unselected package python3-rlpycairo. 160s Preparing to unpack .../050-python3-rlpycairo_0.3.0-3_all.deb ... 160s Unpacking python3-rlpycairo (0.3.0-3) ... 160s Selecting previously unselected package python3-reportlab. 160s Preparing to unpack .../051-python3-reportlab_4.3.1-1_all.deb ... 160s Unpacking python3-reportlab (4.3.1-1) ... 160s Selecting previously unselected package xml-core. 160s Preparing to unpack .../052-xml-core_0.19_all.deb ... 160s Unpacking xml-core (0.19) ... 160s Selecting previously unselected package w3c-sgml-lib. 160s Preparing to unpack .../053-w3c-sgml-lib_1.3-3_all.deb ... 160s Unpacking w3c-sgml-lib (1.3-3) ... 161s Selecting previously unselected package python3-biopython. 161s Preparing to unpack .../054-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 161s Unpacking python3-biopython (1.85+dfsg-2build1) ... 161s Selecting previously unselected package libjs-jquery. 161s Preparing to unpack .../055-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 161s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 161s Selecting previously unselected package libjs-jquery-ui. 161s Preparing to unpack .../056-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 161s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 161s Selecting previously unselected package fonts-lyx. 161s Preparing to unpack .../057-fonts-lyx_2.4.3-1_all.deb ... 161s Unpacking fonts-lyx (2.4.3-1) ... 161s Selecting previously unselected package python-matplotlib-data. 161s Preparing to unpack .../058-python-matplotlib-data_3.8.3-7build1_all.deb ... 161s Unpacking python-matplotlib-data (3.8.3-7build1) ... 161s Selecting previously unselected package python3-dateutil. 161s Preparing to unpack .../059-python3-dateutil_2.9.0-3_all.deb ... 161s Unpacking python3-dateutil (2.9.0-3) ... 161s Selecting previously unselected package python3-contourpy. 161s Preparing to unpack .../060-python3-contourpy_1.3.1-1build1_amd64.deb ... 161s Unpacking python3-contourpy (1.3.1-1build1) ... 161s Selecting previously unselected package python3-cycler. 161s Preparing to unpack .../061-python3-cycler_0.12.1-1_all.deb ... 161s Unpacking python3-cycler (0.12.1-1) ... 161s Selecting previously unselected package python3-brotli. 161s Preparing to unpack .../062-python3-brotli_1.1.0-2build4_amd64.deb ... 161s Unpacking python3-brotli (1.1.0-2build4) ... 161s Selecting previously unselected package python3-platformdirs. 161s Preparing to unpack .../063-python3-platformdirs_4.3.6-1_all.deb ... 161s Unpacking python3-platformdirs (4.3.6-1) ... 161s Selecting previously unselected package python3-fs. 161s Preparing to unpack .../064-python3-fs_2.4.16-7_all.deb ... 161s Unpacking python3-fs (2.4.16-7) ... 161s Selecting previously unselected package libxslt1.1:amd64. 161s Preparing to unpack .../065-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 161s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 161s Selecting previously unselected package python3-lxml:amd64. 161s Preparing to unpack .../066-python3-lxml_5.3.1-1build1_amd64.deb ... 161s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 161s Selecting previously unselected package python3-lz4. 161s Preparing to unpack .../067-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 161s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 161s Selecting previously unselected package python3-decorator. 161s Preparing to unpack .../068-python3-decorator_5.1.1-5_all.deb ... 161s Unpacking python3-decorator (5.1.1-5) ... 161s Selecting previously unselected package liblbfgsb0:amd64. 161s Preparing to unpack .../069-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 161s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 161s Selecting previously unselected package python3-scipy. 161s Preparing to unpack .../070-python3-scipy_1.14.1-4ubuntu2_amd64.deb ... 161s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 162s Selecting previously unselected package python3-mpmath. 162s Preparing to unpack .../071-python3-mpmath_1.3.0-1_all.deb ... 162s Unpacking python3-mpmath (1.3.0-1) ... 162s Selecting previously unselected package python3-sympy. 162s Preparing to unpack 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unselected package python3-pandas-lib:amd64. 163s Preparing to unpack .../083-python3-pandas-lib_2.2.3+dfsg-8build1_amd64.deb ... 163s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 163s Selecting previously unselected package python3-pandas. 163s Preparing to unpack .../084-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 163s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 164s Selecting previously unselected package cython3. 164s Preparing to unpack .../085-cython3_3.0.11+dfsg-2ubuntu2_amd64.deb ... 164s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 164s Selecting previously unselected package python3-joblib. 164s Preparing to unpack .../086-python3-joblib_1.4.2-3_all.deb ... 164s Unpacking python3-joblib (1.4.2-3) ... 164s Selecting previously unselected package python3-networkx. 164s Preparing to unpack .../087-python3-networkx_3.2.1-4ubuntu1_all.deb ... 164s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 164s Selecting previously unselected package python3-pomegranate. 164s Preparing to unpack .../088-python3-pomegranate_0.15.0-1build1_amd64.deb ... 164s Unpacking python3-pomegranate (0.15.0-1build1) ... 165s Selecting previously unselected package python3-importlib-metadata. 165s Preparing to unpack .../089-python3-importlib-metadata_8.6.1-1_all.deb ... 165s Unpacking python3-importlib-metadata (8.6.1-1) ... 165s Selecting previously unselected package python3-pyfaidx. 165s Preparing to unpack .../090-python3-pyfaidx_0.8.1.3-1_all.deb ... 165s Unpacking python3-pyfaidx (0.8.1.3-1) ... 165s Selecting previously unselected package libhtscodecs2:amd64. 165s Preparing to unpack .../091-libhtscodecs2_1.6.1-2_amd64.deb ... 165s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 165s Selecting previously unselected package libhts3t64:amd64. 165s Preparing to unpack .../092-libhts3t64_1.21+ds-1_amd64.deb ... 165s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 165s Selecting previously unselected package python3-pysam. 165s Preparing to unpack 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(6.0-28ubuntu6) ... 165s Selecting previously unselected package libpaper2:amd64. 165s Preparing to unpack .../099-libpaper2_2.2.5-0.3_amd64.deb ... 165s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 165s Selecting previously unselected package libpaper-utils. 165s Preparing to unpack .../100-libpaper-utils_2.2.5-0.3_amd64.deb ... 165s Unpacking libpaper-utils (2.2.5-0.3) ... 165s Selecting previously unselected package xdg-utils. 165s Preparing to unpack .../101-xdg-utils_1.2.1-2ubuntu1_all.deb ... 165s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 165s Selecting previously unselected package fontconfig. 165s Preparing to unpack .../102-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 165s Unpacking fontconfig (2.15.0-2ubuntu1) ... 165s Selecting previously unselected package libthai-data. 165s Preparing to unpack .../103-libthai-data_0.1.29-2build1_all.deb ... 165s Unpacking libthai-data (0.1.29-2build1) ... 165s Selecting previously unselected package libdatrie1:amd64. 165s Preparing to unpack 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166s Preparing to unpack .../115-cnvkit_0.9.12-1_all.deb ... 166s Unpacking cnvkit (0.9.12-1) ... 167s Selecting previously unselected package libgpgmepp6t64:amd64. 167s Preparing to unpack .../116-libgpgmepp6t64_1.24.2-1ubuntu2_amd64.deb ... 167s Unpacking libgpgmepp6t64:amd64 (1.24.2-1ubuntu2) ... 167s Selecting previously unselected package libpoppler147:amd64. 167s Preparing to unpack .../117-libpoppler147_25.03.0-2_amd64.deb ... 167s Unpacking libpoppler147:amd64 (25.03.0-2) ... 167s Selecting previously unselected package poppler-utils. 167s Preparing to unpack .../118-poppler-utils_25.03.0-2_amd64.deb ... 167s Unpacking poppler-utils (25.03.0-2) ... 167s Setting up libhtscodecs2:amd64 (1.6.1-2) ... 167s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 167s Setting up liblcms2-2:amd64 (2.16-2) ... 167s Setting up libpixman-1-0:amd64 (0.44.0-3) ... 167s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ... 167s Setting up libgpgmepp6t64:amd64 (1.24.2-1ubuntu2) ... 167s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 167s Setting up python3-importlib-metadata (8.6.1-1) ... 167s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 167s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 167s Setting up python3-joblib (1.4.2-3) ... 167s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 167s Setting up libxcb-render0:amd64 (1.17.0-2) ... 167s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 167s Setting up fonts-lyx (2.4.3-1) ... 167s Setting up unzip (6.0-28ubuntu6) ... 167s Setting up python3-threadpoolctl (3.1.0-1) ... 167s Setting up x11-common (1:7.7+23ubuntu3) ... 168s Setting up libdeflate0:amd64 (1.23-1) ... 168s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 168s Setting up python3-pytz (2025.1-3) ... 168s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 168s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 168s Setting up python3-freetype (2.5.1-1) ... 168s Setting up python3-networkx (3.2.1-4ubuntu1) ... 169s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 169s Setting up python3-platformdirs (4.3.6-1) ... 169s Setting up python3-tz (2025.1-3) ... 169s Setting up python3-fs (2.4.16-7) ... 169s Setting up unicode-data (15.1.0-1) ... 169s Setting up python3-decorator (5.1.1-5) ... 169s Setting up zip (3.0-14ubuntu2) ... 169s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 169s Setting up libblas3:amd64 (3.12.1-2) ... 169s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 169s Setting up python3-packaging (24.2-1) ... 170s Setting up python3-brotli (1.1.0-2build4) ... 170s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 170s Setting up python3-cycler (0.12.1-1) ... 170s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 170s Setting up fonts-dejavu-mono (2.37-8) ... 170s Setting up python3-kiwisolver (1.4.7-3build1) ... 170s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 170s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 171s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 171s Setting up fonts-dejavu-core (2.37-8) ... 171s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 171s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 171s Setting up libwebp7:amd64 (1.5.0-0.1) ... 171s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 171s Setting up libhts3t64:amd64 (1.21+ds-1) ... 171s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 171s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 171s Setting up libthai-data (0.1.29-2build1) ... 171s Setting up python3-dateutil (2.9.0-3) ... 171s Setting up sgml-base (1.31) ... 171s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 171s Setting up libpaper2:amd64 (2.2.5-0.3) ... 171s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 171s Setting up python3-mpmath (1.3.0-1) ... 171s Setting up python-matplotlib-data (3.8.3-7build1) ... 171s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 171s Setting up xdg-utils (1.2.1-2ubuntu1) ... 171s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 171s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 171s Setting up python3-pyfaidx (0.8.1.3-1) ... 171s Setting up python3-sympy (1.13.3-5) ... 176s Setting up libice6:amd64 (2:1.1.1-1) ... 176s Setting up liblapack3:amd64 (3.12.1-2) ... 176s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 176s Setting up python3-pysam (0.23.0+ds-1build1) ... 176s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 177s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 177s Setting up libpaper-utils (2.2.5-0.3) ... 177s Setting up xfonts-utils (1:7.7+7) ... 177s Setting up libthai0:amd64 (0.1.29-2build1) ... 177s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 177s Setting up libraqm0:amd64 (0.10.2-1) ... 177s Setting up python3-numpy (1:2.2.3+ds-5) ... 178s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 178s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 178s Setting up xml-core (0.19) ... 179s Setting up python3-contourpy (1.3.1-1build1) ... 179s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 179s Setting up libsm6:amd64 (2:1.2.4-1) ... 179s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 179s Setting up fontconfig (2.15.0-2ubuntu1) ... 181s Regenerating fonts cache... done. 181s Setting up libxft2:amd64 (2.3.6-1build1) ... 181s Setting up python3-scipy (1.14.1-4ubuntu2) ... 184s Setting up libpoppler147:amd64 (25.03.0-2) ... 184s Setting up python3-pomegranate (0.15.0-1build1) ... 184s Setting up libtk8.6:amd64 (8.6.16-1) ... 184s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 184s Setting up libpango-1.0-0:amd64 (1.56.2-1) ... 184s Setting up python3.12-tk (3.12.9-1) ... 184s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 184s Setting up fonts-urw-base35 (20200910-8) ... 184s Setting up libcairo2:amd64 (1.18.2-2) ... 184s Setting up python3.13-tk (3.13.2-2) ... 184s Setting up python3-pil:amd64 (11.1.0-5build1) ... 184s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 188s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 188s Setting up python3-sklearn (1.4.2+dfsg-8) ... 190s Setting up poppler-utils (25.03.0-2) ... 190s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 190s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 190s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 190s Setting up python3-cairo (1.26.1-2build2) ... 190s Setting up blt (2.5.3+dfsg-8) ... 190s Setting up python3-tk:amd64 (3.13.1-1) ... 190s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 190s Setting up python3-rlpycairo (0.3.0-3) ... 190s Setting up r-base-core (4.4.3-1) ... 190s Creating config file /etc/R/Renviron with new version 190s Setting up python3-reportlab (4.3.1-1) ... 191s Setting up r-bioc-biocgenerics (0.52.0-2) ... 191s Setting up r-bioc-dnacopy (1.80.0-2) ... 191s Setting up python3-fonttools (4.55.3-2build1) ... 192s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 192s Setting up python3-matplotlib (3.8.3-7build1) ... 193s Processing triggers for libc-bin (2.41-1ubuntu1) ... 193s Processing triggers for man-db (2.13.0-1) ... 194s Processing triggers for install-info (7.1.1-1) ... 194s Processing triggers for sgml-base (1.31) ... 195s Setting up w3c-sgml-lib (1.3-3) ... 222s Setting up python3-biopython (1.85+dfsg-2build1) ... 222s Setting up cnvkit (0.9.12-1) ... 223s autopkgtest [01:42:46]: testbed environment configured for cross-architecture building 223s autopkgtest [01:42:46]: test run-unit-test: [----------------------- 224s cnvkit.py batch -n -f formats/chrM-Y-trunc.hg19.fa -m wgs formats/na12878-chrM-Y-trunc.bam -d build 226s CNVkit 0.9.12 226s WGS protocol: recommend '--annotate' option (e.g. refFlat.txt) to help locate genes in output files. 226s chrM: Scanning for accessible regions 226s Accessible region chrM:0-121 (size 121) 226s Accessible region chrM:122-1271 (size 1149) 226s Accessible region chrM:1274-1288 (size 14) 226s Accessible region chrM:1289-1547 (size 258) 226s Accessible region chrM:1553-16571 (size 15018) 226s chrY: Scanning for accessible regions 226s Accessible region chrY:500-14900 (size 14400) 226s Accessible region chrY:15600-22966 (size 7366) 226s chrY: Joining over small gaps 226s Joining chrY 500-14900 and 15600-22966 (gap size 700) 226s Wrote chrM-Y-trunc.hg19.bed with 1 regions 226s Detected file format: bed 226s Splitting large targets 226s Created directory build 226s Wrote build/chrM-Y-trunc.hg19.target.bed with 4 regions 226s Wrote build/chrM-Y-trunc.hg19.antitarget.bed with 0 regions 226s Building a flat reference... 226s Detected file format: bed 226s Calculating GC and RepeatMasker content in formats/chrM-Y-trunc.hg19.fa ... 226s Extracting sequences from chromosome chrY 226s Wrote build/reference.cnn with 4 regions 226s Running 1 samples in serial 226s Running the CNVkit pipeline on formats/na12878-chrM-Y-trunc.bam ... 226s Indexing BAM file formats/na12878-chrM-Y-trunc.bam 226s Processing reads in na12878-chrM-Y-trunc.bam 226s Time: 0.007 seconds (5310 reads/sec, 574 bins/sec) 226s Summary: #bins=4, #reads=37, mean=9.2500, min=0.0, max=21.0 226s Percent reads in regions: 0.063 (of 58636 mapped) 226s Wrote build/na12878-chrM-Y-trunc.targetcoverage.cnn with 4 regions 226s Skip processing na12878-chrM-Y-trunc.bam with empty regions file build/chrM-Y-trunc.hg19.antitarget.bed 226s Wrote build/na12878-chrM-Y-trunc.antitargetcoverage.cnn with 0 regions 226s Processing target: na12878-chrM-Y-trunc 226s Keeping 4 of 4 bins 226s Correcting for GC bias... 226s Processing antitarget: na12878-chrM-Y-trunc 226s Wrote build/na12878-chrM-Y-trunc.cnr with 4 regions 226s Segmenting build/na12878-chrM-Y-trunc.cnr ... 226s Segmenting with method 'cbs', significance threshold 1e-06, in 1 processes 226s Post-processing build/na12878-chrM-Y-trunc.cns ... 226s Wrote build/na12878-chrM-Y-trunc.cns with 1 regions 226s Applying filter 'ci' 226s Filtered by 'ci' from 1 to 1 rows 226s Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 226s Wrote build/na12878-chrM-Y-trunc.call.cns with 1 regions 226s Significant hits in 4/4 bins (100%) 226s Wrote build/na12878-chrM-Y-trunc.bintest.cns with 4 regions 226s cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/ 228s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 228s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 228s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 228s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 228s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 228s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 228s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 228s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 228s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 228s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 230s Number of target and antitarget files: 3, 3 230s No FASTA reference genome provided; skipping GC, RM calculations 230s Sample sex not provided; inferring from samples. 230s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 230s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 230s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 230s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 230s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 230s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 230s Loading build/p2-20_5.targetcoverage.cnn 230s Correcting for GC bias for p2-20_5... 230s Correcting for density bias for p2-20_5... 230s Loading build/p2-5_5.targetcoverage.cnn 230s Correcting for GC bias for p2-5_5... 230s Correcting for density bias for p2-5_5... 230s Loading build/p2-9_5.targetcoverage.cnn 230s Correcting for GC bias for p2-9_5... 230s Correcting for density bias for p2-9_5... 230s Loading build/p2-20_5.antitargetcoverage.cnn 230s Correcting for GC bias for p2-20_5... 230s Loading build/p2-5_5.antitargetcoverage.cnn 230s Correcting for GC bias for p2-5_5... 231s Loading build/p2-9_5.antitargetcoverage.cnn 231s Correcting for GC bias for p2-9_5... 231s Calculating average bin coverages 237s Calculating bin spreads 238s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 238s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 238s " chr1:2435319-2436685 log2=-0.709 spread=0.503 238s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 238s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 238s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 238s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 238s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 238s " chr1:120611883-120612051 log2=0.070 spread=0.050 238s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 238s " chr1:156842391-156842479 log2=-0.398 spread=0.290 238s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 238s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 238s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 238s " chr1:183481886-183481951 log2=-0.040 spread=0.119 238s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 238s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 238s " chr1:243800859-243801066 log2=0.023 spread=0.063 238s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 238s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 238s " chr2:25536716-25536891 log2=0.702 spread=0.033 238s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 238s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 238s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 238s REL chr2:61108881-61109061 log2=1.026 spread=0.559 238s " chr2:61128072-61128256 log2=0.115 spread=0.173 238s " chr2:61145275-61145462 log2=0.014 spread=0.099 238s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 238s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 238s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 238s " chr2:128095237-128095425 log2=0.215 spread=0.212 238s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 238s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 238s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 238s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 238s " chr3:97160189-97160367 log2=-0.050 spread=0.191 238s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 238s " chr3:142286854-142287031 log2=-0.076 spread=0.116 238s GAK chr4:896278-896357 log2=-1.505 spread=1.261 238s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 238s " chr4:1803044-1803507 log2=-0.073 spread=0.117 238s " chr4:1808792-1809022 log2=0.252 spread=0.108 238s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 238s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 238s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 238s " chr4:178514600-178514725 log2=-0.098 spread=0.096 238s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 238s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 238s " chr5:1295312-1295381 log2=-0.690 spread=0.462 238s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 238s " chr5:25519857-25520034 log2=-0.015 spread=0.095 238s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 238s " chr5:38962338-38962525 log2=0.005 spread=0.019 238s " chr5:38966685-38966862 log2=0.006 spread=0.165 238s " chr5:38978620-38978763 log2=0.040 spread=0.030 238s " chr5:39074133-39074327 log2=-0.158 spread=0.139 238s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 238s " chr5:51030131-51030313 log2=-0.034 spread=0.192 238s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 238s " chr5:56168412-56168590 log2=0.479 spread=0.038 238s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 238s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 238s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 238s " chr5:86637023-86637168 log2=0.054 spread=0.111 238s " chr5:86642414-86642592 log2=0.254 spread=0.162 238s " chr5:86648912-86649096 log2=0.092 spread=0.062 238s " chr5:86670598-86670778 log2=0.222 spread=0.198 238s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 238s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 238s APC chr5:112101965-112102138 log2=0.104 spread=0.217 238s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 238s " chr5:170837567-170837631 log2=0.085 spread=0.349 238s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 238s " chr5:180046203-180046404 log2=-1.531 spread=0.722 238s " chr5:180076418-180076603 log2=-2.224 spread=1.416 238s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 238s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 238s " chr6:31939599-31940313 log2=-19.582 spread=0.181 238s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 238s " chr6:31946632-31946824 log2=-20.052 spread=0.088 238s " chr6:31947142-31947366 log2=-20.114 spread=0.066 238s " chr6:31948176-31948360 log2=-19.982 spread=0.149 238s " chr6:31948382-31948612 log2=-19.757 spread=0.165 238s " chr6:31948730-31949253 log2=-20.048 spread=0.014 238s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 238s " chr6:32164046-32164227 log2=-19.755 spread=0.189 238s " chr6:32164652-32164888 log2=-19.984 spread=0.154 238s " chr6:32165021-32165403 log2=-19.625 spread=0.196 238s " chr6:32166163-32166545 log2=-20.043 spread=0.072 238s " chr6:32166648-32166962 log2=-3.514 spread=5.742 238s " chr6:32168554-32168821 log2=-19.601 spread=0.197 238s " chr6:32168844-32169306 log2=-19.683 spread=0.166 238s " chr6:32169801-32170391 log2=-19.405 spread=0.205 238s " chr6:32171492-32171691 log2=-20.095 spread=0.101 238s " chr6:32171861-32172198 log2=-3.141 spread=7.288 238s " chr6:32178478-32178749 log2=-19.927 spread=0.164 238s " chr6:32180197-32180441 log2=-10.902 spread=9.532 238s " chr6:32180544-32180722 log2=-19.675 spread=0.186 238s " chr6:32180857-32181062 log2=-19.562 spread=0.227 238s " chr6:32181411-32181646 log2=-19.966 spread=0.171 238s " chr6:32181832-32182066 log2=-19.961 spread=0.172 238s " chr6:32182948-32183194 log2=-19.935 spread=0.168 238s " chr6:32184667-32185079 log2=-19.923 spread=0.165 238s " chr6:32185720-32185919 log2=-19.707 spread=0.197 238s " chr6:32187317-32187601 log2=-19.765 spread=0.173 238s " chr6:32187871-32188094 log2=-19.660 spread=0.188 238s " chr6:32188127-32188451 log2=-19.622 spread=0.169 238s " chr6:32188481-32188693 log2=-19.902 spread=0.132 238s " chr6:32188704-32189133 log2=-19.501 spread=0.193 238s " chr6:32190258-32190616 log2=-19.570 spread=0.209 238s " chr6:32190724-32190908 log2=-19.540 spread=0.232 238s " chr6:32191570-32191668 log2=-19.773 spread=0.178 238s " chr6:32191676-32191753 log2=-19.374 spread=0.201 238s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 238s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 238s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 238s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 238s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 238s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 238s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 238s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 238s " chr6:128316545-128316699 log2=-0.070 spread=0.050 238s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 238s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 238s " chr6:157099442-157099991 log2=-0.846 spread=0.504 238s " chr6:157100042-157100634 log2=-1.570 spread=0.825 238s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 238s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 238s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 238s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 238s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 238s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 238s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 238s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 238s " chr7:98491365-98491541 log2=0.209 spread=0.153 238s " chr7:98493314-98493496 log2=0.389 spread=0.207 238s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 238s " chr7:128829048-128829358 log2=-0.474 spread=0.315 238s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 238s " chr7:140484736-140484912 log2=0.081 spread=0.150 238s " chr7:140487956-140488430 log2=-0.089 spread=0.142 238s " chr7:140493336-140493442 log2=-0.340 spread=0.283 238s " chr7:140624315-140624540 log2=-0.497 spread=0.342 238s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 238s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 238s " chr8:30941153-30941335 log2=0.079 spread=0.294 238s " chr8:30942625-30942802 log2=0.044 spread=0.247 238s " chr8:30947918-30948092 log2=0.151 spread=0.124 238s " chr8:31000128-31000252 log2=-0.099 spread=0.098 238s " chr8:31001006-31001182 log2=-0.002 spread=0.062 238s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 238s " chr8:37698557-37699898 log2=-0.612 spread=0.029 238s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 238s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 238s " chr8:48845528-48845758 log2=0.056 spread=0.196 238s " chr8:48866846-48867043 log2=-0.067 spread=0.097 238s " chr8:48868369-48868526 log2=-0.239 spread=0.174 238s " chr8:48872485-48872722 log2=-0.636 spread=0.464 238s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 238s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 238s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 238s " chr9:2101491-2101640 log2=0.244 spread=0.104 238s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 238s " chr9:5067014-5067883 log2=0.146 spread=0.089 238s " chr9:5068184-5070306 log2=0.133 spread=0.092 238s " chr9:5076944-5077152 log2=0.046 spread=0.137 238s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 238s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 238s " chr9:21986759-21986899 log2=0.058 spread=0.175 238s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 238s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 238s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 238s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 238s " chr9:87425375-87425452 log2=0.494 spread=0.066 238s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 238s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 238s " chr9:139250747-139251032 log2=-0.223 spread=0.273 238s " chr9:139252418-139252703 log2=-0.512 spread=0.264 238s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 238s " chr9:139417262-139417677 log2=-0.173 spread=0.191 238s " chr9:139440110-139440287 log2=-1.257 spread=0.500 238s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 238s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 238s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 238s " chr10:43600360-43600677 log2=-0.341 spread=0.222 238s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 238s " chr10:89685254-89685374 log2=0.244 spread=0.259 238s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 238s " chr10:93579008-93579121 log2=0.166 spread=0.220 238s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 238s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 238s " chr10:112679716-112679934 log2=-0.008 spread=0.028 238s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 238s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 238s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 238s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 238s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 238s " chr11:94170270-94170454 log2=0.095 spread=0.285 238s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 238s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 238s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 238s " chr11:108164020-108164234 log2=-0.056 spread=0.040 238s " chr11:108217986-108218135 log2=0.359 spread=0.277 238s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 238s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 238s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 238s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 238s " chr12:25391004-25391186 log2=0.368 spread=0.128 238s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 238s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 238s " chr12:51206782-51207287 log2=-0.012 spread=0.101 238s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 238s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 238s " chr13:26970356-26970536 log2=0.137 spread=0.121 238s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 238s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 238s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 238s " chr13:32903506-32903689 log2=0.019 spread=0.232 238s " chr13:32918645-32918823 log2=0.158 spread=0.114 238s " chr13:32920899-32921077 log2=0.014 spread=0.247 238s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 238s " chr13:48919164-48919369 log2=0.025 spread=0.094 238s " chr13:48921877-48922044 log2=0.106 spread=0.147 238s " chr13:48923026-48923204 log2=0.360 spread=0.016 238s " chr13:48938965-48939147 log2=0.084 spread=0.356 238s " chr13:48941578-48941767 log2=0.238 spread=0.212 238s " chr13:48947486-48947665 log2=0.025 spread=0.126 238s " chr13:48954166-48954251 log2=0.061 spread=0.273 238s " chr13:49037815-49038005 log2=0.063 spread=0.062 238s " chr13:49047410-49047589 log2=0.053 spread=0.170 238s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 238s " chr13:85527771-85527948 log2=0.007 spread=0.222 238s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 238s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 238s " chr13:110438332-110438432 log2=-3.643 spread=2.325 238s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 238s " chr14:20291466-20291612 log2=0.697 spread=0.248 238s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 238s " chr14:36989195-36989373 log2=0.023 spread=0.162 238s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 238s " chr14:50619741-50619923 log2=0.003 spread=0.272 238s " chr14:50697856-50698044 log2=0.277 spread=0.334 238s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 238s " chr14:71275790-71275923 log2=-2.815 spread=1.938 238s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 238s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 238s " chr15:38544477-38545455 log2=-0.348 spread=0.179 238s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 238s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 238s " chr15:41803968-41804185 log2=-2.202 spread=0.188 238s " chr15:41804261-41804494 log2=-0.402 spread=0.392 238s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 238s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 238s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 238s " chr16:2611404-2611585 log2=-5.171 spread=1.963 238s " chr16:2611721-2611943 log2=-11.810 spread=9.172 238s " chr16:2615504-2615725 log2=-20.113 spread=0.007 238s " chr16:2616307-2616486 log2=-20.054 spread=0.072 238s " chr16:2631267-2631414 log2=-20.009 spread=0.061 238s " chr16:2631583-2631734 log2=-20.089 spread=0.090 238s " chr16:2633363-2633616 log2=-20.101 spread=0.089 238s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 238s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 238s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 238s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 238s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 238s " chr16:50826460-50826650 log2=0.239 spread=0.204 238s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 238s " chr16:60005694-60005857 log2=-0.366 spread=0.298 238s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 238s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 238s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 238s " chr17:12011053-12011253 log2=0.028 spread=0.232 238s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 238s " chr17:29496854-29497046 log2=0.226 spread=0.193 238s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 238s " chr17:30519172-30519355 log2=0.163 spread=0.289 238s " chr17:30525911-30526093 log2=-0.157 spread=0.046 238s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 238s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 238s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 238s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 238s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 238s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 238s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 238s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 238s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 238s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 238s " chr19:2210351-2210545 log2=-0.860 spread=0.261 238s " chr19:2226130-2227152 log2=-0.113 spread=0.120 238s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 238s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 238s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 238s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 238s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 238s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 238s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 238s " chr19:15311544-15311749 log2=-1.887 spread=1.202 238s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 238s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 238s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 238s " chr19:33792774-33793010 log2=-1.781 spread=0.127 238s " chr19:33793014-33793356 log2=-0.541 spread=0.385 238s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 238s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 238s " chr19:45873698-45873881 log2=-0.522 spread=0.327 238s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 238s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 238s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 238s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 238s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 238s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 238s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 238s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 238s " chr21:36265140-36265318 log2=0.042 spread=0.039 238s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 238s " chr22:29115325-29115465 log2=0.055 spread=0.390 238s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 238s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 238s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 238s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 238s " chrX:1317372-1317594 log2=-21.121 spread=0.049 238s " chrX:1321225-1321435 log2=-20.851 spread=0.196 238s " chrX:1325274-1325530 log2=-21.121 spread=0.011 238s " chrX:1327651-1327830 log2=-21.000 spread=0.029 238s " chrX:1331391-1331576 log2=-21.018 spread=0.052 238s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 238s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 238s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 238s " chrX:123185143-123185290 log2=-1.018 spread=0.062 238s " chrX:123202378-123202544 log2=-0.959 spread=0.103 238s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 238s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 238s " chrY:9008607-9008759 log2=-1.012 spread=0.097 238s " chrY:13131970-13132039 log2=-1.004 spread=0.074 238s " chrY:19506485-19506650 log2=-1.018 spread=0.034 238s " chrY:21033918-21034071 log2=-1.013 spread=0.057 238s " chrY:28463435-28463622 log2=-0.952 spread=0.039 238s " chrY:28514033-28514208 log2=-0.992 spread=0.026 238s Antitargets: 108 (0.8597%) bins failed filters 238s Wrote build/reference-picard.cnn with 19209 regions 239s cnvkit.py fix build/p2-5_5.targetcoverage.cnn build/p2-5_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-5_5.cnr 240s Processing target: p2-5_5 240s Keeping 6308 of 6646 bins 240s Correcting for GC bias... 240s Correcting for density bias... 240s Processing antitarget: p2-5_5 241s Keeping 12455 of 12563 bins 241s Correcting for GC bias... 241s WARNING: Skipping correction for RepeatMasker bias 241s Targets are 1.18 x more variable than antitargets 241s Wrote build/p2-5_5.cnr with 18763 regions 241s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 243s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 243s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 243s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 244s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 245s cnvkit.py fix build/p2-9_2.targetcoverage.cnn build/p2-9_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-9_2.cnr 246s Processing target: p2-9_2 246s Keeping 6308 of 6646 bins 246s Correcting for GC bias... 246s Correcting for density bias... 246s Processing antitarget: p2-9_2 246s Keeping 12455 of 12563 bins 246s Correcting for GC bias... 246s WARNING: Skipping correction for RepeatMasker bias 247s Targets are 1.72 x more variable than antitargets 247s Wrote build/p2-9_2.cnr with 18763 regions 247s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 250s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 250s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 250s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 250s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 251s cnvkit.py fix build/p2-20_1.targetcoverage.cnn build/p2-20_1.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_1.cnr 252s Processing target: p2-20_1 252s Keeping 6308 of 6646 bins 252s Correcting for GC bias... 252s Correcting for density bias... 252s Processing antitarget: p2-20_1 252s Keeping 12455 of 12563 bins 252s Correcting for GC bias... 253s WARNING: Skipping correction for RepeatMasker bias 253s Targets are 1.12 x more variable than antitargets 253s Wrote build/p2-20_1.cnr with 18763 regions 253s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 254s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 255s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 255s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 256s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 257s cnvkit.py fix build/p2-20_2.targetcoverage.cnn build/p2-20_2.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_2.cnr 258s Processing target: p2-20_2 258s Keeping 6308 of 6646 bins 258s Correcting for GC bias... 258s Correcting for density bias... 258s Processing antitarget: p2-20_2 258s Keeping 12455 of 12563 bins 258s Correcting for GC bias... 258s WARNING: Skipping correction for RepeatMasker bias 259s Targets are 1.10 x more variable than antitargets 259s Wrote build/p2-20_2.cnr with 18763 regions 259s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 260s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 260s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 261s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 262s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 262s cnvkit.py fix build/p2-20_3.targetcoverage.cnn build/p2-20_3.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_3.cnr 264s Processing target: p2-20_3 264s Keeping 6308 of 6646 bins 264s Correcting for GC bias... 264s Correcting for density bias... 264s Processing antitarget: p2-20_3 264s Keeping 12455 of 12563 bins 264s Correcting for GC bias... 264s WARNING: Skipping correction for RepeatMasker bias 264s Antitargets are 1.09 x more variable than targets 265s Wrote build/p2-20_3.cnr with 18763 regions 265s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 266s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 266s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 267s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 268s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 268s cnvkit.py fix build/p2-20_4.targetcoverage.cnn build/p2-20_4.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_4.cnr 270s Processing target: p2-20_4 270s Keeping 6308 of 6646 bins 270s Correcting for GC bias... 270s Correcting for density bias... 270s Processing antitarget: p2-20_4 270s Keeping 12455 of 12563 bins 270s Correcting for GC bias... 270s WARNING: Skipping correction for RepeatMasker bias 270s Targets are 1.43 x more variable than antitargets 271s Wrote build/p2-20_4.cnr with 18763 regions 271s cnvkit.py fix build/p2-20_5.targetcoverage.cnn build/p2-20_5.antitargetcoverage.cnn build/reference-picard.cnn -o build/p2-20_5.cnr 272s Processing target: p2-20_5 272s Keeping 6308 of 6646 bins 272s Correcting for GC bias... 272s Correcting for density bias... 272s Processing antitarget: p2-20_5 273s Keeping 12455 of 12563 bins 273s Correcting for GC bias... 273s WARNING: Skipping correction for RepeatMasker bias 273s Targets are 2.50 x more variable than antitargets 273s Wrote build/p2-20_5.cnr with 18763 regions 273s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 274s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 281s Dropped 8 / 49 bins on chromosome chrY 281s Wrote build/p2-5_5.cns with 71 regions 282s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 283s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 285s Dropped 1 / 949 bins on chromosome chr6 290s Dropped 27 / 49 bins on chromosome chrY 290s Wrote build/p2-9_2.cns with 103 regions 290s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 292s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 299s Dropped 6 / 49 bins on chromosome chrY 299s Wrote build/p2-20_1.cns with 121 regions 299s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 301s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 307s Dropped 7 / 49 bins on chromosome chrY 308s Wrote build/p2-20_2.cns with 117 regions 308s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 309s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 316s Dropped 11 / 49 bins on chromosome chrY 316s Wrote build/p2-20_3.cns with 64 regions 316s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 318s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 325s Dropped 8 / 49 bins on chromosome chrY 325s Wrote build/p2-20_4.cns with 143 regions 325s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 327s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 333s Smoothing overshot at 1 / 123 indices: (-0.30060035404086394, 0.32508880185194683) vs. original (-0.363302, 0.311218) 334s Dropped 6 / 49 bins on chromosome chrY 334s Wrote build/p2-20_5.cns with 120 regions 334s cnvkit.py scatter -s build/p2-5_5.cns build/p2-5_5.cnr -t --y-min=-2.5 -o p2-5_5-scatter.pdf 337s Wrote p2-5_5-scatter.pdf 337s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -t --y-min=-2.5 -o p2-9_2-scatter.pdf 339s Smoothing overshot at 3 / 97 indices: (-19.90010586862171, -3.3099069223720505) vs. original (-19.294, -0.16431) 340s Wrote p2-9_2-scatter.pdf 340s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 342s Showing 1480 probes and 0 selected genes in region chr1 342s Wrote p2-9_2-chr1-scatter.pdf 342s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 344s Showing 201 probes and 0 selected genes in region chr21 344s Wrote p2-9_2-chr21-scatter.pdf 344s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c 'chr9:150000-45000000' -o p2-9_2-chr9p-scatter.pdf 346s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 346s Wrote p2-9_2-chr9p-scatter.pdf 346s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -g SMARCA2,PTPRD -w 4e6 -o p2-9_2-SMARCA2-PTPRD-scatter.pdf 348s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 348s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 348s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -l regions.bed -o p2-9_2-bed_regions-scatter.pdf 349s Detected file format: bed 349s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 350s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 350s which pdfunite && pdfunite p2-5_5-scatter.pdf p2-9_2-scatter.pdf p2-9_2-chr1-scatter.pdf p2-9_2-chr21-scatter.pdf p2-9_2-chr9p-scatter.pdf p2-9_2-SMARCA2-PTPRD-scatter.pdf p2-9_2-bed_regions-scatter.pdf all-scatters.pdf || touch all-scatters.pdf 350s /usr/bin/pdfunite 350s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 351s Treating sample p2-5_5 as female 359s Wrote p2-5_5-diagram.pdf 359s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 360s Treating sample p2-9_2 as female 368s Wrote p2-9_2-diagram.pdf 368s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 369s Treating sample p2-20_1 as female 377s Wrote p2-20_1-diagram.pdf 377s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 378s Treating sample p2-20_2 as female 386s Wrote p2-20_2-diagram.pdf 386s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 387s Treating sample p2-5_5 as female 388s Wrote p2-5_5-cbs-diagram.pdf 388s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 389s Treating sample p2-9_2 as female 389s Wrote p2-9_2-cbs-diagram.pdf 390s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 391s Treating sample p2-20_1 as female 391s Wrote p2-20_1-cbs-diagram.pdf 391s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 393s Treating sample p2-20_2 as female 393s Wrote p2-20_2-cbs-diagram.pdf 393s cnvkit.py diagram -y --segment=build/p2-5_5.cns build/p2-5_5.cnr -t 0.3 -o p2-5_5-both-diagram.pdf 395s Treating sample p2-5_5 as female 399s Wrote p2-5_5-both-diagram.pdf 400s cnvkit.py diagram -y --segment=build/p2-9_2.cns build/p2-9_2.cnr -t 0.3 -o p2-9_2-both-diagram.pdf 401s Treating sample p2-9_2 as female 406s Wrote p2-9_2-both-diagram.pdf 406s cnvkit.py diagram -y --segment=build/p2-20_1.cns build/p2-20_1.cnr -t 0.3 -o p2-20_1-both-diagram.pdf 408s Treating sample p2-20_1 as female 412s Wrote p2-20_1-both-diagram.pdf 413s cnvkit.py diagram -y --segment=build/p2-20_2.cns build/p2-20_2.cnr -t 0.3 -o p2-20_2-both-diagram.pdf 414s Treating sample p2-20_2 as female 419s Wrote p2-20_2-both-diagram.pdf 419s which pdfunite && pdfunite p2-5_5-diagram.pdf p2-9_2-diagram.pdf p2-20_1-diagram.pdf p2-20_2-diagram.pdf p2-5_5-cbs-diagram.pdf p2-9_2-cbs-diagram.pdf p2-20_1-cbs-diagram.pdf p2-20_2-cbs-diagram.pdf p2-5_5-both-diagram.pdf p2-9_2-both-diagram.pdf p2-20_1-both-diagram.pdf p2-20_2-both-diagram.pdf all-diagrams.pdf || touch all-diagrams.pdf 419s /usr/bin/pdfunite 419s cnvkit.py heatmap build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -y -o heatmap-picard.pdf 421s Treating sample p2-5_5 as female 421s Treating sample p2-9_2 as female 421s Treating sample p2-20_1 as female 421s Treating sample p2-20_2 as female 421s Treating sample p2-20_3 as female 421s Treating sample p2-20_4 as female 421s Treating sample p2-20_5 as female 422s Wrote heatmap-picard.pdf 423s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 424s Found 14 gene breakpoints 424s Wrote p2-9_2-breaks.txt 425s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 426s Treating sample p2-9_2 as female 427s Found 323 gene-level gains and losses 427s Wrote p2-9_2-genemetrics.txt 428s cnvkit.py sex -y build/p2-5_5.cnr build/p2-5_5.cns build/p2-9_2.cnr build/p2-9_2.cns build/p2-20_5.cnr build/p2-20_5.cns -o gender-picard.txt 429s Wrote gender-picard.txt 429s cnvkit.py export cdt build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all.cdt 433s Wrote p2-all.cdt 434s cnvkit.py export jtv build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -o p2-all-jtv.txt 438s Wrote p2-all-jtv.txt 438s cnvkit.py export seg build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-all.seg 439s Wrote p2-all.seg 440s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 441s Wrote p2-9_2.nexus 442s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 443s Selected test sample NA12882 and control sample NA12878 443s Loaded 3654 records; skipped: 514 somatic, 394 depth 443s Kept 2631 heterozygous of 3654 VCF records 446s Placed 705 variants into 18763 bins 446s Wrote p2-9_2.nexus-ogt 446s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 448s Treating sample p2-5_5 as female 448s Rescaling sample with purity 0.65, ploidy 2 448s Wrote build/p2-5_5.call.cns with 71 regions 448s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 449s Treating sample p2-9_2 as female 449s Rescaling sample with purity 0.65, ploidy 2 449s Wrote build/p2-9_2.call.cns with 103 regions 450s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 451s Treating sample p2-20_1 as female 451s Rescaling sample with purity 0.65, ploidy 2 451s Wrote build/p2-20_1.call.cns with 121 regions 452s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 456s Treating sample p2-20_2 as female 456s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 456s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 456s Rescaling sample with purity 0.65, ploidy 2 456s Wrote build/p2-20_2.call.cns with 117 regions 456s Treating sample p2-20_3 as female 456s Rescaling sample with purity 0.65, ploidy 2 456s Wrote build/p2-20_3.call.cns with 64 regions 456s Treating sample p2-20_4 as female 456s Rescaling sample with purity 0.65, ploidy 2 456s Wrote build/p2-20_4.call.cns with 143 regions 457s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 458s Treating sample p2-20_5 as female 458s Rescaling sample with purity 0.65, ploidy 2 458s Wrote build/p2-20_5.call.cns with 120 regions 458s cnvkit.py export bed build/p2-5_5.call.cns build/p2-9_2.call.cns build/p2-20_1.call.cns build/p2-20_2.call.cns build/p2-20_3.call.cns build/p2-20_4.call.cns build/p2-20_5.call.cns -y --show variant -o p2-all.bed 460s Treating sample p2-5_5.call as female 460s Treating sample p2-9_2.call as female 460s Treating sample p2-20_1.call as female 460s Treating sample p2-20_2.call as female 460s Treating sample p2-20_3.call as female 460s Treating sample p2-20_4.call as female 460s Treating sample p2-20_5.call as female 460s Wrote p2-all.bed 460s cnvkit.py export vcf -o p2-9_2.vcf -y --cnr build/p2-9_2.cnr build/p2-9_2.call.cns -y -o p2-9_2.vcf 461s Treating sample p2-9_2.call as female 462s Wrote p2-9_2.vcf 462s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 463s Wrote p2-9_2.theta2.input 464s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 464s --mean --median --mode --t-test \ 464s --stdev --mad --mse --iqr --bivar \ 464s --ci --pi --sem --smooth-bootstrap 466s Wrote p2-9_2-segmetrics.cns with 103 regions 466s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 466s --ci -b 50 -a 0.5 468s Wrote p2-5_5-segmetrics.cns with 71 regions 468s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 469s Wrote p2-5_5-metrics.tsv 470s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 471s Wrote p2-9_2-metrics.tsv 472s cnvkit.py metrics build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr -s build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns -o p2-20-metrics.tsv 473s Wrote p2-20-metrics.tsv 474s PASS 474s autopkgtest [01:46:57]: test run-unit-test: -----------------------] 474s autopkgtest [01:46:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 474s run-unit-test PASS 474s autopkgtest [01:46:57]: test pybuild-autopkgtest: preparing testbed 535s autopkgtest [01:47:58]: testbed dpkg architecture: amd64 535s autopkgtest [01:47:58]: testbed apt version: 2.9.31ubuntu1 535s autopkgtest [01:47:58]: @@@@@@@@@@@@@@@@@@@@ test bed setup 535s autopkgtest [01:47:58]: testbed release detected to be: plucky 535s autopkgtest [01:47:58]: updating testbed package index (apt update) 536s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 536s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 536s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 536s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 536s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 536s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 536s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 536s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [84.0 kB] 536s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [66.6 kB] 536s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1844 B] 536s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 536s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [338 kB] 536s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [168 kB] 536s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [14.9 kB] 536s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [18.0 kB] 536s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9324 B] 536s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 536s Fetched 1252 kB in 0s (5804 kB/s) 537s Reading package lists... 537s + lsb_release --codename --short 537s + RELEASE=plucky 537s + cat 537s + [ plucky != trusty ] 537s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade 537s Reading package lists... 537s Building dependency tree... 537s Reading state information... 538s Calculating upgrade... 538s Calculating upgrade... 538s The following package was automatically installed and is no longer required: 538s libnl-genl-3-200 538s Use 'sudo apt autoremove' to remove it. 538s The following NEW packages will be installed: 538s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 538s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 538s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 538s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 538s The following packages will be upgraded: 538s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 538s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 538s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 538s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 538s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 538s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 538s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 538s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 538s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 538s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 538s linux-headers-generic linux-headers-virtual linux-image-generic 538s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 538s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 538s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 538s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 538s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 538s python3.13-minimal rsync rsyslog strace xz-utils 538s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 538s Need to get 807 MB of archives. 538s After this operation, 326 MB of additional disk space will be used. 538s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 538s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 538s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 538s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 538s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 538s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 538s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 538s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 538s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 538s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 538s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 538s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 538s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 538s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 538s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 538s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 538s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 538s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 539s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 539s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 539s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 539s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 539s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 539s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 539s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 539s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 539s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 539s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 539s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 539s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 539s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 539s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 539s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 539s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 539s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 539s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 539s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 539s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 539s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 539s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 539s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 539s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 539s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 539s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 539s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 539s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 539s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 539s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 539s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 539s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 539s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 539s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 539s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 539s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 539s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 539s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 539s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 539s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 539s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 539s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 539s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 539s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 539s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 539s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 539s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 539s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 539s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 539s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 539s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 539s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 539s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 539s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 539s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 539s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 539s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 539s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 539s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 539s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 545s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 546s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 546s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 547s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 547s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 547s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 547s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 547s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 547s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 547s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 547s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 547s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 547s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 547s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 547s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 547s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 547s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 547s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 547s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 547s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 547s Preconfiguring packages ... 547s Fetched 807 MB in 9s (92.8 MB/s) 548s (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 ... 109138 files and directories currently installed.) 548s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 548s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 548s Setting up ncurses-bin (6.5+20250216-2) ... 548s (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 ... 109138 files and directories currently installed.) 548s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 548s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 548s Setting up ncurses-base (6.5+20250216-2) ... 548s (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 ... 109138 files and directories currently installed.) 548s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 548s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 549s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 549s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 549s Setting up liblz4-1:amd64 (1.10.0-4) ... 549s (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 ... 109138 files and directories currently installed.) 549s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 549s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 549s Setting up liblzma5:amd64 (5.6.4-1) ... 549s (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 ... 109138 files and directories currently installed.) 549s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 549s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 549s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 549s (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 ... 109138 files and directories currently installed.) 549s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 549s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 549s Setting up apt (2.9.33) ... 550s (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 ... 109138 files and directories currently installed.) 550s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 550s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 550s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 550s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 550s Setting up python3-minimal (3.13.2-2) ... 550s (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 ... 109138 files and directories currently installed.) 550s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 550s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 550s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 550s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 550s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 550s Unpacking media-types (13.0.0) over (12.0.0) ... 550s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 550s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 550s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 550s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 550s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 550s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 550s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 551s (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 ... 109138 files and directories currently installed.) 551s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 551s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 551s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 551s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 551s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 551s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 551s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 551s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 551s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 551s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 551s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 551s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 551s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 551s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 551s Selecting previously unselected package libdebuginfod-common. 551s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 551s Unpacking libdebuginfod-common (0.192-4) ... 551s Preparing to unpack .../8-libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ... 551s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 551s Setting up libaudit-common (1:4.0.2-2ubuntu2) ... 551s (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 ... 109147 files and directories currently installed.) 551s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 551s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 551s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 551s (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 ... 109147 files and directories currently installed.) 552s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 552s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 552s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 552s (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 ... 109147 files and directories currently installed.) 552s Preparing to unpack .../libselinux1_3.7-3ubuntu3_amd64.deb ... 552s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 552s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 552s (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 ... 109147 files and directories currently installed.) 552s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 552s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 552s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 552s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 552s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 552s Unpacking libglib2.0-0t64:amd64 (2.84.0-1) over (2.83.5-1) ... 552s Preparing to unpack .../03-libgirepository-1.0-1_1.83.4-1_amd64.deb ... 552s Unpacking libgirepository-1.0-1:amd64 (1.83.4-1) over (1.82.0-4) ... 552s Preparing to unpack .../04-libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ... 552s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu6) ... 552s Preparing to unpack .../05-libestr0_0.1.11-2_amd64.deb ... 552s Unpacking libestr0:amd64 (0.1.11-2) over (0.1.11-1build1) ... 552s Preparing to unpack .../06-libglib2.0-data_2.84.0-1_all.deb ... 552s Unpacking libglib2.0-data (2.84.0-1) over (2.83.5-1) ... 552s Preparing to unpack .../07-libxml2_2.12.7+dfsg+really2.9.14-0.2ubuntu5_amd64.deb ... 552s Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) over (2.12.7+dfsg+really2.9.14-0.2ubuntu4) ... 552s Preparing to unpack .../08-python-apt-common_2.9.9build1_all.deb ... 552s Unpacking python-apt-common (2.9.9build1) over (2.9.9) ... 552s Preparing to unpack .../09-python3-apt_2.9.9build1_amd64.deb ... 552s Unpacking python3-apt (2.9.9build1) over (2.9.9) ... 552s Preparing to unpack .../10-python3-cffi-backend_1.17.1-2build2_amd64.deb ... 552s Unpacking python3-cffi-backend:amd64 (1.17.1-2build2) over (1.17.1-2build1) ... 552s Preparing to unpack .../11-python3-dbus_1.3.2-5build5_amd64.deb ... 552s Unpacking python3-dbus (1.3.2-5build5) over (1.3.2-5build4) ... 552s Preparing to unpack .../12-python3-gi_3.50.0-4build1_amd64.deb ... 552s Unpacking python3-gi (3.50.0-4build1) over (3.50.0-4) ... 553s Preparing to unpack .../13-python3-yaml_6.0.2-1build2_amd64.deb ... 553s Unpacking python3-yaml (6.0.2-1build2) over (6.0.2-1build1) ... 553s Preparing to unpack .../14-rsyslog_8.2412.0-2ubuntu2_amd64.deb ... 553s Unpacking rsyslog (8.2412.0-2ubuntu2) over (8.2412.0-2ubuntu1) ... 553s Preparing to unpack .../15-apparmor_4.1.0~beta5-0ubuntu8_amd64.deb ... 554s Unpacking apparmor (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu6) ... 554s Preparing to unpack .../16-dosfstools_4.2-1.2_amd64.deb ... 554s Unpacking dosfstools (4.2-1.2) over (4.2-1.1build1) ... 554s Preparing to unpack .../17-libnl-genl-3-200_3.7.0-1_amd64.deb ... 554s Unpacking libnl-genl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 554s Preparing to unpack .../18-libnl-route-3-200_3.7.0-1_amd64.deb ... 554s Unpacking libnl-route-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 554s Preparing to unpack .../19-libnl-3-200_3.7.0-1_amd64.deb ... 554s Unpacking libnl-3-200:amd64 (3.7.0-1) over (3.7.0-0.3build2) ... 554s Preparing to unpack .../20-pci.ids_0.0~2025.03.09-1_all.deb ... 554s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 554s Preparing to unpack .../21-pciutils_1%3a3.13.0-2_amd64.deb ... 554s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 554s Preparing to unpack .../22-libpci3_1%3a3.13.0-2_amd64.deb ... 554s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 554s Preparing to unpack .../23-strace_6.13+ds-1ubuntu1_amd64.deb ... 554s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 554s Preparing to unpack .../24-xz-utils_5.6.4-1_amd64.deb ... 554s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 554s Preparing to unpack .../25-libgprofng0_2.44-3ubuntu1_amd64.deb ... 554s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 554s Preparing to unpack .../26-libctf0_2.44-3ubuntu1_amd64.deb ... 554s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 554s Preparing to unpack .../27-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 554s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 554s Preparing to unpack .../28-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 554s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 554s Preparing to unpack .../29-libbinutils_2.44-3ubuntu1_amd64.deb ... 554s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 555s Preparing to unpack .../30-binutils_2.44-3ubuntu1_amd64.deb ... 555s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 555s Preparing to unpack .../31-binutils-common_2.44-3ubuntu1_amd64.deb ... 555s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 555s Preparing to unpack .../32-libsframe1_2.44-3ubuntu1_amd64.deb ... 555s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 555s Preparing to unpack .../33-hwdata_0.393-3_all.deb ... 555s Unpacking hwdata (0.393-3) over (0.393-1) ... 555s Selecting previously unselected package pnp.ids. 555s Preparing to unpack .../34-pnp.ids_0.393-3_all.deb ... 555s Unpacking pnp.ids (0.393-3) ... 555s Preparing to unpack .../35-linux-tools-common_6.14.0-10.10_all.deb ... 555s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 555s Selecting previously unselected package bpftool. 555s Preparing to unpack .../36-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 555s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 555s Preparing to unpack .../37-python3-markupsafe_2.1.5-1build4_amd64.deb ... 555s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 555s Preparing to unpack .../38-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 555s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 555s Preparing to unpack .../39-cloud-init-base_25.1-0ubuntu3_all.deb ... 555s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 555s Preparing to unpack .../40-libbrotli1_1.1.0-2build4_amd64.deb ... 555s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 555s Preparing to unpack .../41-curl_8.12.1-3ubuntu1_amd64.deb ... 555s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 555s Preparing to unpack .../42-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 555s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 556s Preparing to unpack .../43-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 556s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 556s Preparing to unpack .../44-fwupd_2.0.6-4_amd64.deb ... 556s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 556s Preparing to unpack .../45-libfwupd3_2.0.6-4_amd64.deb ... 556s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 556s Preparing to unpack .../46-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 556s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 556s Preparing to unpack .../47-htop_3.4.0-2_amd64.deb ... 556s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 556s Selecting previously unselected package libdebuginfod1t64:amd64. 556s Preparing to unpack .../48-libdebuginfod1t64_0.192-4_amd64.deb ... 556s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 556s Preparing to unpack .../49-libjemalloc2_5.3.0-3_amd64.deb ... 556s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 556s Preparing to unpack .../50-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 556s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 559s Selecting previously unselected package linux-modules-6.14.0-10-generic. 559s Preparing to unpack .../51-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 559s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 560s Selecting previously unselected package linux-image-6.14.0-10-generic. 560s Preparing to unpack .../52-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 560s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 560s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 560s Preparing to unpack .../53-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 560s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 561s Preparing to unpack .../54-linux-generic_6.14.0-10.10_amd64.deb ... 561s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 561s Preparing to unpack .../55-linux-image-generic_6.14.0-10.10_amd64.deb ... 561s Unpacking linux-image-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 561s Preparing to unpack .../56-linux-virtual_6.14.0-10.10_amd64.deb ... 561s Unpacking linux-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 561s Preparing to unpack .../57-linux-image-virtual_6.14.0-10.10_amd64.deb ... 561s Unpacking linux-image-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 561s Preparing to unpack .../58-linux-headers-virtual_6.14.0-10.10_amd64.deb ... 561s Unpacking linux-headers-virtual (6.14.0-10.10) over (6.12.0-16.16+2) ... 561s Selecting previously unselected package linux-headers-6.14.0-10. 561s Preparing to unpack .../59-linux-headers-6.14.0-10_6.14.0-10.10_all.deb ... 561s Unpacking linux-headers-6.14.0-10 (6.14.0-10.10) ... 564s Selecting previously unselected package linux-headers-6.14.0-10-generic. 564s Preparing to unpack .../60-linux-headers-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 564s Unpacking linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 565s Preparing to unpack .../61-linux-headers-generic_6.14.0-10.10_amd64.deb ... 565s Unpacking linux-headers-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 565s Preparing to unpack .../62-linux-libc-dev_6.14.0-10.10_amd64.deb ... 565s Unpacking linux-libc-dev:amd64 (6.14.0-10.10) over (6.12.0-16.16) ... 565s Selecting previously unselected package linux-perf. 565s Preparing to unpack .../63-linux-perf_6.14.0-10.10_amd64.deb ... 565s Unpacking linux-perf (6.14.0-10.10) ... 565s Selecting previously unselected package linux-tools-6.14.0-10. 565s Preparing to unpack .../64-linux-tools-6.14.0-10_6.14.0-10.10_amd64.deb ... 565s Unpacking linux-tools-6.14.0-10 (6.14.0-10.10) ... 565s Selecting previously unselected package linux-tools-6.14.0-10-generic. 565s Preparing to unpack .../65-linux-tools-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 565s Unpacking linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 566s Preparing to unpack .../66-pinentry-curses_1.3.1-2ubuntu3_amd64.deb ... 566s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 566s Preparing to unpack .../67-python3-lazr.uri_1.0.6-6_all.deb ... 566s Unpacking python3-lazr.uri (1.0.6-6) over (1.0.6-5) ... 566s Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 566s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 566s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 566s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 566s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 566s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 566s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 566s Setting up media-types (13.0.0) ... 566s Installing new version of config file /etc/mime.types ... 566s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 566s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 566s Setting up pci.ids (0.0~2025.03.09-1) ... 566s Setting up apt-utils (2.9.33) ... 566s Setting up libdebuginfod-common (0.192-4) ... 566s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 566s Setting up bpftool (7.6.0+6.14.0-10.10) ... 566s Setting up libestr0:amd64 (0.1.11-2) ... 566s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 566s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 566s Setting up dosfstools (4.2-1.2) ... 566s Setting up rsyslog (8.2412.0-2ubuntu2) ... 566s info: The user `syslog' is already a member of `adm'. 567s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 567s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 567s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 567s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 567s Setting up linux-headers-generic (6.14.0-10.10) ... 567s Setting up libjemalloc2:amd64 (5.3.0-3) ... 567s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 567s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 567s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 567s Installing new version of config file /etc/apparmor.d/openvpn ... 568s Reloading AppArmor profiles 570s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 570s No schema files found: doing nothing. 570s Setting up libglib2.0-data (2.84.0-1) ... 570s Setting up libncurses6:amd64 (6.5+20250216-2) ... 570s Setting up strace (6.13+ds-1ubuntu1) ... 570s Setting up xz-utils (5.6.4-1) ... 570s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 570s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 572s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 572s Setting up libpci3:amd64 (1:3.13.0-2) ... 572s Setting up python-apt-common (2.9.9build1) ... 572s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 572s Setting up pnp.ids (0.393-3) ... 572s Setting up libnl-3-200:amd64 (3.7.0-1) ... 572s Setting up python3.13-minimal (3.13.2-2) ... 572s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 572s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 572s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 572s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 572s Setting up rsync (3.4.1+ds1-3) ... 573s rsync.service is a disabled or a static unit not running, not starting it. 573s Setting up python3.13-gdbm (3.13.2-2) ... 573s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 573s Setting up ncurses-term (6.5+20250216-2) ... 573s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 573s Setting up libpython3.13:amd64 (3.13.2-2) ... 573s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 573s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 573s Setting up linux-headers-virtual (6.14.0-10.10) ... 573s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 573s Setting up python3.13 (3.13.2-2) ... 574s Setting up htop (3.4.0-2) ... 574s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 576s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 576s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 576s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 576s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 576s Setting up libfwupd3:amd64 (2.0.6-4) ... 576s Setting up python3 (3.13.2-2) ... 576s Setting up python3-markupsafe (2.1.5-1build4) ... 576s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 578s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 578s Setting up hwdata (0.393-3) ... 578s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 579s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 579s Setting up linux-perf (6.14.0-10.10) ... 579s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 579s Setting up python3-gi (3.50.0-4build1) ... 579s Setting up pciutils (1:3.13.0-2) ... 579s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 579s Setting up curl (8.12.1-3ubuntu1) ... 579s Setting up linux-image-virtual (6.14.0-10.10) ... 579s Setting up linux-tools-common (6.14.0-10.10) ... 579s Setting up fwupd (2.0.6-4) ... 579s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 579s fwupd.service is a disabled or a static unit not running, not starting it. 579s Setting up python3-systemd (235-1build6) ... 580s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 580s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 580s Setting up linux-image-generic (6.14.0-10.10) ... 580s Setting up python3-dbus (1.3.2-5build5) ... 580s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 580s Setting up linux-generic (6.14.0-10.10) ... 580s Setting up python3-apt (2.9.9build1) ... 580s Setting up python3-yaml (6.0.2-1build2) ... 580s Setting up python3-lazr.uri (1.0.6-6) ... 580s Setting up binutils (2.44-3ubuntu1) ... 580s Setting up cloud-init-base (25.1-0ubuntu3) ... 582s Setting up linux-virtual (6.14.0-10.10) ... 582s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 582s Setting up cloud-init (25.1-0ubuntu3) ... 582s Processing triggers for systemd (257.3-1ubuntu3) ... 582s Processing triggers for man-db (2.13.0-1) ... 583s Processing triggers for dbus (1.16.2-1ubuntu1) ... 583s Processing triggers for libc-bin (2.41-1ubuntu1) ... 583s Processing triggers for initramfs-tools (0.146ubuntu1) ... 583s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 583s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 593s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 593s /etc/kernel/postinst.d/initramfs-tools: 593s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 593s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 603s /etc/kernel/postinst.d/zz-update-grub: 603s Sourcing file `/etc/default/grub' 603s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 603s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 603s Generating grub configuration file ... 603s Found linux image: /boot/vmlinuz-6.14.0-10-generic 603s Found initrd image: /boot/initrd.img-6.14.0-10-generic 603s Found linux image: /boot/vmlinuz-6.12.0-16-generic 603s Found initrd image: /boot/initrd.img-6.12.0-16-generic 603s Found linux image: /boot/vmlinuz-6.11.0-8-generic 603s Found initrd image: /boot/initrd.img-6.11.0-8-generic 603s Warning: os-prober will not be executed to detect other bootable partitions. 603s Systems on them will not be added to the GRUB boot configuration. 603s Check GRUB_DISABLE_OS_PROBER documentation entry. 603s Adding boot menu entry for UEFI Firmware Settings ... 603s done 604s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref 604s + /usr/lib/apt/apt-helper analyze-pattern ?true 604s + uname -r 604s + sed s/\./\\./g 604s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.* 604s + + tail -n+2 604s + grep -v ^linux-.*6\.12\.0-16-generic.* 604s apt list ?obsolete 604s + cut -d/ -f1 605s + obsolete_pkgs=linux-headers-6.11.0-8-generic 605s linux-headers-6.11.0-8 605s linux-headers-6.12.0-16 605s linux-image-6.11.0-8-generic 605s linux-modules-6.11.0-8-generic 605s linux-tools-6.11.0-8-generic 605s linux-tools-6.11.0-8 605s linux-tools-6.12.0-16 605s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-headers-6.12.0-16 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 linux-tools-6.12.0-16 605s Reading package lists... 605s Building dependency tree... 605s Reading state information... 605s Solving dependencies... 606s The following packages will be REMOVED: 606s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 606s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 606s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 606s linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic* 606s linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 606s linux-tools-6.12.0-16-generic* 606s 0 upgraded, 0 newly installed, 15 to remove and 0 not upgraded. 606s After this operation, 371 MB disk space will be freed. 606s (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 ... 148643 files and directories currently installed.) 606s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 606s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 606s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 606s Removing libpython3.12t64:amd64 (3.12.9-1) ... 606s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 606s Removing libnsl2:amd64 (1.3.0-3build3) ... 606s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 606s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 607s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 609s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 609s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 611s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 611s /etc/kernel/postrm.d/initramfs-tools: 611s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 611s /etc/kernel/postrm.d/zz-update-grub: 611s Sourcing file `/etc/default/grub' 611s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 611s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 611s Generating grub configuration file ... 612s Found linux image: /boot/vmlinuz-6.14.0-10-generic 612s Found initrd image: /boot/initrd.img-6.14.0-10-generic 612s Found linux image: /boot/vmlinuz-6.12.0-16-generic 612s Found initrd image: /boot/initrd.img-6.12.0-16-generic 612s Warning: os-prober will not be executed to detect other bootable partitions. 612s Systems on them will not be added to the GRUB boot configuration. 612s Check GRUB_DISABLE_OS_PROBER documentation entry. 612s Adding boot menu entry for UEFI Firmware Settings ... 612s done 612s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 612s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 612s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 612s Processing triggers for libc-bin (2.41-1ubuntu1) ... 612s (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 ... 84830 files and directories currently installed.) 612s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 612s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 612s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 613s + grep -q trusty /etc/lsb-release 613s + [ ! -d /usr/share/doc/unattended-upgrades ] 613s + [ ! -d /usr/share/doc/lxd ] 613s + [ ! -d /usr/share/doc/lxd-client ] 613s + [ ! -d /usr/share/doc/snapd ] 613s + type iptables 613s + cat 613s + chmod 755 /etc/rc.local 613s + . /etc/rc.local 613s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu 613s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP 613s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP 613s + uname -m 613s + [ x86_64 = ppc64le ] 613s + [ -d /run/systemd/system ] 613s + systemd-detect-virt --quiet --vm 613s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/ 613s + cat 613s + grep -q lz4 /etc/initramfs-tools/initramfs.conf 613s + echo COMPRESS=lz4 613s autopkgtest [01:49:16]: upgrading testbed (apt dist-upgrade and autopurge) 613s Reading package lists... 613s Building dependency tree... 613s Reading state information... 613s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 613s Starting 2 pkgProblemResolver with broken count: 0 613s Done 614s Entering ResolveByKeep 614s 614s Calculating upgrade... 614s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 614s Reading package lists... 615s Building dependency tree... 615s Reading state information... 615s Starting pkgProblemResolver with broken count: 0 615s Starting 2 pkgProblemResolver with broken count: 0 615s Done 615s Solving dependencies... 616s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 616s autopkgtest [01:49:19]: rebooting testbed after setup commands that affected boot 619s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 632s Reading package lists... 632s Building dependency tree... 632s Reading state information... 633s Starting pkgProblemResolver with broken count: 0 633s Starting 2 pkgProblemResolver with broken count: 0 633s Done 633s The following NEW packages will be installed: 633s autoconf automake autopoint autotools-dev binutils-i686-linux-gnu blt 633s build-essential cnvkit cpp cpp-14 cpp-14-i686-linux-gnu 633s cpp-14-x86-64-linux-gnu cpp-i686-linux-gnu cpp-x86-64-linux-gnu cross-config 633s crossbuild-essential-i386 cython3 debhelper debugedit dh-autoreconf 633s dh-python dh-strip-nondeterminism dpkg-cross dwz fontconfig 633s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 633s fonts-urw-base35 g++ g++-14 g++-14-i686-linux-gnu g++-14-x86-64-linux-gnu 633s g++-i686-linux-gnu g++-x86-64-linux-gnu gcc gcc-12-base:i386 gcc-14 633s gcc-14-cross-base gcc-14-i686-linux-gnu gcc-14-i686-linux-gnu-base 633s gcc-14-x86-64-linux-gnu gcc-15-base:i386 gcc-15-cross-base 633s gcc-i686-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 633s libarchive-zip-perl libasan8 libasan8:i386 libasan8-i386-cross 633s libatomic1:i386 libatomic1-i386-cross libblas3 libc6:i386 libc6-dev:i386 633s libc6-dev-i386-cross libc6-i386-cross libcairo2 libcc1-0 libconfig-auto-perl 633s libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdatrie1 633s libdebhelper-perl libdebian-dpkgcross-perl libdeflate0 libfile-homedir-perl 633s libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 633s libfontenc1 libgcc-12-dev:i386 libgcc-14-dev libgcc-14-dev-i386-cross 633s libgcc-s1:i386 libgcc-s1-i386-cross libgfortran5 libgomp1 libgomp1:i386 633s libgomp1-i386-cross libgpgmepp6t64 libgraphite2-3 libharfbuzz0b libhts3t64 633s libhtscodecs2 libhwasan0 libice6 libimagequant0 libio-string-perl libisl23 633s libitm1 libitm1:i386 libitm1-i386-cross libjbig0 libjpeg-turbo8 libjpeg8 633s libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblerc4 633s liblsan0 libmpc3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 633s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpoppler147 633s libqhull-r8.0 libquadmath0 libquadmath0:i386 libquadmath0-i386-cross 633s libraqm0 libsharpyuv0 libsm6 libstdc++-12-dev:i386 libstdc++-14-dev 633s libstdc++-14-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libtcl8.6 633s libthai-data libthai0 libtiff6 libtk8.6 libtool libtsan2 libubsan1 633s libubsan1:i386 libubsan1-i386-cross libwebp7 libwebpdemux2 libwebpmux3 633s libxcb-render0 libxcb-shm0 libxft2 libxml-libxml-perl 633s libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl 633s libxml-simple-perl libxrender1 libxslt1.1 libxss1 libxt6t64 libyaml-perl 633s linux-libc-dev:i386 linux-libc-dev-i386-cross m4 po-debconf poppler-utils 633s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python-matplotlib-data 633s python3-all python3-biopython python3-brotli python3-build python3-cairo 633s python3-contourpy python3-cycler python3-dateutil python3-decorator 633s python3-fonttools python3-freetype python3-fs python3-importlib-metadata 633s python3-iniconfig python3-installer python3-joblib python3-kiwisolver 633s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-networkx 633s python3-numpy python3-numpy-dev python3-packaging python3-pandas 633s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 633s python3-pluggy python3-pomegranate python3-pyfaidx python3-pyproject-hooks 633s python3-pysam python3-pytest python3-pytz python3-reportlab 633s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 633s python3-sympy python3-threadpoolctl python3-tk python3-toml python3-tz 633s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-tk 633s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 633s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 633s xfonts-encodings xfonts-utils xml-core zip 633s 0 upgraded, 228 newly installed, 0 to remove and 0 not upgraded. 633s Need to get 341 MB of archives. 633s After this operation, 1318 MB of additional disk space will be used. 633s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 633s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 633s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 633s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 633s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 633s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 633s Get:7 http://ftpmaster.internal/ubuntu plucky/main i386 gcc-15-base i386 15-20250222-0ubuntu1 [53.4 kB] 633s Get:8 http://ftpmaster.internal/ubuntu plucky/main i386 libgcc-s1 i386 15-20250222-0ubuntu1 [93.9 kB] 633s Get:9 http://ftpmaster.internal/ubuntu plucky/main i386 libc6 i386 2.41-1ubuntu1 [3076 kB] 633s Get:10 http://ftpmaster.internal/ubuntu plucky/main i386 libcrypt1 i386 1:4.4.38-1 [91.6 kB] 633s Get:11 http://ftpmaster.internal/ubuntu plucky/main i386 libatomic1 i386 15-20250222-0ubuntu1 [8352 B] 633s Get:12 http://ftpmaster.internal/ubuntu plucky/main i386 libstdc++6 i386 15-20250222-0ubuntu1 [873 kB] 633s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-7 [263 kB] 633s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3ubuntu1 [383 kB] 633s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 633s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.17-3ubuntu1 [572 kB] 633s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.23.1-1 [619 kB] 633s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 633s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 633s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 633s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 633s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 633s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 633s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 633s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 634s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 634s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 634s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 634s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 634s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 634s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 634s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 634s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 634s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 634s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 634s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 634s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 634s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 634s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 634s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 634s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 634s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 634s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 634s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 634s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 634s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 634s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 634s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 634s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 634s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 634s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 634s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 634s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 634s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 634s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 634s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 634s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 634s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 634s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 634s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 634s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 634s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 634s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 634s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 634s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 634s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 634s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 634s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 634s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 634s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 634s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 634s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 634s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 634s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 634s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 634s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 634s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 634s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 634s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 634s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 634s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 634s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 634s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 634s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 634s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build2 [124 kB] 634s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 634s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 634s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 634s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 634s Get:90 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 634s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 634s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 634s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 634s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 634s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 634s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 634s Get:97 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 634s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 634s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 634s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 634s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 634s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 634s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 634s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 634s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 634s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 634s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 635s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 635s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 635s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 635s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 635s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 635s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 635s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 635s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 635s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 635s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 635s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 635s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 635s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 635s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8build1 [5332 kB] 635s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 635s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 635s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 635s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 635s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 635s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 635s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 635s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 635s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 635s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 635s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 635s Get:133 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 635s Get:134 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 635s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 635s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 635s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 635s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 635s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 635s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 635s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 635s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 635s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 635s Get:144 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 635s Get:145 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 635s Get:146 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 635s Get:147 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 635s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 635s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 635s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 635s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 635s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 635s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 635s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-i686-linux-gnu-base amd64 14.2.0-12ubuntu1cross1 [52.9 kB] 635s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-i686-linux-gnu amd64 14.2.0-12ubuntu1cross1 [12.6 MB] 636s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-i686-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 636s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-i686-linux-gnu amd64 2.44-3ubuntu1 [1720 kB] 636s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-cross-base all 14.2.0-12ubuntu1cross1 [47.9 kB] 636s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-cross-base all 15-20250213-1ubuntu1cross1 [48.5 kB] 636s Get:160 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-i386-cross all 2.41-1ubuntu1cross1 [1558 kB] 636s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgcc-s1-i386-cross all 15-20250213-1ubuntu1cross1 [93.9 kB] 636s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgomp1-i386-cross all 15-20250213-1ubuntu1cross1 [150 kB] 636s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 libitm1-i386-cross all 15-20250213-1ubuntu1cross1 [30.3 kB] 636s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 libatomic1-i386-cross all 15-20250213-1ubuntu1cross1 [8086 B] 636s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 libasan8-i386-cross all 15-20250213-1ubuntu1cross1 [2901 kB] 636s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 libstdc++6-i386-cross all 15-20250213-1ubuntu1cross1 [823 kB] 636s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 libubsan1-i386-cross all 15-20250213-1ubuntu1cross1 [1173 kB] 636s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 libquadmath0-i386-cross all 15-20250213-1ubuntu1cross1 [245 kB] 636s Get:169 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev-i386-cross all 14.2.0-12ubuntu1cross1 [2719 kB] 636s Get:170 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-i686-linux-gnu amd64 14.2.0-12ubuntu1cross1 [24.7 MB] 636s Get:171 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-i686-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 636s Get:172 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev-i386-cross all 6.12.0-15.15cross1 [1433 kB] 636s Get:173 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev-i386-cross all 2.41-1ubuntu1cross1 [1958 kB] 636s Get:174 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev-i386-cross all 14.2.0-12ubuntu1cross1 [2591 kB] 636s Get:175 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-i686-linux-gnu amd64 14.2.0-12ubuntu1cross1 [14.1 MB] 636s Get:176 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-i686-linux-gnu amd64 4:14.2.0-1ubuntu1 [958 B] 636s Get:177 http://ftpmaster.internal/ubuntu plucky/main amd64 libconfig-inifiles-perl all 3.000003-3 [38.4 kB] 636s Get:178 http://ftpmaster.internal/ubuntu plucky/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 636s Get:179 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml-namespacesupport-perl all 1.12-2 [13.5 kB] 636s Get:180 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml-sax-base-perl all 1.09-3 [18.9 kB] 636s Get:181 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml-sax-perl all 1.02+dfsg-4 [52.4 kB] 636s Get:182 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5build1 [305 kB] 636s Get:183 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml-simple-perl all 2.25-2 [64.1 kB] 636s Get:184 http://ftpmaster.internal/ubuntu plucky/main amd64 libyaml-perl all 1.31-1 [65.7 kB] 636s Get:185 http://ftpmaster.internal/ubuntu plucky/main amd64 libconfig-auto-perl all 0.44-2 [17.1 kB] 636s Get:186 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-which-perl all 1.27-2 [12.5 kB] 636s Get:187 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-homedir-perl all 1.006-2 [37.0 kB] 636s Get:188 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.6 kB] 636s Get:189 http://ftpmaster.internal/ubuntu plucky/main amd64 cross-config all 2.6.20 [16.5 kB] 636s Get:190 http://ftpmaster.internal/ubuntu plucky/main amd64 dpkg-cross all 2.6.20 [22.2 kB] 636s Get:191 http://ftpmaster.internal/ubuntu plucky/universe amd64 crossbuild-essential-i386 all 12.10ubuntu1 [3870 B] 636s Get:192 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 636s Get:193 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.5.4-4 [168 kB] 636s Get:194 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 636s Get:195 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 636s Get:196 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 636s Get:197 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 636s Get:198 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 636s Get:199 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 636s Get:200 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.23.1-1 [1086 kB] 636s Get:201 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 636s Get:202 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 636s Get:203 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 636s Get:204 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20250308 [118 kB] 636s Get:205 http://ftpmaster.internal/ubuntu plucky/universe i386 gcc-12-base i386 12.4.0-4ubuntu1 [47.4 kB] 636s Get:206 http://ftpmaster.internal/ubuntu plucky/main i386 libasan8 i386 15-20250222-0ubuntu1 [2908 kB] 636s Get:207 http://ftpmaster.internal/ubuntu plucky/main i386 linux-libc-dev i386 6.14.0-10.10 [1724 kB] 636s Get:208 http://ftpmaster.internal/ubuntu plucky/main i386 libcrypt-dev i386 1:4.4.38-1 [121 kB] 636s Get:209 http://ftpmaster.internal/ubuntu plucky/main i386 libc6-dev i386 2.41-1ubuntu1 [1917 kB] 636s Get:210 http://ftpmaster.internal/ubuntu plucky/main i386 libgomp1 i386 15-20250222-0ubuntu1 [153 kB] 636s Get:211 http://ftpmaster.internal/ubuntu plucky/main i386 libitm1 i386 15-20250222-0ubuntu1 [30.9 kB] 636s Get:212 http://ftpmaster.internal/ubuntu plucky/main i386 libubsan1 i386 15-20250222-0ubuntu1 [1172 kB] 636s Get:213 http://ftpmaster.internal/ubuntu plucky/main i386 libquadmath0 i386 15-20250222-0ubuntu1 [245 kB] 636s Get:214 http://ftpmaster.internal/ubuntu plucky/universe i386 libgcc-12-dev i386 12.4.0-4ubuntu1 [2552 kB] 636s Get:215 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgmepp6t64 amd64 1.24.2-1ubuntu2 [126 kB] 636s Get:216 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler147 amd64 25.03.0-2 [1295 kB] 636s Get:217 http://ftpmaster.internal/ubuntu plucky/universe i386 libstdc++-12-dev i386 12.4.0-4ubuntu1 [2273 kB] 636s Get:218 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 25.03.0-2 [232 kB] 636s Get:219 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20250308 [1744 B] 636s Get:220 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 636s Get:221 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 636s Get:222 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.45.1-1 [57.7 kB] 636s Get:223 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 636s Get:224 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 636s Get:225 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20250308 [1726 B] 636s Get:226 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 636s Get:227 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 636s Get:228 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.5-1 [252 kB] 637s Preconfiguring packages ... 637s Fetched 341 MB in 3s (117 MB/s) 637s Selecting previously unselected package python3-numpy-dev:amd64. 637s (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 ... 84827 files and directories currently installed.) 637s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 637s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 637s Selecting previously unselected package libblas3:amd64. 637s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 637s Unpacking libblas3:amd64 (3.12.1-2) ... 637s Selecting previously unselected package libgfortran5:amd64. 637s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 637s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 637s Selecting previously unselected package liblapack3:amd64. 637s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 637s Unpacking liblapack3:amd64 (3.12.1-2) ... 637s Selecting previously unselected package python3-numpy. 637s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 637s Unpacking python3-numpy (1:2.2.3+ds-5) ... 637s Selecting previously unselected package sgml-base. 637s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 637s Unpacking sgml-base (1.31) ... 638s Selecting previously unselected package gcc-15-base:i386. 638s Preparing to unpack .../006-gcc-15-base_15-20250222-0ubuntu1_i386.deb ... 638s Unpacking gcc-15-base:i386 (15-20250222-0ubuntu1) ... 638s Selecting previously unselected package libgcc-s1:i386. 638s Preparing to unpack .../007-libgcc-s1_15-20250222-0ubuntu1_i386.deb ... 638s Unpacking libgcc-s1:i386 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unpack .../040-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 639s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 640s Selecting previously unselected package libitm1:amd64. 640s Preparing to unpack .../041-libitm1_15-20250222-0ubuntu1_amd64.deb ... 640s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 640s Selecting previously unselected package libasan8:amd64. 640s Preparing to unpack .../042-libasan8_15-20250222-0ubuntu1_amd64.deb ... 640s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 640s Selecting previously unselected package liblsan0:amd64. 640s Preparing to unpack .../043-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 640s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 640s Selecting previously unselected package libtsan2:amd64. 640s Preparing to unpack .../044-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 640s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 640s Selecting previously unselected package libubsan1:amd64. 640s Preparing to unpack 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Selecting previously unselected package liblcms2-2:amd64. 641s Preparing to unpack .../066-liblcms2-2_2.16-2_amd64.deb ... 641s Unpacking liblcms2-2:amd64 (2.16-2) ... 641s Selecting previously unselected package libopenjp2-7:amd64. 641s Preparing to unpack .../067-libopenjp2-7_2.5.3-2_amd64.deb ... 641s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 641s Selecting previously unselected package libgraphite2-3:amd64. 641s Preparing to unpack .../068-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 641s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 641s Selecting previously unselected package libharfbuzz0b:amd64. 641s Preparing to unpack .../069-libharfbuzz0b_10.2.0-1_amd64.deb ... 641s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 641s Selecting previously unselected package libraqm0:amd64. 641s Preparing to unpack .../070-libraqm0_0.10.2-1_amd64.deb ... 641s Unpacking libraqm0:amd64 (0.10.2-1) ... 641s Selecting previously unselected package libdeflate0:amd64. 641s Preparing to unpack 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unselected package libxcb-shm0:amd64. 642s Preparing to unpack .../082-libxcb-shm0_1.17.0-2_amd64.deb ... 642s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 642s Selecting previously unselected package libcairo2:amd64. 642s Preparing to unpack .../083-libcairo2_1.18.2-2_amd64.deb ... 642s Unpacking libcairo2:amd64 (1.18.2-2) ... 642s Selecting previously unselected package python3-cairo. 642s Preparing to unpack .../084-python3-cairo_1.26.1-2build2_amd64.deb ... 642s Unpacking python3-cairo (1.26.1-2build2) ... 642s Selecting previously unselected package python3-freetype. 642s Preparing to unpack .../085-python3-freetype_2.5.1-1_all.deb ... 642s Unpacking python3-freetype (2.5.1-1) ... 642s Selecting previously unselected package python3-rlpycairo. 642s Preparing to unpack .../086-python3-rlpycairo_0.3.0-3_all.deb ... 642s Unpacking python3-rlpycairo (0.3.0-3) ... 642s Selecting previously unselected package python3-reportlab. 642s Preparing to unpack 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.../098-python3-brotli_1.1.0-2build4_amd64.deb ... 643s Unpacking python3-brotli (1.1.0-2build4) ... 643s Selecting previously unselected package python3-platformdirs. 643s Preparing to unpack .../099-python3-platformdirs_4.3.6-1_all.deb ... 643s Unpacking python3-platformdirs (4.3.6-1) ... 643s Selecting previously unselected package python3-fs. 643s Preparing to unpack .../100-python3-fs_2.4.16-7_all.deb ... 643s Unpacking python3-fs (2.4.16-7) ... 643s Selecting previously unselected package libxslt1.1:amd64. 643s Preparing to unpack .../101-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 643s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 643s Selecting previously unselected package python3-lxml:amd64. 643s Preparing to unpack .../102-python3-lxml_5.3.1-1build1_amd64.deb ... 643s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 643s Selecting previously unselected package python3-lz4. 643s Preparing to unpack .../103-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 643s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 643s Selecting previously unselected package python3-decorator. 643s Preparing to unpack .../104-python3-decorator_5.1.1-5_all.deb ... 643s Unpacking python3-decorator (5.1.1-5) ... 643s Selecting previously unselected package liblbfgsb0:amd64. 643s Preparing to unpack .../105-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 643s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 643s Selecting previously unselected package python3-scipy. 643s Preparing to unpack .../106-python3-scipy_1.14.1-4ubuntu2_amd64.deb ... 643s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 643s Selecting previously unselected package python3-mpmath. 643s Preparing to unpack .../107-python3-mpmath_1.3.0-1_all.deb ... 643s Unpacking python3-mpmath (1.3.0-1) ... 643s Selecting previously unselected package python3-sympy. 644s Preparing to unpack .../108-python3-sympy_1.13.3-5_all.deb ... 644s Unpacking python3-sympy (1.13.3-5) ... 644s Selecting previously unselected package python3-ufolib2. 644s Preparing to unpack .../109-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 644s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 644s Selecting previously unselected package python3-unicodedata2. 644s Preparing to unpack .../110-python3-unicodedata2_15.1.0+ds-1build3_amd64.deb ... 644s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 644s Selecting previously unselected package python3-all. 644s Preparing to unpack .../111-python3-all_3.13.2-2_amd64.deb ... 644s Unpacking python3-all (3.13.2-2) ... 644s Selecting previously unselected package unicode-data. 644s Preparing to unpack .../112-unicode-data_15.1.0-1_all.deb ... 644s Unpacking unicode-data (15.1.0-1) ... 644s Selecting previously unselected package python3-fonttools. 644s Preparing to unpack .../113-python3-fonttools_4.55.3-2build1_amd64.deb ... 644s Unpacking python3-fonttools (4.55.3-2build1) ... 644s Selecting previously unselected package python3-kiwisolver. 644s Preparing to unpack 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python3-tz (2025.1-3) ... 645s Selecting previously unselected package python3-pandas-lib:amd64. 645s Preparing to unpack .../120-python3-pandas-lib_2.2.3+dfsg-8build1_amd64.deb ... 645s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 645s Selecting previously unselected package python3-pandas. 645s Preparing to unpack .../121-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 645s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 645s Selecting previously unselected package cython3. 645s Preparing to unpack .../122-cython3_3.0.11+dfsg-2ubuntu2_amd64.deb ... 645s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 645s Selecting previously unselected package python3-joblib. 645s Preparing to unpack .../123-python3-joblib_1.4.2-3_all.deb ... 645s Unpacking python3-joblib (1.4.2-3) ... 645s Selecting previously unselected package python3-networkx. 646s Preparing to unpack .../124-python3-networkx_3.2.1-4ubuntu1_all.deb ... 646s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 646s Selecting previously unselected package python3-pomegranate. 646s Preparing to unpack .../125-python3-pomegranate_0.15.0-1build1_amd64.deb ... 646s Unpacking python3-pomegranate (0.15.0-1build1) ... 646s Selecting previously unselected package python3-importlib-metadata. 646s Preparing to unpack .../126-python3-importlib-metadata_8.6.1-1_all.deb ... 646s Unpacking python3-importlib-metadata (8.6.1-1) ... 646s Selecting previously unselected package python3-pyfaidx. 646s Preparing to unpack .../127-python3-pyfaidx_0.8.1.3-1_all.deb ... 646s Unpacking python3-pyfaidx (0.8.1.3-1) ... 646s Selecting previously unselected package libhtscodecs2:amd64. 646s Preparing to unpack .../128-libhtscodecs2_1.6.1-2_amd64.deb ... 646s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 646s Selecting previously unselected package libhts3t64:amd64. 646s Preparing to unpack .../129-libhts3t64_1.21+ds-1_amd64.deb ... 646s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 647s Selecting previously unselected package python3-pysam. 647s Preparing to unpack .../130-python3-pysam_0.23.0+ds-1build1_amd64.deb ... 647s Unpacking python3-pysam (0.23.0+ds-1build1) ... 647s Selecting previously unselected package python3-threadpoolctl. 647s Preparing to unpack .../131-python3-threadpoolctl_3.1.0-1_all.deb ... 647s Unpacking python3-threadpoolctl (3.1.0-1) ... 647s Selecting previously unselected package python3-sklearn-lib:amd64. 647s Preparing to unpack .../132-python3-sklearn-lib_1.4.2+dfsg-8_amd64.deb ... 647s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 647s Selecting previously unselected package python3-sklearn. 647s Preparing to unpack .../133-python3-sklearn_1.4.2+dfsg-8_all.deb ... 647s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 647s Selecting previously unselected package zip. 647s Preparing to unpack .../134-zip_3.0-14ubuntu2_amd64.deb ... 647s Unpacking zip (3.0-14ubuntu2) ... 647s Selecting previously unselected package unzip. 647s Preparing to unpack .../135-unzip_6.0-28ubuntu6_amd64.deb ... 647s Unpacking unzip (6.0-28ubuntu6) ... 647s Selecting previously unselected package libpaper2:amd64. 647s Preparing to unpack .../136-libpaper2_2.2.5-0.3_amd64.deb ... 647s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 647s Selecting previously unselected package libpaper-utils. 647s Preparing to unpack .../137-libpaper-utils_2.2.5-0.3_amd64.deb ... 647s Unpacking libpaper-utils (2.2.5-0.3) ... 647s Selecting previously unselected package xdg-utils. 647s Preparing to unpack .../138-xdg-utils_1.2.1-2ubuntu1_all.deb ... 647s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 647s Selecting previously unselected package fontconfig. 647s Preparing to unpack .../139-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 647s Unpacking fontconfig (2.15.0-2ubuntu1) ... 647s Selecting previously unselected package libthai-data. 647s Preparing to unpack .../140-libthai-data_0.1.29-2build1_all.deb ... 647s Unpacking libthai-data (0.1.29-2build1) ... 647s Selecting previously unselected package libdatrie1:amd64. 647s Preparing to unpack .../141-libdatrie1_0.2.13-3build1_amd64.deb ... 647s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 647s Selecting previously unselected package libthai0:amd64. 647s Preparing to unpack .../142-libthai0_0.1.29-2build1_amd64.deb ... 647s Unpacking libthai0:amd64 (0.1.29-2build1) ... 647s Selecting previously unselected package libpango-1.0-0:amd64. 647s Preparing to unpack .../143-libpango-1.0-0_1.56.2-1_amd64.deb ... 647s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 647s Selecting previously unselected package libpangoft2-1.0-0:amd64. 647s Preparing to unpack .../144-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 647s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 647s Selecting previously unselected package libpangocairo-1.0-0:amd64. 647s Preparing to unpack .../145-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 647s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 648s Selecting previously unselected package libice6:amd64. 648s Preparing to unpack .../146-libice6_2%3a1.1.1-1_amd64.deb ... 648s Unpacking libice6:amd64 (2:1.1.1-1) ... 648s Selecting previously unselected package libsm6:amd64. 648s Preparing to unpack .../147-libsm6_2%3a1.2.4-1_amd64.deb ... 648s Unpacking libsm6:amd64 (2:1.2.4-1) ... 648s Selecting previously unselected package libxt6t64:amd64. 648s Preparing to unpack .../148-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 648s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 648s Selecting previously unselected package r-base-core. 648s Preparing to unpack .../149-r-base-core_4.4.3-1_amd64.deb ... 648s Unpacking r-base-core (4.4.3-1) ... 648s Selecting previously unselected package r-bioc-biocgenerics. 648s Preparing to unpack .../150-r-bioc-biocgenerics_0.52.0-2_all.deb ... 648s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 648s Selecting previously unselected package r-bioc-dnacopy. 648s Preparing to unpack .../151-r-bioc-dnacopy_1.80.0-2_amd64.deb ... 648s Unpacking r-bioc-dnacopy (1.80.0-2) ... 648s Selecting previously unselected package cnvkit. 648s Preparing to unpack .../152-cnvkit_0.9.12-1_all.deb ... 648s Unpacking cnvkit (0.9.12-1) ... 649s Selecting previously unselected package gcc-14-i686-linux-gnu-base:amd64. 649s Preparing to unpack .../153-gcc-14-i686-linux-gnu-base_14.2.0-12ubuntu1cross1_amd64.deb ... 649s Unpacking gcc-14-i686-linux-gnu-base:amd64 (14.2.0-12ubuntu1cross1) ... 649s Selecting previously unselected package cpp-14-i686-linux-gnu. 649s Preparing to unpack .../154-cpp-14-i686-linux-gnu_14.2.0-12ubuntu1cross1_amd64.deb ... 649s Unpacking cpp-14-i686-linux-gnu (14.2.0-12ubuntu1cross1) ... 649s Selecting previously unselected package cpp-i686-linux-gnu. 649s Preparing to unpack .../155-cpp-i686-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 649s Unpacking cpp-i686-linux-gnu (4:14.2.0-1ubuntu1) ... 649s Selecting previously unselected package binutils-i686-linux-gnu. 649s Preparing to unpack .../156-binutils-i686-linux-gnu_2.44-3ubuntu1_amd64.deb ... 649s Unpacking binutils-i686-linux-gnu (2.44-3ubuntu1) ... 649s Selecting previously unselected package gcc-14-cross-base. 649s Preparing to unpack .../157-gcc-14-cross-base_14.2.0-12ubuntu1cross1_all.deb ... 649s Unpacking gcc-14-cross-base (14.2.0-12ubuntu1cross1) ... 649s Selecting previously unselected package gcc-15-cross-base. 649s Preparing to unpack .../158-gcc-15-cross-base_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking gcc-15-cross-base (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libc6-i386-cross. 649s Preparing to unpack .../159-libc6-i386-cross_2.41-1ubuntu1cross1_all.deb ... 649s Unpacking libc6-i386-cross (2.41-1ubuntu1cross1) ... 649s Selecting previously unselected package libgcc-s1-i386-cross. 649s Preparing to unpack .../160-libgcc-s1-i386-cross_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking libgcc-s1-i386-cross (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libgomp1-i386-cross. 649s Preparing to unpack .../161-libgomp1-i386-cross_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking libgomp1-i386-cross (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libitm1-i386-cross. 649s Preparing to unpack .../162-libitm1-i386-cross_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking libitm1-i386-cross (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libatomic1-i386-cross. 649s Preparing to unpack .../163-libatomic1-i386-cross_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking libatomic1-i386-cross (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libasan8-i386-cross. 649s Preparing to unpack .../164-libasan8-i386-cross_15-20250213-1ubuntu1cross1_all.deb ... 649s Unpacking libasan8-i386-cross (15-20250213-1ubuntu1cross1) ... 649s Selecting previously unselected package libstdc++6-i386-cross. 649s Preparing to unpack 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650s Unpacking gcc-14-i686-linux-gnu (14.2.0-12ubuntu1cross1) ... 650s Selecting previously unselected package gcc-i686-linux-gnu. 650s Preparing to unpack .../170-gcc-i686-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 650s Unpacking gcc-i686-linux-gnu (4:14.2.0-1ubuntu1) ... 650s Selecting previously unselected package linux-libc-dev-i386-cross. 650s Preparing to unpack .../171-linux-libc-dev-i386-cross_6.12.0-15.15cross1_all.deb ... 650s Unpacking linux-libc-dev-i386-cross (6.12.0-15.15cross1) ... 650s Selecting previously unselected package libc6-dev-i386-cross. 650s Preparing to unpack .../172-libc6-dev-i386-cross_2.41-1ubuntu1cross1_all.deb ... 650s Unpacking libc6-dev-i386-cross (2.41-1ubuntu1cross1) ... 650s Selecting previously unselected package libstdc++-14-dev-i386-cross. 650s Preparing to unpack .../173-libstdc++-14-dev-i386-cross_14.2.0-12ubuntu1cross1_all.deb ... 650s Unpacking libstdc++-14-dev-i386-cross (14.2.0-12ubuntu1cross1) ... 651s Selecting previously unselected package g++-14-i686-linux-gnu. 651s Preparing to unpack .../174-g++-14-i686-linux-gnu_14.2.0-12ubuntu1cross1_amd64.deb ... 651s Unpacking g++-14-i686-linux-gnu (14.2.0-12ubuntu1cross1) ... 651s Selecting previously unselected package g++-i686-linux-gnu. 651s Preparing to unpack .../175-g++-i686-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 651s Unpacking g++-i686-linux-gnu (4:14.2.0-1ubuntu1) ... 651s Selecting previously unselected package libconfig-inifiles-perl. 651s Preparing to unpack .../176-libconfig-inifiles-perl_3.000003-3_all.deb ... 651s Unpacking libconfig-inifiles-perl (3.000003-3) ... 651s Selecting previously unselected package libio-string-perl. 651s Preparing to unpack .../177-libio-string-perl_1.08-4_all.deb ... 651s Unpacking libio-string-perl (1.08-4) ... 651s Selecting previously unselected package libxml-namespacesupport-perl. 651s Preparing to unpack .../178-libxml-namespacesupport-perl_1.12-2_all.deb ... 651s Unpacking libxml-namespacesupport-perl (1.12-2) ... 651s Selecting previously unselected package libxml-sax-base-perl. 651s Preparing to unpack .../179-libxml-sax-base-perl_1.09-3_all.deb ... 651s Unpacking libxml-sax-base-perl (1.09-3) ... 651s Selecting previously unselected package libxml-sax-perl. 651s Preparing to unpack .../180-libxml-sax-perl_1.02+dfsg-4_all.deb ... 651s Unpacking libxml-sax-perl (1.02+dfsg-4) ... 651s Selecting previously unselected package libxml-libxml-perl. 651s Preparing to unpack .../181-libxml-libxml-perl_2.0207+dfsg+really+2.0134-5build1_amd64.deb ... 651s Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-5build1) ... 651s Selecting previously unselected package libxml-simple-perl. 651s Preparing to unpack .../182-libxml-simple-perl_2.25-2_all.deb ... 651s Unpacking libxml-simple-perl (2.25-2) ... 651s Selecting previously unselected package libyaml-perl. 651s Preparing to unpack .../183-libyaml-perl_1.31-1_all.deb ... 651s Unpacking libyaml-perl (1.31-1) ... 651s Selecting previously unselected package libconfig-auto-perl. 651s Preparing to unpack .../184-libconfig-auto-perl_0.44-2_all.deb ... 651s Unpacking libconfig-auto-perl (0.44-2) ... 651s Selecting previously unselected package libfile-which-perl. 651s Preparing to unpack .../185-libfile-which-perl_1.27-2_all.deb ... 651s Unpacking libfile-which-perl (1.27-2) ... 651s Selecting previously unselected package libfile-homedir-perl. 651s Preparing to unpack .../186-libfile-homedir-perl_1.006-2_all.deb ... 651s Unpacking libfile-homedir-perl (1.006-2) ... 651s Selecting previously unselected package libdebian-dpkgcross-perl. 651s Preparing to unpack .../187-libdebian-dpkgcross-perl_2.6.20_all.deb ... 651s Unpacking libdebian-dpkgcross-perl (2.6.20) ... 651s Selecting previously unselected package cross-config. 651s Preparing to unpack .../188-cross-config_2.6.20_all.deb ... 651s Unpacking cross-config (2.6.20) ... 651s Selecting previously unselected package dpkg-cross. 651s Preparing to unpack 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Selecting previously unselected package libfile-stripnondeterminism-perl. 651s Preparing to unpack .../195-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 651s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 651s Selecting previously unselected package dh-strip-nondeterminism. 652s Preparing to unpack .../196-dh-strip-nondeterminism_1.14.1-2_all.deb ... 652s Unpacking dh-strip-nondeterminism (1.14.1-2) ... 652s Selecting previously unselected package debugedit. 652s Preparing to unpack .../197-debugedit_1%3a5.1-2_amd64.deb ... 652s Unpacking debugedit (1:5.1-2) ... 652s Selecting previously unselected package dwz. 652s Preparing to unpack .../198-dwz_0.15-1build6_amd64.deb ... 652s Unpacking dwz (0.15-1build6) ... 652s Selecting previously unselected package gettext. 652s Preparing to unpack .../199-gettext_0.23.1-1_amd64.deb ... 652s Unpacking gettext (0.23.1-1) ... 652s Selecting previously unselected package intltool-debian. 652s Preparing to unpack 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652s Selecting previously unselected package linux-libc-dev:i386. 652s Preparing to unpack .../206-linux-libc-dev_6.14.0-10.10_i386.deb ... 652s Unpacking linux-libc-dev:i386 (6.14.0-10.10) ... 652s Selecting previously unselected package libcrypt-dev:i386. 652s Preparing to unpack .../207-libcrypt-dev_1%3a4.4.38-1_i386.deb ... 652s Unpacking libcrypt-dev:i386 (1:4.4.38-1) ... 652s Selecting previously unselected package libc6-dev:i386. 653s Preparing to unpack .../208-libc6-dev_2.41-1ubuntu1_i386.deb ... 653s Unpacking libc6-dev:i386 (2.41-1ubuntu1) ... 653s Selecting previously unselected package libgomp1:i386. 653s Preparing to unpack .../209-libgomp1_15-20250222-0ubuntu1_i386.deb ... 653s Unpacking libgomp1:i386 (15-20250222-0ubuntu1) ... 653s Selecting previously unselected package libitm1:i386. 653s Preparing to unpack .../210-libitm1_15-20250222-0ubuntu1_i386.deb ... 653s Unpacking libitm1:i386 (15-20250222-0ubuntu1) ... 653s Selecting previously unselected package 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(c++) in auto mode 680s Setting up r-bioc-dnacopy (1.80.0-2) ... 680s Setting up gcc-i686-linux-gnu (4:14.2.0-1ubuntu1) ... 680s Setting up build-essential (12.10ubuntu1) ... 680s Setting up libstdc++-14-dev-i386-cross (14.2.0-12ubuntu1cross1) ... 680s Setting up dpkg-cross (2.6.20) ... 680s Setting up g++-14-i686-linux-gnu (14.2.0-12ubuntu1cross1) ... 680s Setting up g++-i686-linux-gnu (4:14.2.0-1ubuntu1) ... 680s Setting up debhelper (13.24.1ubuntu2) ... 680s Setting up crossbuild-essential-i386 (12.10ubuntu1) ... 680s Setting up pybuild-plugin-autopkgtest (6.20250308) ... 680s Setting up libgcc-s1:i386 (15-20250222-0ubuntu1) ... 680s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 680s Setting up libc6:i386 (2.41-1ubuntu1) ... 680s Setting up libasan8:i386 (15-20250222-0ubuntu1) ... 680s Setting up libstdc++6:i386 (15-20250222-0ubuntu1) ... 680s Setting up libitm1:i386 (15-20250222-0ubuntu1) ... 680s Setting up libcrypt1:i386 (1:4.4.38-1) ... 680s Setting up libgomp1:i386 (15-20250222-0ubuntu1) ... 680s Setting up python3-fonttools (4.55.3-2build1) ... 681s Setting up libquadmath0:i386 (15-20250222-0ubuntu1) ... 681s Setting up libatomic1:i386 (15-20250222-0ubuntu1) ... 681s Setting up libubsan1:i386 (15-20250222-0ubuntu1) ... 681s Setting up libcrypt-dev:i386 (1:4.4.38-1) ... 681s Setting up libc6-dev:i386 (2.41-1ubuntu1) ... 681s Setting up python3-matplotlib (3.8.3-7build1) ... 682s Setting up libgcc-12-dev:i386 (12.4.0-4ubuntu1) ... 682s Setting up libstdc++-12-dev:i386 (12.4.0-4ubuntu1) ... 682s Processing triggers for libc-bin (2.41-1ubuntu1) ... 682s Processing triggers for man-db (2.13.0-1) ... 684s Processing triggers for install-info (7.1.1-1) ... 684s Processing triggers for sgml-base (1.31) ... 684s Setting up w3c-sgml-lib (1.3-3) ... 711s Setting up python3-biopython (1.85+dfsg-2build1) ... 711s Setting up cnvkit (0.9.12-1) ... 712s Processing triggers for systemd (257.3-1ubuntu3) ... 716s autopkgtest [01:50:59]: testbed environment configured for cross-architecture building 716s autopkgtest [01:50:59]: test pybuild-autopkgtest: pybuild-autopkgtest 716s autopkgtest [01:50:59]: test pybuild-autopkgtest: [----------------------- 716s pybuild-autopkgtest 716s I: pybuild base:311: cd /tmp/autopkgtest.Uz2vHW/autopkgtest_tmp/build; python3.13 -m pytest test 717s ============================= test session starts ============================== 717s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 717s rootdir: /tmp/autopkgtest.Uz2vHW/autopkgtest_tmp/build 717s configfile: pyproject.toml 717s plugins: typeguard-4.4.2 717s collected 10 items / 4 errors 717s 717s ==================================== ERRORS ==================================== 717s _____________________ ERROR collecting test/test_cnvlib.py _____________________ 717s ImportError while importing test module '/tmp/autopkgtest.Uz2vHW/autopkgtest_tmp/build/test/test_cnvlib.py'. 717s Hint: make sure your test modules/packages have valid Python names. 717s Traceback: 717s /usr/lib/python3.13/importlib/__init__.py:88: in import_module 717s return _bootstrap._gcd_import(name[level:], package, level) 717s test/test_cnvlib.py:15: in 717s from skgenome import GenomicArray, tabio 717s /usr/lib/python3/dist-packages/skgenome/__init__.py:1: in 717s from . import tabio 717s /usr/lib/python3/dist-packages/skgenome/tabio/__init__.py:10: in 717s import pandas as pd 717s /usr/lib/python3/dist-packages/pandas/__init__.py:19: in 717s raise ImportError( 717s E ImportError: Unable to import required dependencies: 717s E pytz: No module named '_sysconfigdata__i386-linux-gnu' 717s ____________________ ERROR collecting test/test_commands.py ____________________ 717s test/test_commands.py:21: in 717s import cnvlib 717s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 717s from .cmdutil import read_cna as read 717s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 717s from .cnary import CopyNumArray as CNA 717s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 717s from scipy.stats import median_test 717s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 717s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 717s E TypeError: can only concatenate str (not "NoneType") to str 717s _____________________ ERROR collecting test/test_genome.py _____________________ 717s test/test_genome.py:15: in 717s from cnvlib import read_ga 717s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 717s from .cmdutil import read_cna as read 717s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 717s from .cnary import CopyNumArray as CNA 717s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 717s from scipy.stats import median_test 717s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 717s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 717s E TypeError: can only concatenate str (not "NoneType") to str 717s _______________________ ERROR collecting test/test_r.py ________________________ 717s test/test_r.py:14: in 717s import cnvlib 717s /usr/lib/python3/dist-packages/cnvlib/__init__.py:4: in 717s from .cmdutil import read_cna as read 717s /usr/lib/python3/dist-packages/cnvlib/cmdutil.py:7: in 717s from .cnary import CopyNumArray as CNA 717s /usr/lib/python3/dist-packages/cnvlib/cnary.py:6: in 717s from scipy.stats import median_test 717s /usr/lib/python3/dist-packages/scipy/__init__.py:52: in 717s __config__ = _importlib.import_module('scipy.__config__' + _sysconfig.get_config_var('SOABI') + '__') 717s E TypeError: can only concatenate str (not "NoneType") to str 717s =========================== short test summary info ============================ 717s ERROR test/test_cnvlib.py 717s ERROR test/test_commands.py - TypeError: can only concatenate str (not "NoneT... 717s ERROR test/test_genome.py - TypeError: can only concatenate str (not "NoneTyp... 717s ERROR test/test_r.py - TypeError: can only concatenate str (not "NoneType") t... 717s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 717s ============================== 4 errors in 0.51s =============================== 717s E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /tmp/autopkgtest.Uz2vHW/autopkgtest_tmp/build; python3.13 -m pytest test 717s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i python{version} -p 3.13 returned exit code 13 717s make: *** [/tmp/ArUyEJ1bKN/run:4: pybuild-autopkgtest] Error 25 717s pybuild-autopkgtest: error: /tmp/ArUyEJ1bKN/run pybuild-autopkgtest returned exit code 2 717s autopkgtest [01:51:00]: test pybuild-autopkgtest: -----------------------] 718s autopkgtest [01:51:01]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 718s pybuild-autopkgtest FAIL non-zero exit status 25 718s autopkgtest [01:51:01]: @@@@@@@@@@@@@@@@@@@@ summary 718s run-unit-test PASS 718s pybuild-autopkgtest FAIL non-zero exit status 25 735s nova [W] Skipping flock for amd64 735s Creating nova instance adt-plucky-i386-cnvkit-20250316-013902-juju-7f2275-prod-proposed-migration-environment-15-f810ddf9-1f1c-4889-88fb-59aa0d227647 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 735s nova [W] Timed out waiting for 519ece6c-6ec0-4c33-a697-96e695f1e552 to get deleted. 735s nova [W] Skipping flock for amd64 735s Creating nova instance adt-plucky-i386-cnvkit-20250316-013902-juju-7f2275-prod-proposed-migration-environment-15-f810ddf9-1f1c-4889-88fb-59aa0d227647 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 735s nova [W] Timed out waiting for f31c9e29-148a-4a73-bec6-d712d830229e to get deleted.