0s autopkgtest [01:44:02]: starting date and time: 2025-03-16 01:44:02+0000 0s autopkgtest [01:44:02]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:44:02]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ennjgyph/out --timeout-copy=6000 --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-20@lcy02-3.secgroup --name adt-plucky-amd64-cnvkit-20250316-012924-juju-7f2275-prod-proposed-migration-environment-20-4b327b99-8874-485a-9860-3780c48cf5ea --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 51s autopkgtest [01:44:53]: testbed dpkg architecture: amd64 51s autopkgtest [01:44:53]: testbed apt version: 2.9.31ubuntu1 51s autopkgtest [01:44:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s autopkgtest [01:44:53]: testbed release detected to be: None 51s autopkgtest [01:44:53]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [66.6 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [84.0 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1844 B] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [338 kB] 51s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [168 kB] 51s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [14.9 kB] 51s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [18.0 kB] 51s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9324 B] 51s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 52s Fetched 1252 kB in 0s (5191 kB/s) 53s Reading package lists... 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 54s Calculating upgrade... 55s The following package was automatically installed and is no longer required: 55s libnl-genl-3-200 55s Use 'sudo apt autoremove' to remove it. 55s The following NEW packages will be installed: 55s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 55s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 55s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 55s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 55s The following packages will be upgraded: 55s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 55s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 55s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 55s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 55s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 55s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 55s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 55s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 55s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 55s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 55s linux-headers-generic linux-headers-virtual linux-image-generic 55s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 55s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 55s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 55s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 55s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 55s python3.13-minimal rsync rsyslog strace xz-utils 55s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 807 MB of archives. 55s After this operation, 326 MB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 55s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 55s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 55s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 55s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 55s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 55s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 55s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 55s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 55s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 55s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 55s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 55s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 55s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 55s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 55s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 55s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 55s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 55s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 55s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 55s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 55s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 55s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 55s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 55s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 55s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 55s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 55s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 55s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 55s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 55s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 55s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 55s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 55s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 55s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 55s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 55s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 55s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 55s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 55s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 55s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 55s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 55s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 55s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 55s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 55s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 55s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 55s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 55s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 55s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 55s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 55s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 55s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 55s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 55s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 55s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 55s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 55s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 55s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 55s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 55s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 55s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 55s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 55s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 55s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 55s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 55s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 55s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 55s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 55s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 55s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 55s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 55s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 55s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 55s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 55s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 55s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 60s 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] 60s 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] 61s 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] 62s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 62s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 62s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 62s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 62s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 62s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 62s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 62s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 62s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 62s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 62s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 62s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 62s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 62s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 62s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 62s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 62s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 63s Preconfiguring packages ... 63s Fetched 807 MB in 7s (111 MB/s) 63s (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.) 63s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 63s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 63s Setting up ncurses-bin (6.5+20250216-2) ... 63s (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.) 63s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 63s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 63s Setting up ncurses-base (6.5+20250216-2) ... 63s (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.) 63s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 63s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 64s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 64s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 64s Setting up liblz4-1:amd64 (1.10.0-4) ... 64s (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.) 64s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 64s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 64s Setting up liblzma5:amd64 (5.6.4-1) ... 64s (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.) 64s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 64s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 64s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 64s (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.) 64s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 65s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 65s Setting up apt (2.9.33) ... 65s (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.) 65s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 65s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 66s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 66s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 66s Setting up python3-minimal (3.13.2-2) ... 66s (Reading database ... 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 85s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 85s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 85s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 85s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 85s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 85s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 85s Setting up media-types (13.0.0) ... 85s Installing new version of config file /etc/mime.types ... 85s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 85s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 85s Setting up pci.ids (0.0~2025.03.09-1) ... 85s Setting up apt-utils (2.9.33) ... 85s Setting up libdebuginfod-common (0.192-4) ... 85s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 85s Setting up bpftool (7.6.0+6.14.0-10.10) ... 85s Setting up libestr0:amd64 (0.1.11-2) ... 85s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 85s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 85s Setting up dosfstools (4.2-1.2) ... 85s Setting up rsyslog (8.2412.0-2ubuntu2) ... 85s info: The user `syslog' is already a member of `adm'. 87s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 87s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 87s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 87s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 87s Setting up linux-headers-generic (6.14.0-10.10) ... 87s Setting up libjemalloc2:amd64 (5.3.0-3) ... 87s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 87s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 87s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 87s Installing new version of config file /etc/apparmor.d/openvpn ... 88s Reloading AppArmor profiles 90s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 90s No schema files found: doing nothing. 90s Setting up libglib2.0-data (2.84.0-1) ... 90s Setting up libncurses6:amd64 (6.5+20250216-2) ... 90s Setting up strace (6.13+ds-1ubuntu1) ... 90s Setting up xz-utils (5.6.4-1) ... 90s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 90s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 93s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 93s Setting up libpci3:amd64 (1:3.13.0-2) ... 93s Setting up python-apt-common (2.9.9build1) ... 93s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 93s Setting up pnp.ids (0.393-3) ... 93s Setting up libnl-3-200:amd64 (3.7.0-1) ... 93s Setting up python3.13-minimal (3.13.2-2) ... 94s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 94s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 94s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 94s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 94s Setting up rsync (3.4.1+ds1-3) ... 95s rsync.service is a disabled or a static unit not running, not starting it. 95s Setting up python3.13-gdbm (3.13.2-2) ... 95s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 95s Setting up ncurses-term (6.5+20250216-2) ... 95s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 95s Setting up libpython3.13:amd64 (3.13.2-2) ... 95s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 95s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 95s Setting up linux-headers-virtual (6.14.0-10.10) ... 95s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 95s Setting up python3.13 (3.13.2-2) ... 96s Setting up htop (3.4.0-2) ... 96s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 99s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 99s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 99s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 99s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 99s Setting up libfwupd3:amd64 (2.0.6-4) ... 99s Setting up python3 (3.13.2-2) ... 100s Setting up python3-markupsafe (2.1.5-1build4) ... 100s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 102s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 102s Setting up hwdata (0.393-3) ... 102s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 103s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 103s Setting up linux-perf (6.14.0-10.10) ... 103s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 103s Setting up python3-gi (3.50.0-4build1) ... 103s Setting up pciutils (1:3.13.0-2) ... 103s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 103s Setting up curl (8.12.1-3ubuntu1) ... 103s Setting up linux-image-virtual (6.14.0-10.10) ... 103s Setting up linux-tools-common (6.14.0-10.10) ... 103s Setting up fwupd (2.0.6-4) ... 103s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 103s fwupd.service is a disabled or a static unit not running, not starting it. 103s Setting up python3-systemd (235-1build6) ... 104s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 104s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 104s Setting up linux-image-generic (6.14.0-10.10) ... 104s Setting up python3-dbus (1.3.2-5build5) ... 104s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 104s Setting up linux-generic (6.14.0-10.10) ... 104s Setting up python3-apt (2.9.9build1) ... 104s Setting up python3-yaml (6.0.2-1build2) ... 104s Setting up python3-lazr.uri (1.0.6-6) ... 104s Setting up binutils (2.44-3ubuntu1) ... 104s Setting up cloud-init-base (25.1-0ubuntu3) ... 106s Setting up linux-virtual (6.14.0-10.10) ... 106s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 106s Setting up cloud-init (25.1-0ubuntu3) ... 106s Processing triggers for systemd (257.3-1ubuntu3) ... 106s Processing triggers for man-db (2.13.0-1) ... 108s Processing triggers for dbus (1.16.2-1ubuntu1) ... 108s Processing triggers for libc-bin (2.41-1ubuntu1) ... 108s Processing triggers for initramfs-tools (0.146ubuntu1) ... 108s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 108s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 122s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 122s /etc/kernel/postinst.d/initramfs-tools: 122s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 122s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 136s /etc/kernel/postinst.d/zz-update-grub: 136s Sourcing file `/etc/default/grub' 136s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 136s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 136s Generating grub configuration file ... 136s Found linux image: /boot/vmlinuz-6.14.0-10-generic 136s Found initrd image: /boot/initrd.img-6.14.0-10-generic 137s Found linux image: /boot/vmlinuz-6.12.0-16-generic 137s Found initrd image: /boot/initrd.img-6.12.0-16-generic 137s Found linux image: /boot/vmlinuz-6.11.0-8-generic 137s Found initrd image: /boot/initrd.img-6.11.0-8-generic 137s Warning: os-prober will not be executed to detect other bootable partitions. 137s Systems on them will not be added to the GRUB boot configuration. 137s Check GRUB_DISABLE_OS_PROBER documentation entry. 137s Adding boot menu entry for UEFI Firmware Settings ... 137s done 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Solving dependencies... 140s The following packages will be REMOVED: 140s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 140s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 140s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 140s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 140s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 140s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 140s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 140s linux-tools-6.12.0-16-generic* 140s 0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded. 140s After this operation, 545 MB disk space will be freed. 140s (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.) 140s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 140s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 140s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 140s Removing libpython3.12t64:amd64 (3.12.9-1) ... 140s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 140s Removing libnsl2:amd64 (1.3.0-3build3) ... 140s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 140s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 141s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 144s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 145s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 147s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 147s /etc/kernel/postrm.d/initramfs-tools: 147s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 148s /etc/kernel/postrm.d/zz-update-grub: 148s Sourcing file `/etc/default/grub' 148s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 148s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 148s Generating grub configuration file ... 148s Found linux image: /boot/vmlinuz-6.14.0-10-generic 148s Found initrd image: /boot/initrd.img-6.14.0-10-generic 148s Found linux image: /boot/vmlinuz-6.12.0-16-generic 148s Found initrd image: /boot/initrd.img-6.12.0-16-generic 148s Warning: os-prober will not be executed to detect other bootable partitions. 148s Systems on them will not be added to the GRUB boot configuration. 148s Check GRUB_DISABLE_OS_PROBER documentation entry. 148s Adding boot menu entry for UEFI Firmware Settings ... 148s done 148s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 149s W: Removing the running kernel 149s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 149s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 149s /etc/kernel/postrm.d/initramfs-tools: 149s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 149s /etc/kernel/postrm.d/zz-update-grub: 149s Sourcing file `/etc/default/grub' 149s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 149s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 149s Generating grub configuration file ... 149s Found linux image: /boot/vmlinuz-6.14.0-10-generic 149s Found initrd image: /boot/initrd.img-6.14.0-10-generic 149s Warning: os-prober will not be executed to detect other bootable partitions. 149s Systems on them will not be added to the GRUB boot configuration. 149s Check GRUB_DISABLE_OS_PROBER documentation entry. 149s Adding boot menu entry for UEFI Firmware Settings ... 149s done 149s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 150s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 152s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 152s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 152s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 152s Processing triggers for libc-bin (2.41-1ubuntu1) ... 152s (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 ... 76972 files and directories currently installed.) 152s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 152s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 152s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 152s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 152s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 152s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 152s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 152s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 152s autopkgtest [01:46:34]: upgrading testbed (apt dist-upgrade and autopurge) 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 154s Starting 2 pkgProblemResolver with broken count: 0 154s Done 154s Entering ResolveByKeep 155s 155s Calculating upgrade... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 155s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 156s Solving dependencies... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s autopkgtest [01:46:39]: rebooting testbed after setup commands that affected boot 161s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 173s autopkgtest [01:46:55]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 174s autopkgtest [01:46:56]: @@@@@@@@@@@@@@@@@@@@ apt-source cnvkit 175s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (dsc) [2483 B] 175s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (tar) [32.1 MB] 175s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cnvkit 0.9.12-1 (diff) [20.8 kB] 176s gpgv: Signature made Thu Feb 6 14:25:04 2025 UTC 176s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 176s gpgv: issuer "crusoe@debian.org" 176s gpgv: Can't check signature: No public key 176s dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.12-1.dsc: no acceptable signature found 177s autopkgtest [01:46:59]: testing package cnvkit version 0.9.12-1 177s autopkgtest [01:46:59]: build not needed 179s autopkgtest [01:47:01]: test run-unit-test: preparing testbed 179s Reading package lists... 180s Building dependency tree... 180s Reading state information... 180s Starting pkgProblemResolver with broken count: 0 180s Starting 2 pkgProblemResolver with broken count: 0 180s Done 181s The following NEW packages will be installed: 181s blt cnvkit cython3 fontconfig fontconfig-config fonts-dejavu-core 181s fonts-dejavu-mono fonts-lyx fonts-urw-base35 libblas3 libcairo2 libdatrie1 181s libdeflate0 libfontconfig1 libfontenc1 libgfortran5 libgomp1 libgpgmepp6t64 181s libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libice6 libimagequant0 181s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 181s liblbfgsb0 liblcms2-2 liblerc4 libopenjp2-7 libpango-1.0-0 181s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 181s libpoppler147 libqhull-r8.0 libraqm0 libsharpyuv0 libsm6 libtcl8.6 181s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 181s libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64 181s poppler-utils python-matplotlib-data python3-biopython python3-brotli 181s python3-cairo python3-contourpy python3-cycler python3-dateutil 181s python3-decorator python3-fonttools python3-freetype python3-fs 181s python3-importlib-metadata python3-joblib python3-kiwisolver python3-lxml 181s python3-lz4 python3-matplotlib python3-mpmath python3-networkx python3-numpy 181s python3-numpy-dev python3-packaging python3-pandas python3-pandas-lib 181s python3-pil python3-pil.imagetk python3-platformdirs python3-pomegranate 181s python3-pyfaidx python3-pysam python3-pytz python3-reportlab 181s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 181s python3-sympy python3-threadpoolctl python3-tk python3-tz python3-ufolib2 181s python3-unicodedata2 python3.12-tk python3.13-tk r-base-core 181s r-bioc-biocgenerics r-bioc-dnacopy sgml-base tk8.6-blt2.5 unicode-data unzip 181s w3c-sgml-lib x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zip 181s 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. 181s Need to get 183 MB of archives. 181s After this operation, 760 MB of additional disk space will be used. 181s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 181s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 181s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 181s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 181s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 181s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 181s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 182s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 182s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 182s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 182s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 182s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 182s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 182s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 182s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 182s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 182s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 182s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 182s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 182s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 182s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 182s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 182s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 182s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 182s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 182s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 182s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 182s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 182s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 182s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 182s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 182s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 182s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 182s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 182s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 182s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 182s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 182s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 182s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 182s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 182s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 182s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 182s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 182s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 182s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 182s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 182s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 182s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 182s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build2 [124 kB] 182s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 182s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 182s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 182s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 182s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 182s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 182s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 182s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 182s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 182s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 182s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 182s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 182s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 182s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 182s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 182s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 182s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 182s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 182s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 182s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 182s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 182s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 183s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 183s Get:73 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 183s Get:74 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 183s Get:75 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 183s Get:76 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 183s Get:77 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 183s Get:78 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 183s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 183s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 183s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 183s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 183s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 183s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8build1 [5332 kB] 183s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 183s Get:86 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 183s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 183s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 183s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 183s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 183s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 183s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 183s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 183s Get:94 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 183s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 183s Get:96 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 183s Get:97 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 183s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 183s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 183s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 183s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 183s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 183s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 183s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 183s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 183s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 183s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 183s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 183s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 183s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 183s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 183s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 183s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 184s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 184s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 184s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 184s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgmepp6t64 amd64 1.24.2-1ubuntu2 [126 kB] 184s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler147 amd64 25.03.0-2 [1295 kB] 184s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 25.03.0-2 [232 kB] 185s Preconfiguring packages ... 185s Fetched 183 MB in 3s (56.2 MB/s) 185s Selecting previously unselected package python3-numpy-dev:amd64. 185s (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 ... 76968 files and directories currently installed.) 185s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 185s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 185s Selecting previously unselected package libblas3:amd64. 185s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 185s Unpacking libblas3:amd64 (3.12.1-2) ... 185s Selecting previously unselected package libgfortran5:amd64. 185s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 185s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 185s Selecting previously unselected package liblapack3:amd64. 185s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 185s Unpacking liblapack3:amd64 (3.12.1-2) ... 185s Selecting previously unselected package python3-numpy. 185s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 185s Unpacking python3-numpy (1:2.2.3+ds-5) ... 185s Selecting previously unselected package sgml-base. 185s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 185s Unpacking sgml-base (1.31) ... 185s Selecting previously unselected package libtcl8.6:amd64. 185s Preparing to unpack .../006-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 185s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 186s Selecting previously unselected package fonts-dejavu-mono. 186s Preparing to unpack .../007-fonts-dejavu-mono_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-mono (2.37-8) ... 186s Selecting previously unselected package fonts-dejavu-core. 186s Preparing to unpack .../008-fonts-dejavu-core_2.37-8_all.deb ... 186s Unpacking fonts-dejavu-core (2.37-8) ... 186s Selecting previously unselected package libfontenc1:amd64. 186s Preparing to unpack .../009-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 186s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 186s Selecting previously unselected package x11-common. 186s Preparing to unpack .../010-x11-common_1%3a7.7+23ubuntu3_all.deb ... 186s Unpacking x11-common (1:7.7+23ubuntu3) ... 186s Selecting previously unselected package xfonts-encodings. 186s Preparing to unpack .../011-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 186s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 186s Selecting previously unselected package xfonts-utils. 186s Preparing to unpack .../012-xfonts-utils_1%3a7.7+7_amd64.deb ... 186s Unpacking xfonts-utils (1:7.7+7) ... 186s Selecting previously unselected package fonts-urw-base35. 186s Preparing to unpack .../013-fonts-urw-base35_20200910-8_all.deb ... 186s Unpacking fonts-urw-base35 (20200910-8) ... 186s Selecting previously unselected package fontconfig-config. 186s Preparing to unpack .../014-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 186s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 186s Selecting previously unselected package libfontconfig1:amd64. 186s Preparing to unpack .../015-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 186s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 186s Selecting previously unselected package libxrender1:amd64. 186s Preparing to unpack .../016-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 186s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 186s Selecting previously unselected package libxft2:amd64. 186s Preparing to unpack .../017-libxft2_2.3.6-1build1_amd64.deb ... 186s Unpacking libxft2:amd64 (2.3.6-1build1) ... 187s Selecting previously unselected package libxss1:amd64. 187s Preparing to unpack .../018-libxss1_1%3a1.2.3-1build3_amd64.deb ... 187s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 187s Selecting previously unselected package libtk8.6:amd64. 187s Preparing to unpack .../019-libtk8.6_8.6.16-1_amd64.deb ... 187s Unpacking libtk8.6:amd64 (8.6.16-1) ... 187s Selecting previously unselected package tk8.6-blt2.5. 187s Preparing to unpack .../020-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 187s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 187s Selecting previously unselected package blt. 187s Preparing to unpack .../021-blt_2.5.3+dfsg-8_amd64.deb ... 187s Unpacking blt (2.5.3+dfsg-8) ... 187s Selecting previously unselected package python3.12-tk. 187s Preparing to unpack .../022-python3.12-tk_3.12.9-1_amd64.deb ... 187s Unpacking python3.12-tk (3.12.9-1) ... 187s Selecting previously unselected package python3.13-tk. 187s Preparing to unpack .../023-python3.13-tk_3.13.2-2_amd64.deb ... 187s Unpacking python3.13-tk (3.13.2-2) ... 187s Selecting previously unselected package python3-tk:amd64. 187s Preparing to unpack .../024-python3-tk_3.13.1-1_amd64.deb ... 187s Unpacking python3-tk:amd64 (3.13.1-1) ... 187s Selecting previously unselected package python3-pil.imagetk:amd64. 187s Preparing to unpack .../025-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 187s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 187s Selecting previously unselected package libgomp1:amd64. 187s Preparing to unpack .../026-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 187s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 187s Selecting previously unselected package libimagequant0:amd64. 187s Preparing to unpack .../027-libimagequant0_2.18.0-1build1_amd64.deb ... 187s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 187s Selecting previously unselected package libjpeg-turbo8:amd64. 187s Preparing to unpack .../028-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 187s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 187s Selecting previously unselected package libjpeg8:amd64. 187s Preparing to unpack .../029-libjpeg8_8c-2ubuntu11_amd64.deb ... 187s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 187s Selecting previously unselected package liblcms2-2:amd64. 187s Preparing to unpack .../030-liblcms2-2_2.16-2_amd64.deb ... 187s Unpacking liblcms2-2:amd64 (2.16-2) ... 187s Selecting previously unselected package libopenjp2-7:amd64. 187s Preparing to unpack .../031-libopenjp2-7_2.5.3-2_amd64.deb ... 187s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 187s Selecting previously unselected package libgraphite2-3:amd64. 187s Preparing to unpack .../032-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 187s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 187s Selecting previously unselected package libharfbuzz0b:amd64. 187s Preparing to unpack .../033-libharfbuzz0b_10.2.0-1_amd64.deb ... 187s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 187s Selecting previously unselected package libraqm0:amd64. 187s Preparing to unpack .../034-libraqm0_0.10.2-1_amd64.deb ... 187s Unpacking libraqm0:amd64 (0.10.2-1) ... 187s Selecting previously unselected package libdeflate0:amd64. 187s Preparing to unpack .../035-libdeflate0_1.23-1_amd64.deb ... 187s Unpacking libdeflate0:amd64 (1.23-1) ... 187s Selecting previously unselected package libjbig0:amd64. 187s Preparing to unpack .../036-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 187s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 187s Selecting previously unselected package liblerc4:amd64. 187s Preparing to unpack .../037-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 187s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 187s Selecting previously unselected package libsharpyuv0:amd64. 187s Preparing to unpack .../038-libsharpyuv0_1.5.0-0.1_amd64.deb ... 187s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 187s Selecting previously unselected package libwebp7:amd64. 187s Preparing to unpack .../039-libwebp7_1.5.0-0.1_amd64.deb ... 187s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 187s Selecting previously unselected package libtiff6:amd64. 187s Preparing to unpack .../040-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 187s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 187s Selecting previously unselected package libwebpdemux2:amd64. 187s Preparing to unpack .../041-libwebpdemux2_1.5.0-0.1_amd64.deb ... 187s Unpacking libwebpdemux2:amd64 (1.5.0-0.1) ... 187s Selecting previously unselected package libwebpmux3:amd64. 187s Preparing to unpack .../042-libwebpmux3_1.5.0-0.1_amd64.deb ... 187s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 187s Selecting previously unselected package python3-pil:amd64. 187s Preparing to unpack .../043-python3-pil_11.1.0-5build1_amd64.deb ... 187s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 187s Selecting previously unselected package libpixman-1-0:amd64. 187s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_amd64.deb ... 187s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 187s Selecting previously unselected package libxcb-render0:amd64. 188s Preparing to unpack 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188s Selecting previously unselected package python3-reportlab. 188s Preparing to unpack .../051-python3-reportlab_4.3.1-1_all.deb ... 188s Unpacking python3-reportlab (4.3.1-1) ... 188s Selecting previously unselected package xml-core. 188s Preparing to unpack .../052-xml-core_0.19_all.deb ... 188s Unpacking xml-core (0.19) ... 188s Selecting previously unselected package w3c-sgml-lib. 188s Preparing to unpack .../053-w3c-sgml-lib_1.3-3_all.deb ... 188s Unpacking w3c-sgml-lib (1.3-3) ... 188s Selecting previously unselected package python3-biopython. 188s Preparing to unpack .../054-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 188s Unpacking python3-biopython (1.85+dfsg-2build1) ... 188s Selecting previously unselected package libjs-jquery. 188s Preparing to unpack .../055-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 188s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 188s Selecting previously unselected package libjs-jquery-ui. 188s Preparing to unpack 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python3-cycler (0.12.1-1) ... 189s Selecting previously unselected package python3-brotli. 189s Preparing to unpack .../062-python3-brotli_1.1.0-2build4_amd64.deb ... 189s Unpacking python3-brotli (1.1.0-2build4) ... 189s Selecting previously unselected package python3-platformdirs. 189s Preparing to unpack .../063-python3-platformdirs_4.3.6-1_all.deb ... 189s Unpacking python3-platformdirs (4.3.6-1) ... 189s Selecting previously unselected package python3-fs. 189s Preparing to unpack .../064-python3-fs_2.4.16-7_all.deb ... 189s Unpacking python3-fs (2.4.16-7) ... 189s Selecting previously unselected package libxslt1.1:amd64. 189s Preparing to unpack .../065-libxslt1.1_1.1.39-0exp1ubuntu2_amd64.deb ... 189s Unpacking libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 189s Selecting previously unselected package python3-lxml:amd64. 189s Preparing to unpack .../066-python3-lxml_5.3.1-1build1_amd64.deb ... 189s Unpacking python3-lxml:amd64 (5.3.1-1build1) ... 189s Selecting previously unselected package python3-lz4. 189s Preparing to unpack .../067-python3-lz4_4.4.0+dfsg-1build1_amd64.deb ... 189s Unpacking python3-lz4 (4.4.0+dfsg-1build1) ... 189s Selecting previously unselected package python3-decorator. 189s Preparing to unpack .../068-python3-decorator_5.1.1-5_all.deb ... 189s Unpacking python3-decorator (5.1.1-5) ... 189s Selecting previously unselected package liblbfgsb0:amd64. 189s Preparing to unpack .../069-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 189s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 189s Selecting previously unselected package python3-scipy. 189s Preparing to unpack .../070-python3-scipy_1.14.1-4ubuntu2_amd64.deb ... 189s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 190s Selecting previously unselected package python3-mpmath. 190s Preparing to unpack .../071-python3-mpmath_1.3.0-1_all.deb ... 190s Unpacking python3-mpmath (1.3.0-1) ... 190s Selecting previously unselected package python3-sympy. 190s Preparing to unpack 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unselected package python3-pandas-lib:amd64. 191s Preparing to unpack .../083-python3-pandas-lib_2.2.3+dfsg-8build1_amd64.deb ... 191s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 192s Selecting previously unselected package python3-pandas. 192s Preparing to unpack .../084-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 192s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 192s Selecting previously unselected package cython3. 192s Preparing to unpack .../085-cython3_3.0.11+dfsg-2ubuntu2_amd64.deb ... 192s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 192s Selecting previously unselected package python3-joblib. 192s Preparing to unpack .../086-python3-joblib_1.4.2-3_all.deb ... 192s Unpacking python3-joblib (1.4.2-3) ... 192s Selecting previously unselected package python3-networkx. 192s Preparing to unpack .../087-python3-networkx_3.2.1-4ubuntu1_all.deb ... 192s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 193s Selecting previously unselected package python3-pomegranate. 193s Preparing to unpack .../088-python3-pomegranate_0.15.0-1build1_amd64.deb ... 193s Unpacking python3-pomegranate (0.15.0-1build1) ... 193s Selecting previously unselected package python3-importlib-metadata. 193s Preparing to unpack .../089-python3-importlib-metadata_8.6.1-1_all.deb ... 193s Unpacking python3-importlib-metadata (8.6.1-1) ... 193s Selecting previously unselected package python3-pyfaidx. 193s Preparing to unpack .../090-python3-pyfaidx_0.8.1.3-1_all.deb ... 193s Unpacking python3-pyfaidx (0.8.1.3-1) ... 193s Selecting previously unselected package libhtscodecs2:amd64. 193s Preparing to unpack .../091-libhtscodecs2_1.6.1-2_amd64.deb ... 193s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 193s Selecting previously unselected package libhts3t64:amd64. 193s Preparing to unpack .../092-libhts3t64_1.21+ds-1_amd64.deb ... 193s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 193s Selecting previously unselected package python3-pysam. 193s Preparing to unpack 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liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 196s Setting up python3-importlib-metadata (8.6.1-1) ... 196s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 196s Setting up libdatrie1:amd64 (0.2.13-3build1) ... 196s Setting up python3-joblib (1.4.2-3) ... 196s Setting up python3-lz4 (4.4.0+dfsg-1build1) ... 196s Setting up libxcb-render0:amd64 (1.17.0-2) ... 196s Setting up python3-unicodedata2 (15.1.0+ds-1build3) ... 196s Setting up fonts-lyx (2.4.3-1) ... 196s Setting up unzip (6.0-28ubuntu6) ... 196s Setting up python3-threadpoolctl (3.1.0-1) ... 196s Setting up x11-common (1:7.7+23ubuntu3) ... 197s Setting up libdeflate0:amd64 (1.23-1) ... 197s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 197s Setting up python3-pytz (2025.1-3) ... 197s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 197s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 197s Setting up python3-freetype (2.5.1-1) ... 197s Setting up python3-networkx (3.2.1-4ubuntu1) ... 198s Setting up libjbig0:amd64 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cython3 (3.0.11+dfsg-2ubuntu2) ... 200s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 200s Setting up fonts-dejavu-core (2.37-8) ... 200s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 200s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 200s Setting up libwebp7:amd64 (1.5.0-0.1) ... 200s Setting up libxslt1.1:amd64 (1.1.39-0exp1ubuntu2) ... 200s Setting up libhts3t64:amd64 (1.21+ds-1) ... 200s Setting up libopenjp2-7:amd64 (2.5.3-2) ... 200s Setting up libharfbuzz0b:amd64 (10.2.0-1) ... 200s Setting up libthai-data (0.1.29-2build1) ... 200s Setting up python3-dateutil (2.9.0-3) ... 200s Setting up sgml-base (1.31) ... 201s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 201s Setting up libpaper2:amd64 (2.2.5-0.3) ... 201s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 201s Setting up python3-mpmath (1.3.0-1) ... 201s Setting up python-matplotlib-data (3.8.3-7build1) ... 201s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 201s Setting up xdg-utils (1.2.1-2ubuntu1) ... 201s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 201s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 201s Setting up python3-pyfaidx (0.8.1.3-1) ... 201s Setting up python3-sympy (1.13.3-5) ... 208s Setting up libice6:amd64 (2:1.1.1-1) ... 208s Setting up liblapack3:amd64 (3.12.1-2) ... 208s 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 208s Setting up python3-pysam (0.23.0+ds-1build1) ... 208s Setting up fontconfig-config (2.15.0-2ubuntu1) ... 209s Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... 209s Setting up libpaper-utils (2.2.5-0.3) ... 209s Setting up xfonts-utils (1:7.7+7) ... 209s Setting up libthai0:amd64 (0.1.29-2build1) ... 209s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 209s Setting up libraqm0:amd64 (0.10.2-1) ... 209s Setting up python3-numpy (1:2.2.3+ds-5) ... 211s Setting up python3-lxml:amd64 (5.3.1-1build1) ... 211s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 211s Setting up xml-core (0.19) ... 211s Setting up python3-contourpy (1.3.1-1build1) ... 212s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 212s Setting up libsm6:amd64 (2:1.2.4-1) ... 212s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 212s Setting up fontconfig (2.15.0-2ubuntu1) ... 214s Regenerating fonts cache... done. 214s Setting up libxft2:amd64 (2.3.6-1build1) ... 214s Setting up python3-scipy (1.14.1-4ubuntu2) ... 218s Setting up libpoppler147:amd64 (25.03.0-2) ... 218s Setting up python3-pomegranate (0.15.0-1build1) ... 218s Setting up libtk8.6:amd64 (8.6.16-1) ... 218s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 218s Setting up libpango-1.0-0:amd64 (1.56.2-1) ... 218s Setting up python3.12-tk (3.12.9-1) ... 218s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 218s Setting up fonts-urw-base35 (20200910-8) ... 218s Setting up libcairo2:amd64 (1.18.2-2) ... 218s Setting up python3.13-tk (3.13.2-2) ... 218s Setting up python3-pil:amd64 (11.1.0-5build1) ... 219s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 224s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 224s Setting up python3-sklearn (1.4.2+dfsg-8) ... 225s Setting up poppler-utils (25.03.0-2) ... 225s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 225s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 225s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 225s Setting up python3-cairo (1.26.1-2build2) ... 226s Setting up blt (2.5.3+dfsg-8) ... 226s Setting up python3-tk:amd64 (3.13.1-1) ... 226s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 226s Setting up python3-rlpycairo (0.3.0-3) ... 226s Setting up r-base-core (4.4.3-1) ... 226s Creating config file /etc/R/Renviron with new version 226s Setting up python3-reportlab (4.3.1-1) ... 227s Setting up r-bioc-biocgenerics (0.52.0-2) ... 227s Setting up r-bioc-dnacopy (1.80.0-2) ... 227s Setting up python3-fonttools (4.55.3-2build1) ... 228s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 228s Setting up python3-matplotlib (3.8.3-7build1) ... 229s Processing triggers for libc-bin (2.41-1ubuntu1) ... 229s Processing triggers for man-db (2.13.0-1) ... 232s Processing triggers for install-info (7.1.1-1) ... 232s Processing triggers for sgml-base (1.31) ... 232s Setting up w3c-sgml-lib (1.3-3) ... 264s Setting up python3-biopython (1.85+dfsg-2build1) ... 266s Setting up cnvkit (0.9.12-1) ... 267s autopkgtest [01:48:29]: test run-unit-test: [----------------------- 267s cnvkit.py batch -n -f formats/chrM-Y-trunc.hg19.fa -m wgs formats/na12878-chrM-Y-trunc.bam -d build 269s CNVkit 0.9.12 269s WGS protocol: recommend '--annotate' option (e.g. refFlat.txt) to help locate genes in output files. 269s chrM: Scanning for accessible regions 269s Accessible region chrM:0-121 (size 121) 269s Accessible region chrM:122-1271 (size 1149) 269s Accessible region chrM:1274-1288 (size 14) 269s Accessible region chrM:1289-1547 (size 258) 269s Accessible region chrM:1553-16571 (size 15018) 269s chrY: Scanning for accessible regions 269s Accessible region chrY:500-14900 (size 14400) 269s Accessible region chrY:15600-22966 (size 7366) 269s chrY: Joining over small gaps 269s Joining chrY 500-14900 and 15600-22966 (gap size 700) 269s Wrote chrM-Y-trunc.hg19.bed with 1 regions 269s Detected file format: bed 269s Splitting large targets 269s Created directory build 269s Wrote build/chrM-Y-trunc.hg19.target.bed with 4 regions 269s Wrote build/chrM-Y-trunc.hg19.antitarget.bed with 0 regions 269s Building a flat reference... 269s Detected file format: bed 269s Calculating GC and RepeatMasker content in formats/chrM-Y-trunc.hg19.fa ... 269s Extracting sequences from chromosome chrY 269s Wrote build/reference.cnn with 4 regions 269s Running 1 samples in serial 269s Running the CNVkit pipeline on formats/na12878-chrM-Y-trunc.bam ... 269s Indexing BAM file formats/na12878-chrM-Y-trunc.bam 269s Processing reads in na12878-chrM-Y-trunc.bam 269s Time: 0.009 seconds (4193 reads/sec, 453 bins/sec) 269s Summary: #bins=4, #reads=37, mean=9.2500, min=0.0, max=21.0 269s Percent reads in regions: 0.063 (of 58636 mapped) 269s Wrote build/na12878-chrM-Y-trunc.targetcoverage.cnn with 4 regions 269s Skip processing na12878-chrM-Y-trunc.bam with empty regions file build/chrM-Y-trunc.hg19.antitarget.bed 269s Wrote build/na12878-chrM-Y-trunc.antitargetcoverage.cnn with 0 regions 269s Processing target: na12878-chrM-Y-trunc 269s Keeping 4 of 4 bins 269s Correcting for GC bias... 269s Processing antitarget: na12878-chrM-Y-trunc 269s Wrote build/na12878-chrM-Y-trunc.cnr with 4 regions 269s Segmenting build/na12878-chrM-Y-trunc.cnr ... 269s Segmenting with method 'cbs', significance threshold 1e-06, in 1 processes 270s Post-processing build/na12878-chrM-Y-trunc.cns ... 270s Wrote build/na12878-chrM-Y-trunc.cns with 1 regions 270s Applying filter 'ci' 270s Filtered by 'ci' from 1 to 1 rows 270s Calling copy number with thresholds: -1.1 => 0, -0.25 => 1, 0.2 => 2, 0.7 => 3 270s Wrote build/na12878-chrM-Y-trunc.call.cns with 1 regions 270s Significant hits in 4/4 bins (100%) 270s Wrote build/na12878-chrM-Y-trunc.bintest.cns with 4 regions 270s 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/ 272s Wrote build/p2-20_5.antitargetcoverage.cnn with 12563 regions 272s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 272s Wrote build/p2-20_5.targetcoverage.cnn with 6646 regions 272s Wrote build/p2-5_5.antitargetcoverage.cnn with 12563 regions 272s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 272s Wrote build/p2-5_5.targetcoverage.cnn with 6646 regions 273s Wrote build/p2-9_5.antitargetcoverage.cnn with 12563 regions 273s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 273s Wrote build/p2-9_5.targetcoverage.cnn with 6646 regions 273s cnvkit.py reference build/p2-*_5.*targetcoverage.cnn -y -o build/reference-picard.cnn 275s Number of target and antitarget files: 3, 3 275s No FASTA reference genome provided; skipping GC, RM calculations 275s Sample sex not provided; inferring from samples. 275s Relative log2 coverage of chrX=-0.325, chrY=-6.57 (maleness=0.0191 x 0.532 = 0.0102) --> assuming female 275s Relative log2 coverage of chrX=-0.324, chrY=-11 (maleness=0.0317 x 0.532 = 0.0168) --> assuming female 275s Relative log2 coverage of chrX=-0.17, chrY=-17.9 (maleness=0.0141 x 0.532 = 0.00752) --> assuming female 275s Relative log2 coverage of chrX=-0.522, chrY=-11.2 (maleness=0.179 x 0.809 = 0.145) --> assuming female 275s Relative log2 coverage of chrX=-0.531, chrY=-12.6 (maleness=0.11 x 0.895 = 0.0984) --> assuming female 275s Relative log2 coverage of chrX=-0.412, chrY=-16.1 (maleness=0.0599 x 0.895 = 0.0536) --> assuming female 275s Loading build/p2-20_5.targetcoverage.cnn 275s Correcting for GC bias for p2-20_5... 275s Correcting for density bias for p2-20_5... 275s Loading build/p2-5_5.targetcoverage.cnn 275s Correcting for GC bias for p2-5_5... 275s Correcting for density bias for p2-5_5... 275s Loading build/p2-9_5.targetcoverage.cnn 275s Correcting for GC bias for p2-9_5... 276s Correcting for density bias for p2-9_5... 276s Loading build/p2-20_5.antitargetcoverage.cnn 276s Correcting for GC bias for p2-20_5... 276s Loading build/p2-5_5.antitargetcoverage.cnn 276s Correcting for GC bias for p2-5_5... 276s Loading build/p2-9_5.antitargetcoverage.cnn 277s Correcting for GC bias for p2-9_5... 277s Calculating average bin coverages 284s Calculating bin spreads 286s Targets: 338 (5.086%) bins failed filters (log2 < -5.0, log2 > 5.0, spread > 1.0) 286s PLCH2 chr1:2433503-2433878 log2=-0.586 spread=0.505 286s " chr1:2435319-2436685 log2=-0.709 spread=0.503 286s ARID1A chr1:27022844-27024053 log2=-1.481 spread=0.110 286s MYCL1 chr1:40366439-40367601 log2=0.085 spread=0.245 286s LRRC8B chr1:90000112-90000296 log2=0.225 spread=0.274 286s CGH chr1:106510773-106510953 log2=-0.394 spread=0.325 286s NOTCH2 chr1:120572470-120572622 log2=-2.593 spread=1.502 286s " chr1:120611883-120612051 log2=0.070 spread=0.050 286s NTRK1 chr1:156830676-156830968 log2=-0.814 spread=0.513 286s " chr1:156842391-156842479 log2=-0.398 spread=0.290 286s MPC2 chr1:167906099-167906278 log2=0.166 spread=0.393 286s ABL2 chr1:179198326-179198565 log2=-0.546 spread=0.389 286s SMG7 chr1:183441669-183441848 log2=0.368 spread=0.171 286s " chr1:183481886-183481951 log2=-0.040 spread=0.119 286s CDC73 chr1:193219724-193219907 log2=0.087 spread=0.141 286s AKT3 chr1:243675572-243675743 log2=0.222 spread=0.106 286s " chr1:243800859-243801066 log2=0.023 spread=0.063 286s MYCN chr2:16082132-16082989 log2=-1.145 spread=0.371 286s DNMT3A chr2:25475011-25475213 log2=-1.033 spread=0.468 286s " chr2:25536716-25536891 log2=0.702 spread=0.033 286s MSH2 chr2:47698049-47698231 log2=0.129 spread=0.196 286s MSH6 chr2:48010322-48010657 log2=-0.616 spread=0.644 286s VRK2 chr2:58386820-58386989 log2=0.422 spread=0.287 286s REL chr2:61108881-61109061 log2=1.026 spread=0.559 286s " chr2:61128072-61128256 log2=0.115 spread=0.173 286s " chr2:61145275-61145462 log2=0.014 spread=0.099 286s CGH chr2:82511447-82511627 log2=-0.205 spread=0.129 286s DUSP2 chr2:96810448-96811208 log2=-0.655 spread=0.435 286s MAP3K2 chr2:128081427-128081603 log2=-0.218 spread=0.144 286s " chr2:128095237-128095425 log2=0.215 spread=0.212 286s METTL8 chr2:172291040-172291240 log2=-0.027 spread=0.068 286s VHL chr3:10183481-10183898 log2=-0.155 spread=0.209 286s TGFBR2 chr3:30648320-30648501 log2=0.496 spread=0.504 286s EPHA6 chr3:96585608-96585773 log2=0.045 spread=0.100 286s " chr3:97160189-97160367 log2=-0.050 spread=0.191 286s ATR chr3:142254935-142255077 log2=0.024 spread=0.027 286s " chr3:142286854-142287031 log2=-0.076 spread=0.116 286s GAK chr4:896278-896357 log2=-1.505 spread=1.261 286s FGFR3 chr4:1795608-1795799 log2=-0.750 spread=0.491 286s " chr4:1803044-1803507 log2=-0.073 spread=0.117 286s " chr4:1808792-1809022 log2=0.252 spread=0.108 286s CGH chr4:31509625-31509802 log2=-0.057 spread=0.101 286s EPHA5 chr4:66535226-66535490 log2=-0.681 spread=0.567 286s CGH chr4:163514273-163514460 log2=-0.403 spread=0.271 286s " chr4:178514600-178514725 log2=-0.098 spread=0.096 286s TERT chr5:1293376-1294792 log2=-0.724 spread=0.511 286s TERT Promoter chr5:1294836-1295203 log2=-1.970 spread=0.777 286s " chr5:1295312-1295381 log2=-0.690 spread=0.462 286s CGH chr5:12000292-12000462 log2=-0.342 spread=0.056 286s " chr5:25519857-25520034 log2=-0.015 spread=0.095 286s RICTOR chr5:38958717-38958965 log2=0.011 spread=0.018 286s " chr5:38962338-38962525 log2=0.005 spread=0.019 286s " chr5:38966685-38966862 log2=0.006 spread=0.165 286s " chr5:38978620-38978763 log2=0.040 spread=0.030 286s " chr5:39074133-39074327 log2=-0.158 spread=0.139 286s CGH chr5:42002796-42002944 log2=-0.083 spread=0.071 286s " chr5:51030131-51030313 log2=-0.034 spread=0.192 286s MAP3K1 chr5:56111354-56111894 log2=-1.478 spread=1.050 286s " chr5:56168412-56168590 log2=0.479 spread=0.038 286s CGH chr5:61573234-61573421 log2=-0.072 spread=0.161 286s PIK3R1 chr5:67589487-67589699 log2=0.349 spread=0.264 286s RASA1 chr5:86633752-86633938 log2=0.119 spread=0.112 286s " chr5:86637023-86637168 log2=0.054 spread=0.111 286s " chr5:86642414-86642592 log2=0.254 spread=0.162 286s " chr5:86648912-86649096 log2=0.092 spread=0.062 286s " chr5:86670598-86670778 log2=0.222 spread=0.198 286s MCTP1 chr5:94619518-94620311 log2=-1.064 spread=0.754 286s CGH chr5:99008357-99008506 log2=-0.069 spread=0.390 286s APC chr5:112101965-112102138 log2=0.104 spread=0.217 286s NPM1 chr5:170832371-170832440 log2=-0.398 spread=0.335 286s " chr5:170837567-170837631 log2=0.085 spread=0.349 286s FLT4 chr5:180045962-180046145 log2=-0.884 spread=0.532 286s " chr5:180046203-180046404 log2=-1.531 spread=0.722 286s " chr5:180076418-180076603 log2=-2.224 spread=1.416 286s TPMT chr6:18130863-18131048 log2=0.022 spread=0.099 286s DOM3Z chr6:31938905-31939081 log2=-20.014 spread=0.042 286s " chr6:31939599-31940313 log2=-19.582 spread=0.181 286s STK19 chr6:31940351-31940562 log2=-18.990 spread=0.181 286s " chr6:31946632-31946824 log2=-20.052 spread=0.088 286s " chr6:31947142-31947366 log2=-20.114 spread=0.066 286s " chr6:31948176-31948360 log2=-19.982 spread=0.149 286s " chr6:31948382-31948612 log2=-19.757 spread=0.165 286s " chr6:31948730-31949253 log2=-20.048 spread=0.014 286s NOTCH4 chr6:32163159-32163956 log2=-19.306 spread=0.203 286s " chr6:32164046-32164227 log2=-19.755 spread=0.189 286s " chr6:32164652-32164888 log2=-19.984 spread=0.154 286s " chr6:32165021-32165403 log2=-19.625 spread=0.196 286s " chr6:32166163-32166545 log2=-20.043 spread=0.072 286s " chr6:32166648-32166962 log2=-3.514 spread=5.742 286s " chr6:32168554-32168821 log2=-19.601 spread=0.197 286s " chr6:32168844-32169306 log2=-19.683 spread=0.166 286s " chr6:32169801-32170391 log2=-19.405 spread=0.205 286s " chr6:32171492-32171691 log2=-20.095 spread=0.101 286s " chr6:32171861-32172198 log2=-3.141 spread=7.288 286s " chr6:32178478-32178749 log2=-19.927 spread=0.164 286s " chr6:32180197-32180441 log2=-10.902 spread=9.532 286s " chr6:32180544-32180722 log2=-19.675 spread=0.186 286s " chr6:32180857-32181062 log2=-19.562 spread=0.227 286s " chr6:32181411-32181646 log2=-19.966 spread=0.171 286s " chr6:32181832-32182066 log2=-19.961 spread=0.172 286s " chr6:32182948-32183194 log2=-19.935 spread=0.168 286s " chr6:32184667-32185079 log2=-19.923 spread=0.165 286s " chr6:32185720-32185919 log2=-19.707 spread=0.197 286s " chr6:32187317-32187601 log2=-19.765 spread=0.173 286s " chr6:32187871-32188094 log2=-19.660 spread=0.188 286s " chr6:32188127-32188451 log2=-19.622 spread=0.169 286s " chr6:32188481-32188693 log2=-19.902 spread=0.132 286s " chr6:32188704-32189133 log2=-19.501 spread=0.193 286s " chr6:32190258-32190616 log2=-19.570 spread=0.209 286s " chr6:32190724-32190908 log2=-19.540 spread=0.232 286s " chr6:32191570-32191668 log2=-19.773 spread=0.178 286s " chr6:32191676-32191753 log2=-19.374 spread=0.201 286s FOXP4 chr6:41565467-41565725 log2=-0.259 spread=0.369 286s CCND3 chr6:41909139-41909415 log2=0.039 spread=0.240 286s NFKBIE chr6:44232672-44233479 log2=0.034 spread=0.050 286s CGH chr6:49502071-49502248 log2=-0.093 spread=0.241 286s POU3F2 chr6:99282701-99283145 log2=-1.559 spread=0.536 286s ROS1 chr6:117657131-117657335 log2=-0.377 spread=0.282 286s RSPO3 chr6:127510871-127511054 log2=-0.128 spread=0.105 286s PTPRK chr6:128313744-128313923 log2=0.177 spread=0.190 286s " chr6:128316545-128316699 log2=-0.070 spread=0.050 286s MAP3K5 chr6:137026207-137026289 log2=0.053 spread=0.094 286s ARID1B chr6:157099014-157099324 log2=-0.621 spread=0.410 286s " chr6:157099442-157099991 log2=-0.846 spread=0.504 286s " chr6:157100042-157100634 log2=-1.570 spread=0.825 286s IGF2R chr6:160390228-160390461 log2=-2.660 spread=0.959 286s RAC1 chr7:6414287-6414459 log2=0.162 spread=0.232 286s COL28A1 chr7:7521080-7521229 log2=0.015 spread=0.050 286s FKBP9 chr7:32997131-32997427 log2=-0.367 spread=0.272 286s CGH chr7:52520101-52520286 log2=-1.525 spread=1.176 286s EGFR chr7:55086913-55087091 log2=-0.081 spread=0.180 286s CDK6 chr7:92462355-92462676 log2=0.309 spread=0.198 286s TRRAP chr7:98479525-98479705 log2=0.060 spread=0.087 286s " chr7:98491365-98491541 log2=0.209 spread=0.153 286s " chr7:98493314-98493496 log2=0.389 spread=0.207 286s SMO chr7:128828938-128829041 log2=-2.056 spread=1.317 286s " chr7:128829048-128829358 log2=-0.474 spread=0.315 286s BRAF chr7:140481968-140482374 log2=0.013 spread=0.017 286s " chr7:140484736-140484912 log2=0.081 spread=0.150 286s " chr7:140487956-140488430 log2=-0.089 spread=0.142 286s " chr7:140493336-140493442 log2=-0.340 spread=0.283 286s " chr7:140624315-140624540 log2=-0.497 spread=0.342 286s TNKS chr8:9609998-9610174 log2=0.021 spread=0.082 286s WRN chr8:30925752-30925890 log2=0.120 spread=0.158 286s " chr8:30941153-30941335 log2=0.079 spread=0.294 286s " chr8:30942625-30942802 log2=0.044 spread=0.247 286s " chr8:30947918-30948092 log2=0.151 spread=0.124 286s " chr8:31000128-31000252 log2=-0.099 spread=0.098 286s " chr8:31001006-31001182 log2=-0.002 spread=0.062 286s GPR124 chr8:37654740-37655077 log2=-1.617 spread=1.020 286s " chr8:37698557-37699898 log2=-0.612 spread=0.029 286s ADAM32 chr8:39022338-39022511 log2=-0.103 spread=0.127 286s PRKDC chr8:48827831-48828019 log2=0.018 spread=0.101 286s " chr8:48845528-48845758 log2=0.056 spread=0.196 286s " chr8:48866846-48867043 log2=-0.067 spread=0.097 286s " chr8:48868369-48868526 log2=-0.239 spread=0.174 286s " chr8:48872485-48872722 log2=-0.636 spread=0.464 286s CGH chr8:88503010-88503173 log2=-0.137 spread=0.254 286s FBXO43 chr8:101149746-101149928 log2=0.049 spread=0.082 286s SMARCA2 chr9:2047182-2047507 log2=-0.353 spread=0.368 286s " chr9:2101491-2101640 log2=0.244 spread=0.104 286s JAK2 chr9:5064539-5066968 log2=0.119 spread=0.077 286s " chr9:5067014-5067883 log2=0.146 spread=0.089 286s " chr9:5068184-5070306 log2=0.133 spread=0.092 286s " chr9:5076944-5077152 log2=0.046 spread=0.137 286s PTPRD chr9:8527276-8527424 log2=-0.239 spread=0.237 286s CDKN2A chr9:21973657-21973843 log2=0.148 spread=0.043 286s " chr9:21986759-21986899 log2=0.058 spread=0.175 286s LINGO2 chr9:28505910-28506090 log2=-0.396 spread=0.123 286s CGH chr9:39011524-39011705 log2=-0.205 spread=0.230 286s TRPM3 chr9:73240339-73240498 log2=0.009 spread=0.086 286s NTRK2 chr9:87356721-87356908 log2=0.166 spread=0.265 286s " chr9:87425375-87425452 log2=0.494 spread=0.066 286s PTCH1 chr9:98278654-98278833 log2=-0.560 spread=0.038 286s GPSM1 chr9:139222089-139222248 log2=-4.879 spread=2.118 286s " chr9:139250747-139251032 log2=-0.223 spread=0.273 286s " chr9:139252418-139252703 log2=-0.512 spread=0.264 286s NOTCH1 chr9:139396674-139396979 log2=-0.595 spread=0.295 286s " chr9:139417262-139417677 log2=-0.173 spread=0.191 286s " chr9:139440110-139440287 log2=-1.257 spread=0.500 286s MRC1 chr10:18136438-18136613 log2=-1.945 spread=3.242 286s CGH chr10:22505654-22505837 log2=0.072 spread=0.107 286s RET chr10:43572644-43572830 log2=-1.376 spread=1.092 286s " chr10:43600360-43600677 log2=-0.341 spread=0.222 286s PTEN chr10:89653722-89653907 log2=0.394 spread=0.030 286s " chr10:89685254-89685374 log2=0.244 spread=0.259 286s TNKS2 chr10:93558396-93558682 log2=-0.037 spread=0.051 286s " chr10:93579008-93579121 log2=0.166 spread=0.220 286s SUFU chr10:104263859-104264127 log2=0.269 spread=0.224 286s SHOC2 chr10:112679251-112679451 log2=-0.434 spread=0.304 286s " chr10:112679716-112679934 log2=-0.008 spread=0.028 286s CGH chr10:114003863-114003979 log2=-0.115 spread=0.290 286s WT1 chr11:32456191-32456924 log2=-1.020 spread=0.782 286s CCND1 chr11:69465991-69466081 log2=0.058 spread=0.209 286s GAB2 chr11:78128632-78128813 log2=-0.754 spread=0.552 286s MRE11A chr11:94153219-94153345 log2=-0.021 spread=0.076 286s " chr11:94170270-94170454 log2=0.095 spread=0.285 286s YAP1 chr11:101981528-101981920 log2=-0.331 spread=0.340 286s GUCY1A2 chr11:106888426-106888817 log2=-1.400 spread=0.707 286s ATM chr11:108153392-108153639 log2=0.113 spread=0.136 286s " chr11:108164020-108164234 log2=-0.056 spread=0.040 286s " chr11:108217986-108218135 log2=0.359 spread=0.277 286s MLL chr11:118307178-118307688 log2=-1.486 spread=0.278 286s ARHGAP32 chr11:129003788-129003964 log2=0.053 spread=0.102 286s ETV6 chr12:12018196-12018602 log2=-0.014 spread=0.112 286s KRAS chr12:25362676-25362878 log2=0.128 spread=0.150 286s " chr12:25391004-25391186 log2=0.368 spread=0.128 286s DIP2B chr12:51002431-51002557 log2=0.344 spread=0.188 286s ATF1 chr12:51206642-51206737 log2=0.009 spread=0.024 286s " chr12:51206782-51207287 log2=-0.012 spread=0.101 286s PTPN11 chr12:112856822-112857002 log2=-0.268 spread=0.071 286s CDK8 chr13:26911641-26911828 log2=-0.125 spread=0.167 286s " chr13:26970356-26970536 log2=0.137 spread=0.121 286s FLT3 chr13:28674525-28674708 log2=-2.257 spread=1.745 286s FLT1 chr13:29068850-29069036 log2=-0.914 spread=0.672 286s BRCA2 chr13:32900164-32900478 log2=-0.076 spread=0.110 286s " chr13:32903506-32903689 log2=0.019 spread=0.232 286s " chr13:32918645-32918823 log2=0.158 spread=0.114 286s " chr13:32920899-32921077 log2=0.014 spread=0.247 286s RB1 chr13:48877994-48878223 log2=-0.155 spread=0.250 286s " chr13:48919164-48919369 log2=0.025 spread=0.094 286s " chr13:48921877-48922044 log2=0.106 spread=0.147 286s " chr13:48923026-48923204 log2=0.360 spread=0.016 286s " chr13:48938965-48939147 log2=0.084 spread=0.356 286s " chr13:48941578-48941767 log2=0.238 spread=0.212 286s " chr13:48947486-48947665 log2=0.025 spread=0.126 286s " chr13:48954166-48954251 log2=0.061 spread=0.273 286s " chr13:49037815-49038005 log2=0.063 spread=0.062 286s " chr13:49047410-49047589 log2=0.053 spread=0.170 286s CGH chr13:63016375-63016514 log2=-0.434 spread=0.282 286s " chr13:85527771-85527948 log2=0.007 spread=0.222 286s GPC5 chr13:93003992-93004180 log2=-0.192 spread=0.289 286s IRS2 chr13:110434582-110438324 log2=-0.768 spread=0.252 286s " chr13:110438332-110438432 log2=-3.643 spread=2.325 286s CGH chr14:19220933-19221047 log2=-1.230 spread=1.205 286s " chr14:20291466-20291612 log2=0.697 spread=0.248 286s NKX2-1 chr14:36986433-36987264 log2=-1.444 spread=0.135 286s " chr14:36989195-36989373 log2=0.023 spread=0.162 286s SOS2 chr14:50596601-50596777 log2=0.237 spread=0.146 286s " chr14:50619741-50619923 log2=0.003 spread=0.272 286s " chr14:50697856-50698044 log2=0.277 spread=0.334 286s MAP3K9 chr14:71275435-71275784 log2=-0.385 spread=0.461 286s " chr14:71275790-71275923 log2=-2.815 spread=1.938 286s TSHR chr14:81528428-81528609 log2=0.070 spread=0.244 286s CGH chr15:20870700-20870881 log2=1.102 spread=0.611 286s " chr15:38544477-38545455 log2=-0.348 spread=0.179 286s SPRED1 chr15:38647081-38647177 log2=0.225 spread=0.350 286s LTK chr15:41803310-41803809 log2=-1.956 spread=1.443 286s " chr15:41803968-41804185 log2=-2.202 spread=0.188 286s " chr15:41804261-41804494 log2=-0.402 spread=0.392 286s NTRK3 chr15:88532873-88532940 log2=-0.337 spread=0.240 286s IDH2 chr15:90645456-90645663 log2=-0.951 spread=0.705 286s PDPK1 chr16:2588022-2588201 log2=-1.782 spread=1.082 286s " chr16:2611404-2611585 log2=-5.171 spread=1.963 286s " chr16:2611721-2611943 log2=-11.810 spread=9.172 286s " chr16:2615504-2615725 log2=-20.113 spread=0.007 286s " chr16:2616307-2616486 log2=-20.054 spread=0.072 286s " chr16:2631267-2631414 log2=-20.009 spread=0.061 286s " chr16:2631583-2631734 log2=-20.089 spread=0.090 286s " chr16:2633363-2633616 log2=-20.101 spread=0.089 286s CREBBP chr16:3799553-3799731 log2=0.082 spread=0.155 286s SOCS1 chr16:11349442-11349617 log2=0.110 spread=0.079 286s BOLA2B chr16:29466011-29466278 log2=-18.994 spread=0.172 286s CGH chr16:31526705-31526886 log2=0.057 spread=0.074 286s CYLD chr16:50821673-50821804 log2=0.007 spread=0.188 286s " chr16:50826460-50826650 log2=0.239 spread=0.204 286s CGH chr16:51098326-51098475 log2=-0.578 spread=0.376 286s " chr16:60005694-60005857 log2=-0.366 spread=0.298 286s CDH1 chr16:68771239-68771428 log2=-0.813 spread=0.625 286s CGH chr16:81005282-81005469 log2=-0.134 spread=0.229 286s MAP2K4 chr17:11924151-11924355 log2=-2.093 spread=1.900 286s " chr17:12011053-12011253 log2=0.028 spread=0.232 286s NF1 chr17:29422259-29422433 log2=-0.466 spread=0.381 286s " chr17:29496854-29497046 log2=0.226 spread=0.193 286s RHOT1 chr17:30469629-30469811 log2=-0.034 spread=0.252 286s " chr17:30519172-30519355 log2=0.163 spread=0.289 286s " chr17:30525911-30526093 log2=-0.157 spread=0.046 286s ERBB2 chr17:37856430-37856609 log2=0.221 spread=0.369 286s RPTOR chr17:78896472-78896661 log2=0.267 spread=0.290 286s C18orf56 chr18:657548-657727 log2=-2.406 spread=0.189 286s CDH2 chr18:25756859-25757030 log2=-3.262 spread=0.283 286s KIAA1328 chr18:34512037-34512192 log2=0.081 spread=0.180 286s CGH chr18:42005882-42006049 log2=-0.031 spread=0.038 286s SMAD4 chr18:48575581-48575754 log2=0.224 spread=0.215 286s CGH chr18:58519179-58519311 log2=-0.254 spread=0.214 286s STK11 chr19:1226401-1226680 log2=-0.501 spread=0.149 286s DOT1L chr19:2164127-2164302 log2=-1.071 spread=0.866 286s " chr19:2210351-2210545 log2=-0.860 spread=0.261 286s " chr19:2226130-2227152 log2=-0.113 spread=0.120 286s GNA11 chr19:3094603-3094817 log2=-0.229 spread=0.152 286s GIPC3 chr19:3585549-3585853 log2=-1.516 spread=1.086 286s MAP2K2 chr19:4123728-4123907 log2=-0.004 spread=0.187 286s INSR chr19:7293751-7294042 log2=-2.020 spread=1.538 286s SMARCA4 chr19:11098288-11098630 log2=-0.647 spread=0.206 286s PODNL1 chr19:14063277-14063492 log2=-0.226 spread=0.272 286s NOTCH3 chr19:15288281-15288927 log2=-1.510 spread=0.106 286s " chr19:15311544-15311749 log2=-1.887 spread=1.202 286s JAK3 chr19:17953074-17953444 log2=-0.886 spread=0.423 286s CCNE1 chr19:30303376-30303718 log2=-0.486 spread=0.368 286s CEBPA chr19:33792189-33792764 log2=-0.086 spread=0.251 286s " chr19:33792774-33793010 log2=-1.781 spread=0.127 286s " chr19:33793014-33793356 log2=-0.541 spread=0.385 286s CD79A chr19:42384673-42384848 log2=-1.881 spread=1.227 286s ERCC2 chr19:45866950-45867408 log2=-0.750 spread=0.536 286s " chr19:45873698-45873881 log2=-0.522 spread=0.327 286s BCL2L12 chr19:50173423-50173770 log2=-0.005 spread=0.243 286s SRC chr20:36012507-36012834 log2=-0.373 spread=0.448 286s TOP1 chr20:39657625-39657796 log2=-0.187 spread=0.282 286s PLCG1 chr20:39766233-39766531 log2=-0.105 spread=0.074 286s AURKA chr20:54959250-54959432 log2=0.185 spread=0.183 286s SYCP2 chr20:58505615-58505798 log2=-0.018 spread=0.034 286s ARFRP1 chr20:62339169-62339402 log2=-1.471 spread=0.976 286s RUNX1 chr21:36164379-36164936 log2=0.163 spread=0.307 286s " chr21:36265140-36265318 log2=0.042 spread=0.039 286s CHEK2 chr22:29105918-29106101 log2=0.091 spread=0.114 286s " chr22:29115325-29115465 log2=0.055 spread=0.390 286s SOX10 chr22:38379312-38379815 log2=-0.427 spread=0.308 286s CGH chr22:41487738-41489134 log2=-0.174 spread=0.116 286s EP300 chr22:41562534-41562711 log2=0.160 spread=0.125 286s CRLF2 chrX:1314835-1315039 log2=-21.107 spread=0.037 286s " chrX:1317372-1317594 log2=-21.121 spread=0.049 286s " chrX:1321225-1321435 log2=-20.851 spread=0.196 286s " chrX:1325274-1325530 log2=-21.121 spread=0.011 286s " chrX:1327651-1327830 log2=-21.000 spread=0.029 286s " chrX:1331391-1331576 log2=-21.018 spread=0.052 286s KDM6A chrX:44820507-44820671 log2=-0.582 spread=0.279 286s PAK3 chrX:110435687-110435871 log2=-1.172 spread=0.053 286s STAG2 chrX:123182790-123182965 log2=-0.941 spread=0.228 286s " chrX:123185143-123185290 log2=-1.018 spread=0.062 286s " chrX:123202378-123202544 log2=-0.959 spread=0.103 286s FAM58A chrX:152864353-152864586 log2=-2.437 spread=0.754 286s CGH chrY:4564417-4564597 log2=-1.004 spread=0.063 286s " chrY:9008607-9008759 log2=-1.012 spread=0.097 286s " chrY:13131970-13132039 log2=-1.004 spread=0.074 286s " chrY:19506485-19506650 log2=-1.018 spread=0.034 286s " chrY:21033918-21034071 log2=-1.013 spread=0.057 286s " chrY:28463435-28463622 log2=-0.952 spread=0.039 286s " chrY:28514033-28514208 log2=-0.992 spread=0.026 286s Antitargets: 108 (0.8597%) bins failed filters 286s Wrote build/reference-picard.cnn with 19209 regions 286s 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 288s Processing target: p2-5_5 288s Keeping 6308 of 6646 bins 288s Correcting for GC bias... 288s Correcting for density bias... 288s Processing antitarget: p2-5_5 288s Keeping 12455 of 12563 bins 288s Correcting for GC bias... 288s WARNING: Skipping correction for RepeatMasker bias 289s Targets are 1.18 x more variable than antitargets 289s Wrote build/p2-5_5.cnr with 18763 regions 289s cnvkit.py import-picard picard/p2-9_2.targetcoverage.csv -d build/ 291s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 291s Wrote build/p2-9_2.targetcoverage.cnn with 6646 regions 291s cnvkit.py import-picard picard/p2-9_2.antitargetcoverage.csv -d build/ 293s Wrote build/p2-9_2.antitargetcoverage.cnn with 12563 regions 294s 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 296s Processing target: p2-9_2 296s Keeping 6308 of 6646 bins 296s Correcting for GC bias... 296s Correcting for density bias... 296s Processing antitarget: p2-9_2 296s Keeping 12455 of 12563 bins 296s Correcting for GC bias... 296s WARNING: Skipping correction for RepeatMasker bias 297s Targets are 1.72 x more variable than antitargets 297s Wrote build/p2-9_2.cnr with 18763 regions 297s cnvkit.py import-picard picard/p2-20_1.targetcoverage.csv -d build/ 299s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 299s Wrote build/p2-20_1.targetcoverage.cnn with 6646 regions 299s cnvkit.py import-picard picard/p2-20_1.antitargetcoverage.csv -d build/ 301s Wrote build/p2-20_1.antitargetcoverage.cnn with 12563 regions 302s 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 304s Processing target: p2-20_1 304s Keeping 6308 of 6646 bins 304s Correcting for GC bias... 304s Correcting for density bias... 304s Processing antitarget: p2-20_1 304s Keeping 12455 of 12563 bins 304s Correcting for GC bias... 304s WARNING: Skipping correction for RepeatMasker bias 305s Targets are 1.12 x more variable than antitargets 305s Wrote build/p2-20_1.cnr with 18763 regions 305s cnvkit.py import-picard picard/p2-20_2.targetcoverage.csv -d build/ 307s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 308s Wrote build/p2-20_2.targetcoverage.cnn with 6646 regions 308s cnvkit.py import-picard picard/p2-20_2.antitargetcoverage.csv -d build/ 310s Wrote build/p2-20_2.antitargetcoverage.cnn with 12563 regions 310s 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 312s Processing target: p2-20_2 312s Keeping 6308 of 6646 bins 312s Correcting for GC bias... 312s Correcting for density bias... 312s Processing antitarget: p2-20_2 312s Keeping 12455 of 12563 bins 313s Correcting for GC bias... 313s WARNING: Skipping correction for RepeatMasker bias 313s Targets are 1.10 x more variable than antitargets 313s Wrote build/p2-20_2.cnr with 18763 regions 313s cnvkit.py import-picard picard/p2-20_3.targetcoverage.csv -d build/ 315s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 315s Wrote build/p2-20_3.targetcoverage.cnn with 6646 regions 315s cnvkit.py import-picard picard/p2-20_3.antitargetcoverage.csv -d build/ 317s Wrote build/p2-20_3.antitargetcoverage.cnn with 12563 regions 318s 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 319s Processing target: p2-20_3 319s Keeping 6308 of 6646 bins 319s Correcting for GC bias... 319s Correcting for density bias... 320s Processing antitarget: p2-20_3 320s Keeping 12455 of 12563 bins 320s Correcting for GC bias... 320s WARNING: Skipping correction for RepeatMasker bias 320s Antitargets are 1.09 x more variable than targets 320s Wrote build/p2-20_3.cnr with 18763 regions 320s cnvkit.py import-picard picard/p2-20_4.targetcoverage.csv -d build/ 322s WARNING: Ambiguous gene name 'TERT|TERT Promoter'; using 'TERT Promoter' 322s Wrote build/p2-20_4.targetcoverage.cnn with 6646 regions 323s cnvkit.py import-picard picard/p2-20_4.antitargetcoverage.csv -d build/ 325s Wrote build/p2-20_4.antitargetcoverage.cnn with 12563 regions 325s 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 327s Processing target: p2-20_4 327s Keeping 6308 of 6646 bins 327s Correcting for GC bias... 327s Correcting for density bias... 327s Processing antitarget: p2-20_4 327s Keeping 12455 of 12563 bins 327s Correcting for GC bias... 327s WARNING: Skipping correction for RepeatMasker bias 327s Targets are 1.43 x more variable than antitargets 327s Wrote build/p2-20_4.cnr with 18763 regions 328s 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 329s Processing target: p2-20_5 330s Keeping 6308 of 6646 bins 330s Correcting for GC bias... 330s Correcting for density bias... 330s Processing antitarget: p2-20_5 330s Keeping 12455 of 12563 bins 330s Correcting for GC bias... 330s WARNING: Skipping correction for RepeatMasker bias 330s Targets are 2.50 x more variable than antitargets 330s Wrote build/p2-20_5.cnr with 18763 regions 331s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns 333s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 340s Dropped 8 / 49 bins on chromosome chrY 341s Wrote build/p2-5_5.cns with 71 regions 341s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-9_2.cnr -o build/p2-9_2.cns 343s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 345s Dropped 1 / 949 bins on chromosome chr6 351s Dropped 27 / 49 bins on chromosome chrY 352s Wrote build/p2-9_2.cns with 103 regions 352s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_1.cnr -o build/p2-20_1.cns 354s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 363s Dropped 6 / 49 bins on chromosome chrY 363s Wrote build/p2-20_1.cns with 121 regions 364s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_2.cnr -o build/p2-20_2.cns 366s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 373s Dropped 7 / 49 bins on chromosome chrY 374s Wrote build/p2-20_2.cns with 117 regions 374s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_3.cnr -o build/p2-20_3.cns 376s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 383s Dropped 11 / 49 bins on chromosome chrY 383s Wrote build/p2-20_3.cns with 64 regions 384s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_4.cnr -o build/p2-20_4.cns 385s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 396s Dropped 8 / 49 bins on chromosome chrY 396s Wrote build/p2-20_4.cns with 143 regions 396s cnvkit.py segment --rscript-path Rscript -p 2 --drop-low-coverage -t .01 build/p2-20_5.cnr -o build/p2-20_5.cns 398s Segmenting with method 'cbs', significance threshold 0.01, in 2 processes 406s Smoothing overshot at 1 / 123 indices: (-0.30060035404086394, 0.32508880185194683) vs. original (-0.363302, 0.311218) 407s Dropped 6 / 49 bins on chromosome chrY 408s Wrote build/p2-20_5.cns with 120 regions 408s 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 411s Wrote p2-5_5-scatter.pdf 411s 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 414s Smoothing overshot at 3 / 97 indices: (-19.90010586862171, -3.3099069223720505) vs. original (-19.294, -0.16431) 415s Wrote p2-9_2-scatter.pdf 415s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr1 -t -o p2-9_2-chr1-scatter.pdf 417s Showing 1480 probes and 0 selected genes in region chr1 418s Wrote p2-9_2-chr1-scatter.pdf 418s cnvkit.py scatter -s build/p2-9_2.cns build/p2-9_2.cnr -c chr21 -t -o p2-9_2-chr21-scatter.pdf 420s Showing 201 probes and 0 selected genes in region chr21 420s Wrote p2-9_2-chr21-scatter.pdf 421s 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 423s Showing 330 probes and 13 selected genes in region chr9:149999-45000000 423s Wrote p2-9_2-chr9p-scatter.pdf 424s 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 426s Showing 179 probes and 2 selected genes in region chr9:0-14504268.0 426s Wrote p2-9_2-SMARCA2-PTPRD-scatter.pdf 426s 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 430s Detected file format: bed 430s 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 430s Showing 41 probes and 1 selected genes in region chr9:2000000-4000000 430s Showing 53 probes and 1 selected genes in region chr9:8000000-12000000 430s /usr/bin/pdfunite 430s cnvkit.py diagram -y build/p2-5_5.cnr -o p2-5_5-diagram.pdf 432s Treating sample p2-5_5 as female 442s Wrote p2-5_5-diagram.pdf 442s cnvkit.py diagram -y build/p2-9_2.cnr -o p2-9_2-diagram.pdf 444s Treating sample p2-9_2 as female 453s Wrote p2-9_2-diagram.pdf 454s cnvkit.py diagram -y build/p2-20_1.cnr -o p2-20_1-diagram.pdf 456s Treating sample p2-20_1 as female 466s Wrote p2-20_1-diagram.pdf 466s cnvkit.py diagram -y build/p2-20_2.cnr -o p2-20_2-diagram.pdf 468s Treating sample p2-20_2 as female 478s Wrote p2-20_2-diagram.pdf 478s cnvkit.py diagram -y --segment=build/p2-5_5.cns -o p2-5_5-cbs-diagram.pdf 480s Treating sample p2-5_5 as female 480s Wrote p2-5_5-cbs-diagram.pdf 480s cnvkit.py diagram -y --segment=build/p2-9_2.cns -o p2-9_2-cbs-diagram.pdf 482s Treating sample p2-9_2 as female 482s Wrote p2-9_2-cbs-diagram.pdf 483s cnvkit.py diagram -y --segment=build/p2-20_1.cns -o p2-20_1-cbs-diagram.pdf 484s Treating sample p2-20_1 as female 485s Wrote p2-20_1-cbs-diagram.pdf 485s cnvkit.py diagram -y --segment=build/p2-20_2.cns -o p2-20_2-cbs-diagram.pdf 487s Treating sample p2-20_2 as female 487s 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 487s Wrote p2-20_2-cbs-diagram.pdf 489s Treating sample p2-5_5 as female 495s Wrote p2-5_5-both-diagram.pdf 495s 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 497s Treating sample p2-9_2 as female 503s Wrote p2-9_2-both-diagram.pdf 504s 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 506s Treating sample p2-20_1 as female 512s Wrote p2-20_1-both-diagram.pdf 512s 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 514s Treating sample p2-20_2 as female 520s Wrote p2-20_2-both-diagram.pdf 520s 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 520s /usr/bin/pdfunite 521s 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 522s Treating sample p2-5_5 as female 522s Treating sample p2-9_2 as female 522s Treating sample p2-20_1 as female 522s Treating sample p2-20_2 as female 522s Treating sample p2-20_3 as female 522s Treating sample p2-20_4 as female 522s Treating sample p2-20_5 as female 524s Wrote heatmap-picard.pdf 525s cnvkit.py breaks build/p2-9_2.cnr build/p2-9_2.cns -o p2-9_2-breaks.txt 526s Found 14 gene breakpoints 526s Wrote p2-9_2-breaks.txt 527s cnvkit.py genemetrics -y -m 2 -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-genemetrics.txt 528s Treating sample p2-9_2 as female 530s Found 323 gene-level gains and losses 530s Wrote p2-9_2-genemetrics.txt 530s 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 532s Wrote gender-picard.txt 533s 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 537s Wrote p2-all.cdt 538s 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 543s Wrote p2-all-jtv.txt 543s 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 545s Wrote p2-all.seg 545s cnvkit.py export nexus-basic build/p2-9_2.cnr -o p2-9_2.nexus 547s Wrote p2-9_2.nexus 548s cnvkit.py export nexus-ogt build/p2-9_2.cnr formats/na12878_na12882_mix.vcf -o p2-9_2.nexus-ogt 550s Selected test sample NA12882 and control sample NA12878 550s Loaded 3654 records; skipped: 514 somatic, 394 depth 550s Kept 2631 heterozygous of 3654 VCF records 553s Placed 705 variants into 18763 bins 553s Wrote p2-9_2.nexus-ogt 554s cnvkit.py call build/p2-5_5.cns -y -m clonal --purity 0.65 -o build/p2-5_5.call.cns 556s Treating sample p2-5_5 as female 556s Rescaling sample with purity 0.65, ploidy 2 556s Wrote build/p2-5_5.call.cns with 71 regions 556s cnvkit.py call build/p2-9_2.cns -y -m clonal --purity 0.65 -o build/p2-9_2.call.cns 558s Treating sample p2-9_2 as female 558s Rescaling sample with purity 0.65, ploidy 2 558s Wrote build/p2-9_2.call.cns with 103 regions 558s cnvkit.py call build/p2-20_1.cns -y -m clonal --purity 0.65 -o build/p2-20_1.call.cns 560s Treating sample p2-20_1 as female 560s Rescaling sample with purity 0.65, ploidy 2 560s Wrote build/p2-20_1.call.cns with 121 regions 560s cnvkit.py call build/p2-20_2.cns -y -m clonal --purity 0.65 -o build/p2-20_2.call.cns 562s Treating sample p2-20_2 as female 562s Rescaling sample with purity 0.65, ploidy 2 562s Wrote build/p2-20_2.call.cns with 117 regions 562s cnvkit.py call build/p2-20_3.cns -y -m clonal --purity 0.65 -o build/p2-20_3.call.cns 564s Treating sample p2-20_3 as female 564s Rescaling sample with purity 0.65, ploidy 2 564s Wrote build/p2-20_3.call.cns with 64 regions 564s cnvkit.py call build/p2-20_4.cns -y -m clonal --purity 0.65 -o build/p2-20_4.call.cns 566s Treating sample p2-20_4 as female 566s Rescaling sample with purity 0.65, ploidy 2 566s Wrote build/p2-20_4.call.cns with 143 regions 566s cnvkit.py call build/p2-20_5.cns -y -m clonal --purity 0.65 -o build/p2-20_5.call.cns 568s Treating sample p2-20_5 as female 568s Rescaling sample with purity 0.65, ploidy 2 568s Wrote build/p2-20_5.call.cns with 120 regions 568s 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 570s Treating sample p2-5_5.call as female 570s Treating sample p2-9_2.call as female 570s Treating sample p2-20_1.call as female 570s Treating sample p2-20_2.call as female 570s Treating sample p2-20_3.call as female 570s Treating sample p2-20_4.call as female 570s Treating sample p2-20_5.call as female 570s Wrote p2-all.bed 570s 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 572s Treating sample p2-9_2.call as female 572s Wrote p2-9_2.vcf 572s cnvkit.py export theta build/p2-9_2.cns -r build/reference-picard.cnn -o p2-9_2.theta2.input 574s Wrote p2-9_2.theta2.input 575s cnvkit.py segmetrics -s build/p2-9_2.cns build/p2-9_2.cnr -o p2-9_2-segmetrics.cns \ 575s --mean --median --mode --t-test \ 575s --stdev --mad --mse --iqr --bivar \ 575s --ci --pi --sem --smooth-bootstrap 578s Wrote p2-9_2-segmetrics.cns with 103 regions 578s cnvkit.py segmetrics -s build/p2-5_5.cns build/p2-5_5.cnr -o p2-5_5-segmetrics.cns \ 578s --ci -b 50 -a 0.5 580s Wrote p2-5_5-segmetrics.cns with 71 regions 581s cnvkit.py metrics build/p2-5_5.cnr -s build/p2-5_5.cns -o p2-5_5-metrics.tsv 583s Wrote p2-5_5-metrics.tsv 583s cnvkit.py metrics build/p2-9_2.cnr -s build/p2-9_2.cns -o p2-9_2-metrics.tsv 585s Wrote p2-9_2-metrics.tsv 586s 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 588s Wrote p2-20-metrics.tsv 588s PASS 589s autopkgtest [01:53:51]: test run-unit-test: -----------------------] 589s autopkgtest [01:53:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 589s run-unit-test PASS 589s autopkgtest [01:53:51]: test pybuild-autopkgtest: preparing testbed 648s autopkgtest [01:54:50]: testbed dpkg architecture: amd64 649s autopkgtest [01:54:51]: testbed apt version: 2.9.31ubuntu1 649s autopkgtest [01:54:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 649s autopkgtest [01:54:51]: testbed release detected to be: plucky 649s autopkgtest [01:54:51]: updating testbed package index (apt update) 649s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 649s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 649s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 649s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 649s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [382 kB] 649s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [42.9 kB] 649s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 649s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [84.0 kB] 649s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [66.6 kB] 649s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1788 B] 649s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 649s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [193 kB] 649s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [358 kB] 649s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [14.5 kB] 649s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [9324 B] 649s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [18.0 kB] 649s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [580 B] 649s Fetched 1315 kB in 0s (6330 kB/s) 650s Reading package lists... 650s Reading package lists... 651s Building dependency tree... 651s Reading state information... 651s Calculating upgrade... 651s Calculating upgrade... 651s The following package was automatically installed and is no longer required: 651s libnl-genl-3-200 651s Use 'sudo apt autoremove' to remove it. 651s The following NEW packages will be installed: 651s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 651s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 651s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 651s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 651s The following packages will be upgraded: 651s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 651s cloud-init cloud-init-base cron cron-daemon-common curl dosfstools fwupd 651s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata libapparmor1 651s libapt-pkg7.0 libaudit-common libaudit1 libbinutils libbrotli1 libcap-ng0 651s libctf-nobfd0 libctf0 libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 651s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgprofng0 651s libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 libncursesw6 651s libnl-3-200 libnl-genl-3-200 libnl-route-3-200 libpci3 libpython3-stdlib 651s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libselinux1 651s libsframe1 libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 651s linux-headers-generic linux-headers-virtual linux-image-generic 651s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 651s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 651s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 651s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 651s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 651s python3.13-minimal rsync rsyslog strace xz-utils 651s 88 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 651s Need to get 807 MB of archives. 651s After this operation, 326 MB of additional disk space will be used. 651s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 651s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 651s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 651s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 651s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 651s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 651s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 651s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 651s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 651s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 651s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 651s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 651s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 651s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 651s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 651s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 651s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 651s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 651s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 651s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 651s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 651s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 651s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 cron amd64 3.0pl1-194ubuntu1 [93.9 kB] 651s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 651s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 651s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 651s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 651s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 651s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 651s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 651s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 652s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 652s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 652s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 652s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 652s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 652s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 652s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 652s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 652s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 652s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 652s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 652s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 652s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 652s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 cron-daemon-common all 3.0pl1-194ubuntu1 [14.6 kB] 652s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 652s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 652s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 652s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 652s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 652s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 652s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 652s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 652s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 652s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 652s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 652s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 652s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 652s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 652s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 652s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 652s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 652s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 652s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 652s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 652s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 652s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 652s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 652s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 652s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 652s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 652s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 652s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 652s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 652s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 652s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 652s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 652s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 652s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 652s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 656s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 656s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 656s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 657s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 657s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 657s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 657s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 657s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 657s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 657s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 657s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 657s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 657s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 657s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 657s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 657s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 657s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 657s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 657s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 657s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 658s Preconfiguring packages ... 658s Fetched 807 MB in 6s (138 MB/s) 658s (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.) 658s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 658s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 658s Setting up ncurses-bin (6.5+20250216-2) ... 658s (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.) 658s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 658s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 658s Setting up ncurses-base (6.5+20250216-2) ... 658s (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.) 658s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 658s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 659s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 659s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 659s Setting up liblz4-1:amd64 (1.10.0-4) ... 659s (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.) 659s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 659s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 659s Setting up liblzma5:amd64 (5.6.4-1) ... 659s (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.) 659s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 659s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 659s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 659s (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.) 659s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 659s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 659s Setting up apt (2.9.33) ... 660s (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.) 660s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 660s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 660s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 660s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 660s Setting up python3-minimal (3.13.2-2) ... 660s (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.) 660s Preparing to unpack .../0-python3_3.13.2-2_amd64.deb ... 660s Unpacking python3 (3.13.2-2) over (3.13.2-1) ... 660s Preparing to unpack .../1-libpython3.13_3.13.2-2_amd64.deb ... 660s Unpacking libpython3.13:amd64 (3.13.2-2) over (3.13.2-1) ... 660s Preparing to unpack .../2-media-types_13.0.0_all.deb ... 660s Unpacking media-types (13.0.0) over (12.0.0) ... 660s Preparing to unpack .../3-libncurses6_6.5+20250216-2_amd64.deb ... 660s Unpacking libncurses6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 660s Preparing to unpack .../4-libncursesw6_6.5+20250216-2_amd64.deb ... 660s Unpacking libncursesw6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 660s Preparing to unpack .../5-libtinfo6_6.5+20250216-2_amd64.deb ... 660s Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ... 660s Setting up libtinfo6:amd64 (6.5+20250216-2) ... 661s (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.) 661s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 661s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 661s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 661s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 661s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 661s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 661s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 661s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 661s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 661s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 661s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 661s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 661s Preparing to unpack .../6-libselinux1_3.7-3ubuntu3_amd64.deb ... 661s Unpacking libselinux1:amd64 (3.7-3ubuntu3) over (3.7-3ubuntu2) ... 661s Setting up libselinux1:amd64 (3.7-3ubuntu3) ... 661s (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.) 661s Preparing to unpack .../cron_3.0pl1-194ubuntu1_amd64.deb ... 661s Unpacking cron (3.0pl1-194ubuntu1) over (3.0pl1-192ubuntu1) ... 661s Preparing to unpack .../rsync_3.4.1+ds1-3_amd64.deb ... 661s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 661s Selecting previously unselected package libdebuginfod-common. 661s Preparing to unpack .../libdebuginfod-common_0.192-4_all.deb ... 661s Unpacking libdebuginfod-common (0.192-4) ... 661s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu2_all.deb ... 661s Unpacking libaudit-common (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 661s Setting up libaudit-common (1:4.0.2-2ubuntu2) ... 661s (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.) 661s Preparing to unpack .../libcap-ng0_0.8.5-4build1_amd64.deb ... 661s Unpacking libcap-ng0:amd64 (0.8.5-4build1) over (0.8.5-4) ... 662s Setting up libcap-ng0:amd64 (0.8.5-4build1) ... 662s (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.) 662s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 662s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 662s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 662s (Reading database ... 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package bpftool. 665s Preparing to unpack .../37-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 665s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 665s Preparing to unpack .../38-python3-markupsafe_2.1.5-1build4_amd64.deb ... 665s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 665s Preparing to unpack .../39-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 665s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 665s Preparing to unpack .../40-cloud-init-base_25.1-0ubuntu3_all.deb ... 665s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 665s Preparing to unpack .../41-libbrotli1_1.1.0-2build4_amd64.deb ... 665s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 665s Preparing to unpack .../42-curl_8.12.1-3ubuntu1_amd64.deb ... 665s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 665s Preparing to unpack .../43-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 665s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over 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libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 675s Setting up pci.ids (0.0~2025.03.09-1) ... 675s Setting up apt-utils (2.9.33) ... 675s Setting up libdebuginfod-common (0.192-4) ... 676s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 676s Setting up bpftool (7.6.0+6.14.0-10.10) ... 676s Setting up libestr0:amd64 (0.1.11-2) ... 676s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 676s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 676s Setting up dosfstools (4.2-1.2) ... 676s Setting up rsyslog (8.2412.0-2ubuntu2) ... 676s info: The user `syslog' is already a member of `adm'. 677s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 677s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 677s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 677s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 677s Setting up linux-headers-generic (6.14.0-10.10) ... 677s Setting up libjemalloc2:amd64 (5.3.0-3) ... 677s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 677s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 677s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 677s Installing new version of config file /etc/apparmor.d/openvpn ... 678s Reloading AppArmor profiles 679s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 679s No schema files found: doing nothing. 679s Setting up libglib2.0-data (2.84.0-1) ... 679s Setting up libncurses6:amd64 (6.5+20250216-2) ... 679s Setting up strace (6.13+ds-1ubuntu1) ... 679s Setting up xz-utils (5.6.4-1) ... 679s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 679s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 681s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 681s Setting up libpci3:amd64 (1:3.13.0-2) ... 681s Setting up python-apt-common (2.9.9build1) ... 681s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 681s Setting up pnp.ids (0.393-3) ... 681s Setting up libnl-3-200:amd64 (3.7.0-1) ... 681s Setting up python3.13-minimal (3.13.2-2) ... 682s Setting up libgirepository-1.0-1:amd64 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linux-image-6.14.0-10-generic (6.14.0-10.10) ... 686s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 686s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 686s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 686s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 686s Setting up libfwupd3:amd64 (2.0.6-4) ... 686s Setting up python3 (3.13.2-2) ... 686s Setting up python3-markupsafe (2.1.5-1build4) ... 686s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 689s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 689s Setting up hwdata (0.393-3) ... 689s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 689s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 689s Setting up linux-perf (6.14.0-10.10) ... 689s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 689s Setting up python3-gi (3.50.0-4build1) ... 689s Setting up pciutils (1:3.13.0-2) ... 689s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 689s Setting up curl (8.12.1-3ubuntu1) ... 689s Setting up linux-image-virtual (6.14.0-10.10) ... 689s Setting up linux-tools-common (6.14.0-10.10) ... 689s Setting up fwupd (2.0.6-4) ... 689s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 689s fwupd.service is a disabled or a static unit not running, not starting it. 689s Setting up python3-systemd (235-1build6) ... 690s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 690s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 690s Setting up linux-image-generic (6.14.0-10.10) ... 690s Setting up python3-dbus (1.3.2-5build5) ... 690s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 690s Setting up linux-generic (6.14.0-10.10) ... 690s Setting up python3-apt (2.9.9build1) ... 690s Setting up python3-yaml (6.0.2-1build2) ... 690s Setting up python3-lazr.uri (1.0.6-6) ... 690s Setting up binutils (2.44-3ubuntu1) ... 690s Setting up cloud-init-base (25.1-0ubuntu3) ... 691s Setting up linux-virtual (6.14.0-10.10) ... 691s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 691s Setting up cloud-init (25.1-0ubuntu3) ... 691s Processing triggers for systemd (257.3-1ubuntu3) ... 692s Processing triggers for man-db (2.13.0-1) ... 693s Processing triggers for dbus (1.16.2-1ubuntu1) ... 693s Processing triggers for libc-bin (2.41-1ubuntu1) ... 693s Processing triggers for initramfs-tools (0.146ubuntu1) ... 693s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 693s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 703s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 703s /etc/kernel/postinst.d/initramfs-tools: 703s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 703s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 713s /etc/kernel/postinst.d/zz-update-grub: 713s Sourcing file `/etc/default/grub' 713s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 713s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 713s Generating grub configuration file ... 713s Found linux image: /boot/vmlinuz-6.14.0-10-generic 713s Found initrd image: /boot/initrd.img-6.14.0-10-generic 714s Found linux image: /boot/vmlinuz-6.12.0-16-generic 714s Found initrd image: /boot/initrd.img-6.12.0-16-generic 714s Found linux image: /boot/vmlinuz-6.11.0-8-generic 714s Found initrd image: /boot/initrd.img-6.11.0-8-generic 714s Warning: os-prober will not be executed to detect other bootable partitions. 714s Systems on them will not be added to the GRUB boot configuration. 714s Check GRUB_DISABLE_OS_PROBER documentation entry. 714s Adding boot menu entry for UEFI Firmware Settings ... 714s done 715s Reading package lists... 716s Building dependency tree... 716s Reading state information... 716s Solving dependencies... 716s The following packages will be REMOVED: 716s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 716s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 716s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 716s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 716s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 716s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 716s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 716s linux-tools-6.12.0-16-generic* 717s 0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded. 717s After this operation, 545 MB disk space will be freed. 717s (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.) 717s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 717s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 717s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 717s Removing libpython3.12t64:amd64 (3.12.9-1) ... 717s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 717s Removing libnsl2:amd64 (1.3.0-3build3) ... 717s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 717s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 718s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 719s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 720s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 722s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 722s /etc/kernel/postrm.d/initramfs-tools: 722s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 722s /etc/kernel/postrm.d/zz-update-grub: 722s Sourcing file `/etc/default/grub' 722s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 722s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 722s Generating grub configuration file ... 722s Found linux image: /boot/vmlinuz-6.14.0-10-generic 722s Found initrd image: /boot/initrd.img-6.14.0-10-generic 722s Found linux image: /boot/vmlinuz-6.12.0-16-generic 722s Found initrd image: /boot/initrd.img-6.12.0-16-generic 723s Warning: os-prober will not be executed to detect other bootable partitions. 723s Systems on them will not be added to the GRUB boot configuration. 723s Check GRUB_DISABLE_OS_PROBER documentation entry. 723s Adding boot menu entry for UEFI Firmware Settings ... 723s done 723s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 723s W: Removing the running kernel 723s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 723s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 723s /etc/kernel/postrm.d/initramfs-tools: 723s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 723s /etc/kernel/postrm.d/zz-update-grub: 723s Sourcing file `/etc/default/grub' 723s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 723s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 723s Generating grub configuration file ... 723s Found linux image: /boot/vmlinuz-6.14.0-10-generic 723s Found initrd image: /boot/initrd.img-6.14.0-10-generic 723s Warning: os-prober will not be executed to detect other bootable partitions. 723s Systems on them will not be added to the GRUB boot configuration. 723s Check GRUB_DISABLE_OS_PROBER documentation entry. 723s Adding boot menu entry for UEFI Firmware Settings ... 723s done 723s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 724s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 725s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 725s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 725s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 725s Processing triggers for libc-bin (2.41-1ubuntu1) ... 725s (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 ... 76972 files and directories currently installed.) 725s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 725s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 725s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 725s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 725s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 725s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 725s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 725s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 726s autopkgtest [01:56:08]: upgrading testbed (apt dist-upgrade and autopurge) 726s Reading package lists... 726s Building dependency tree... 726s Reading state information... 726s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 726s Starting 2 pkgProblemResolver with broken count: 0 726s Done 727s Entering ResolveByKeep 727s 727s Calculating upgrade... 727s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 727s Reading package lists... 728s Building dependency tree... 728s Reading state information... 728s Starting pkgProblemResolver with broken count: 0 728s Starting 2 pkgProblemResolver with broken count: 0 728s Done 728s Solving dependencies... 728s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 728s autopkgtest [01:56:10]: rebooting testbed after setup commands that affected boot 732s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 744s Reading package lists... 745s Building dependency tree... 745s Reading state information... 745s Starting pkgProblemResolver with broken count: 0 745s Starting 2 pkgProblemResolver with broken count: 0 745s Done 745s The following NEW packages will be installed: 745s autoconf automake autopoint autotools-dev blt build-essential cnvkit cpp 745s cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu cython3 debhelper 745s debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz fontconfig 745s fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx 745s fonts-urw-base35 g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 745s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gettext intltool-debian 745s libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdatrie1 745s libdebhelper-perl libdeflate0 libfile-stripnondeterminism-perl 745s libfontconfig1 libfontenc1 libgcc-14-dev libgfortran5 libgomp1 745s libgpgmepp6t64 libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 745s libhwasan0 libice6 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8 745s libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 745s liblerc4 liblsan0 libmpc3 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 745s libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 libpoppler147 745s libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libsm6 libstdc++-14-dev 745s libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libtsan2 libubsan1 745s libwebp7 libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 745s libxrender1 libxslt1.1 libxss1 libxt6t64 m4 po-debconf poppler-utils 745s pybuild-plugin-autopkgtest pybuild-plugin-pyproject python-matplotlib-data 745s python3-all python3-biopython python3-brotli python3-build python3-cairo 745s python3-contourpy python3-cycler python3-dateutil python3-decorator 745s python3-fonttools python3-freetype python3-fs python3-importlib-metadata 745s python3-iniconfig python3-installer python3-joblib python3-kiwisolver 745s python3-lxml python3-lz4 python3-matplotlib python3-mpmath python3-networkx 745s python3-numpy python3-numpy-dev python3-packaging python3-pandas 745s python3-pandas-lib python3-pil python3-pil.imagetk python3-platformdirs 745s python3-pluggy python3-pomegranate python3-pyfaidx python3-pyproject-hooks 745s python3-pysam python3-pytest python3-pytz python3-reportlab 745s python3-rlpycairo python3-scipy python3-sklearn python3-sklearn-lib 745s python3-sympy python3-threadpoolctl python3-tk python3-toml python3-tz 745s python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-tk 745s python3.13-tk r-base-core r-bioc-biocgenerics r-bioc-dnacopy sgml-base 745s tk8.6-blt2.5 unicode-data unzip w3c-sgml-lib x11-common xdg-utils 745s xfonts-encodings xfonts-utils xml-core zip 745s 0 upgraded, 173 newly installed, 0 to remove and 0 not upgraded. 745s Need to get 254 MB of archives. 745s After this operation, 998 MB of additional disk space will be used. 745s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-5 [148 kB] 745s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 745s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 745s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 746s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:2.2.3+ds-5 [5702 kB] 746s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 sgml-base all 1.31 [11.4 kB] 746s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 m4 amd64 1.4.19-7 [263 kB] 746s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 autoconf all 2.72-3ubuntu1 [383 kB] 746s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 autotools-dev all 20220109.1 [44.9 kB] 746s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 automake all 1:1.17-3ubuntu1 [572 kB] 746s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 autopoint all 0.23.1-1 [619 kB] 746s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 746s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 746s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 746s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontenc1 amd64 1:1.1.8-1build1 [14.0 kB] 746s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 746s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] 746s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 xfonts-utils amd64 1:7.7+7 [97.1 kB] 746s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-urw-base35 all 20200910-8 [11.0 MB] 746s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 746s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 746s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 746s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 746s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 746s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 746s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [694 kB] 746s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 blt amd64 2.5.3+dfsg-8 [4824 B] 746s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 746s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 746s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 746s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 746s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 746s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 746s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 746s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 746s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 746s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 746s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 746s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 746s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 746s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 746s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 746s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 746s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 746s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 746s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 746s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 746s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 746s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 746s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 746s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 746s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 746s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 746s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-tk amd64 3.12.9-1 [116 kB] 746s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-tk amd64 3.13.2-2 [107 kB] 746s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tk amd64 3.13.1-1 [9770 B] 746s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pil.imagetk amd64 11.1.0-5build1 [9828 B] 746s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 746s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 746s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 746s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblcms2-2 amd64 2.16-2 [212 kB] 746s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libopenjp2-7 amd64 2.5.3-2 [218 kB] 746s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 746s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 746s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libraqm0 amd64 0.10.2-1 [17.2 kB] 746s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 746s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 746s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 746s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 746s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 746s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 746s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [13.0 kB] 746s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [27.6 kB] 746s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pil amd64 11.1.0-5build1 [583 kB] 746s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 746s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 746s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 746s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 746s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cairo amd64 1.26.1-2build2 [124 kB] 746s Get:80 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-freetype all 2.5.1-1 [92.3 kB] 746s Get:81 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-rlpycairo all 0.3.0-3 [9130 B] 746s Get:82 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-reportlab all 4.3.1-1 [1137 kB] 746s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xml-core all 0.19 [20.3 kB] 746s Get:84 http://ftpmaster.internal/ubuntu plucky/universe amd64 w3c-sgml-lib all 1.3-3 [280 kB] 746s Get:85 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biopython amd64 1.85+dfsg-2build1 [1739 kB] 746s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 746s Get:87 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 746s Get:88 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-lyx all 2.4.3-1 [171 kB] 746s Get:89 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-matplotlib-data all 3.8.3-7build1 [2934 kB] 746s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 746s Get:91 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-contourpy amd64 1.3.1-1build1 [218 kB] 746s Get:92 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 746s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-brotli amd64 1.1.0-2build4 [367 kB] 746s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-platformdirs all 4.3.6-1 [16.8 kB] 746s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fs all 2.4.16-7 [90.8 kB] 746s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 libxslt1.1 amd64 1.1.39-0exp1ubuntu2 [175 kB] 746s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lxml amd64 5.3.1-1build1 [1408 kB] 746s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-lz4 amd64 4.4.0+dfsg-1build1 [27.0 kB] 746s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 746s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 746s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu2 [18.7 MB] 746s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 746s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sympy all 1.13.3-5 [4229 kB] 746s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.5 kB] 746s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build3 [360 kB] 746s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.2-2 [884 B] 746s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 747s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-fonttools amd64 4.55.3-2build1 [1536 kB] 747s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-kiwisolver amd64 1.4.7-3build1 [55.6 kB] 747s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.2-1 [51.5 kB] 747s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 747s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-matplotlib amd64 3.8.3-7build1 [17.4 MB] 747s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 747s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 747s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8build1 [5332 kB] 747s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 747s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 cython3 amd64 3.0.11+dfsg-2ubuntu2 [2676 kB] 747s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.4.2-3 [205 kB] 747s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-networkx all 3.2.1-4ubuntu1 [11.5 MB] 747s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pomegranate amd64 0.15.0-1build1 [3356 kB] 747s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-importlib-metadata all 8.6.1-1 [20.7 kB] 747s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyfaidx all 0.8.1.3-1 [29.7 kB] 747s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhtscodecs2 amd64 1.6.1-2 [132 kB] 747s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhts3t64 amd64 1.21+ds-1 [514 kB] 747s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pysam amd64 0.23.0+ds-1build1 [3966 kB] 747s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 747s Get:127 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-8 [4359 kB] 747s Get:128 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 747s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 747s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 747s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 747s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 747s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 747s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 747s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 747s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 747s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 747s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 747s Get:139 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 747s Get:140 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 747s Get:141 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 747s Get:142 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 747s Get:143 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 747s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 747s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 747s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 747s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 cnvkit all 0.9.12-1 [20.6 MB] 747s Get:148 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebhelper-perl all 13.24.1ubuntu2 [95.4 kB] 747s Get:149 http://ftpmaster.internal/ubuntu plucky/main amd64 libtool all 2.5.4-4 [168 kB] 747s Get:150 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-autoreconf all 20 [16.1 kB] 747s Get:151 http://ftpmaster.internal/ubuntu plucky/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] 747s Get:152 http://ftpmaster.internal/ubuntu plucky/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [20.3 kB] 747s Get:153 http://ftpmaster.internal/ubuntu plucky/main amd64 dh-strip-nondeterminism all 1.14.1-2 [5064 B] 747s Get:154 http://ftpmaster.internal/ubuntu plucky/main amd64 debugedit amd64 1:5.1-2 [47.0 kB] 747s Get:155 http://ftpmaster.internal/ubuntu plucky/main amd64 dwz amd64 0.15-1build6 [115 kB] 747s Get:156 http://ftpmaster.internal/ubuntu plucky/main amd64 gettext amd64 0.23.1-1 [1086 kB] 747s Get:157 http://ftpmaster.internal/ubuntu plucky/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] 747s Get:158 http://ftpmaster.internal/ubuntu plucky/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] 747s Get:159 http://ftpmaster.internal/ubuntu plucky/main amd64 debhelper all 13.24.1ubuntu2 [895 kB] 747s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 dh-python all 6.20250308 [118 kB] 747s Get:161 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgmepp6t64 amd64 1.24.2-1ubuntu2 [126 kB] 747s Get:162 http://ftpmaster.internal/ubuntu plucky/main amd64 libpoppler147 amd64 25.03.0-2 [1295 kB] 747s Get:163 http://ftpmaster.internal/ubuntu plucky/main amd64 poppler-utils amd64 25.03.0-2 [232 kB] 747s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-autopkgtest all 6.20250308 [1744 B] 747s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pyproject-hooks all 1.2.0-1 [10.2 kB] 747s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-toml all 0.10.2-1 [16.5 kB] 747s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-wheel all 0.45.1-1 [57.7 kB] 747s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-build all 1.2.2-1 [31.0 kB] 747s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-installer all 0.7.0+dfsg1-3 [17.4 kB] 747s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 pybuild-plugin-pyproject all 6.20250308 [1726 B] 747s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 747s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 747s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.5-1 [252 kB] 748s Preconfiguring packages ... 748s Fetched 254 MB in 2s (128 MB/s) 748s Selecting previously unselected package python3-numpy-dev:amd64. 748s (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 ... 76968 files and directories currently installed.) 748s Preparing to unpack .../000-python3-numpy-dev_1%3a2.2.3+ds-5_amd64.deb ... 748s Unpacking python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 748s Selecting previously unselected package libblas3:amd64. 748s Preparing to unpack .../001-libblas3_3.12.1-2_amd64.deb ... 748s Unpacking libblas3:amd64 (3.12.1-2) ... 748s Selecting previously unselected package libgfortran5:amd64. 748s Preparing to unpack .../002-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 748s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 748s Selecting previously unselected package liblapack3:amd64. 748s Preparing to unpack .../003-liblapack3_3.12.1-2_amd64.deb ... 748s Unpacking liblapack3:amd64 (3.12.1-2) ... 748s Selecting previously unselected package python3-numpy. 748s Preparing to unpack .../004-python3-numpy_1%3a2.2.3+ds-5_amd64.deb ... 748s Unpacking python3-numpy (1:2.2.3+ds-5) ... 749s Selecting previously unselected package sgml-base. 749s Preparing to unpack .../005-sgml-base_1.31_all.deb ... 749s Unpacking sgml-base (1.31) ... 749s Selecting previously unselected package m4. 749s Preparing to unpack .../006-m4_1.4.19-7_amd64.deb ... 749s Unpacking m4 (1.4.19-7) ... 749s Selecting previously unselected package autoconf. 749s Preparing to unpack .../007-autoconf_2.72-3ubuntu1_all.deb ... 749s Unpacking autoconf (2.72-3ubuntu1) ... 749s Selecting previously unselected package autotools-dev. 749s Preparing to unpack .../008-autotools-dev_20220109.1_all.deb ... 749s Unpacking autotools-dev (20220109.1) ... 749s Selecting previously unselected package automake. 749s Preparing to unpack .../009-automake_1%3a1.17-3ubuntu1_all.deb ... 749s Unpacking automake (1:1.17-3ubuntu1) ... 749s Selecting previously unselected package autopoint. 751s Preparing to unpack .../010-autopoint_0.23.1-1_all.deb ... 751s Unpacking autopoint (0.23.1-1) ... 751s Selecting previously unselected package libtcl8.6:amd64. 751s Preparing to unpack .../011-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 751s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 751s Selecting previously unselected package fonts-dejavu-mono. 751s Preparing to unpack .../012-fonts-dejavu-mono_2.37-8_all.deb ... 751s Unpacking fonts-dejavu-mono (2.37-8) ... 751s Selecting previously unselected package fonts-dejavu-core. 751s Preparing to unpack .../013-fonts-dejavu-core_2.37-8_all.deb ... 751s Unpacking fonts-dejavu-core (2.37-8) ... 751s Selecting previously unselected package libfontenc1:amd64. 751s Preparing to unpack .../014-libfontenc1_1%3a1.1.8-1build1_amd64.deb ... 751s Unpacking libfontenc1:amd64 (1:1.1.8-1build1) ... 751s Selecting previously unselected package x11-common. 751s Preparing to unpack .../015-x11-common_1%3a7.7+23ubuntu3_all.deb ... 751s Unpacking x11-common (1:7.7+23ubuntu3) ... 751s Selecting previously unselected package xfonts-encodings. 751s Preparing to unpack .../016-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ... 751s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ... 751s Selecting previously unselected package xfonts-utils. 751s Preparing to unpack .../017-xfonts-utils_1%3a7.7+7_amd64.deb ... 751s Unpacking xfonts-utils (1:7.7+7) ... 751s Selecting previously unselected package fonts-urw-base35. 751s Preparing to unpack .../018-fonts-urw-base35_20200910-8_all.deb ... 751s Unpacking fonts-urw-base35 (20200910-8) ... 751s Selecting previously unselected package fontconfig-config. 751s Preparing to unpack .../019-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 751s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 751s Selecting previously unselected package libfontconfig1:amd64. 751s Preparing to unpack .../020-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 751s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 751s Selecting previously unselected package libxrender1:amd64. 751s Preparing to unpack .../021-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 751s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 751s Selecting previously unselected package libxft2:amd64. 751s Preparing to unpack .../022-libxft2_2.3.6-1build1_amd64.deb ... 751s Unpacking libxft2:amd64 (2.3.6-1build1) ... 751s Selecting previously unselected package libxss1:amd64. 751s Preparing to unpack .../023-libxss1_1%3a1.2.3-1build3_amd64.deb ... 751s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 751s Selecting previously unselected package libtk8.6:amd64. 751s Preparing to unpack .../024-libtk8.6_8.6.16-1_amd64.deb ... 751s Unpacking libtk8.6:amd64 (8.6.16-1) ... 751s Selecting previously unselected package tk8.6-blt2.5. 751s Preparing to unpack .../025-tk8.6-blt2.5_2.5.3+dfsg-8_amd64.deb ... 751s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-8) ... 751s Selecting previously unselected package blt. 751s Preparing to unpack .../026-blt_2.5.3+dfsg-8_amd64.deb ... 751s Unpacking blt (2.5.3+dfsg-8) ... 751s Selecting previously unselected package libisl23:amd64. 751s Preparing to unpack .../027-libisl23_0.27-1_amd64.deb ... 751s Unpacking libisl23:amd64 (0.27-1) ... 751s Selecting previously unselected package libmpc3:amd64. 751s Preparing to unpack .../028-libmpc3_1.3.1-1build2_amd64.deb ... 751s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 751s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 751s Preparing to unpack .../029-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 751s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 751s Selecting previously unselected package cpp-14. 751s Preparing to unpack .../030-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 751s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 751s Selecting previously unselected package cpp-x86-64-linux-gnu. 751s Preparing to unpack .../031-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 751s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 751s Selecting previously unselected package cpp. 751s Preparing to unpack .../032-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 751s Unpacking cpp (4:14.2.0-1ubuntu1) ... 751s Selecting previously unselected package libcc1-0:amd64. 751s Preparing to unpack .../033-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libgomp1:amd64. 751s Preparing to unpack .../034-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libitm1:amd64. 751s Preparing to unpack .../035-libitm1_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libasan8:amd64. 751s Preparing to unpack .../036-libasan8_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package liblsan0:amd64. 751s Preparing to unpack .../037-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libtsan2:amd64. 751s Preparing to unpack .../038-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libubsan1:amd64. 751s Preparing to unpack .../039-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 751s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 751s Selecting previously unselected package libhwasan0:amd64. 751s Preparing to unpack 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unpack .../045-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 751s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 751s Selecting previously unselected package gcc. 751s Preparing to unpack .../046-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 751s Unpacking gcc (4:14.2.0-1ubuntu1) ... 751s Selecting previously unselected package libstdc++-14-dev:amd64. 751s Preparing to unpack .../047-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 751s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 752s Selecting previously unselected package g++-14-x86-64-linux-gnu. 752s Preparing to unpack .../048-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 752s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 752s Selecting previously unselected package g++-14. 752s Preparing to unpack .../049-g++-14_14.2.0-17ubuntu3_amd64.deb ... 752s Unpacking g++-14 (14.2.0-17ubuntu3) ... 752s Selecting previously unselected package g++-x86-64-linux-gnu. 752s Preparing to unpack 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752s Selecting previously unselected package python3-pil.imagetk:amd64. 752s Preparing to unpack .../056-python3-pil.imagetk_11.1.0-5build1_amd64.deb ... 752s Unpacking python3-pil.imagetk:amd64 (11.1.0-5build1) ... 752s Selecting previously unselected package libimagequant0:amd64. 752s Preparing to unpack .../057-libimagequant0_2.18.0-1build1_amd64.deb ... 752s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 752s Selecting previously unselected package libjpeg-turbo8:amd64. 752s Preparing to unpack .../058-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 752s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 752s Selecting previously unselected package libjpeg8:amd64. 752s Preparing to unpack .../059-libjpeg8_8c-2ubuntu11_amd64.deb ... 752s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 752s Selecting previously unselected package liblcms2-2:amd64. 752s Preparing to unpack .../060-liblcms2-2_2.16-2_amd64.deb ... 752s Unpacking liblcms2-2:amd64 (2.16-2) ... 752s Selecting previously unselected package libopenjp2-7:amd64. 752s Preparing to unpack .../061-libopenjp2-7_2.5.3-2_amd64.deb ... 752s Unpacking libopenjp2-7:amd64 (2.5.3-2) ... 752s Selecting previously unselected package libgraphite2-3:amd64. 752s Preparing to unpack .../062-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 752s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 752s Selecting previously unselected package libharfbuzz0b:amd64. 752s Preparing to unpack .../063-libharfbuzz0b_10.2.0-1_amd64.deb ... 752s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 752s Selecting previously unselected package libraqm0:amd64. 752s Preparing to unpack .../064-libraqm0_0.10.2-1_amd64.deb ... 752s Unpacking libraqm0:amd64 (0.10.2-1) ... 752s Selecting previously unselected package libdeflate0:amd64. 752s Preparing to unpack .../065-libdeflate0_1.23-1_amd64.deb ... 752s Unpacking libdeflate0:amd64 (1.23-1) ... 752s Selecting previously unselected package libjbig0:amd64. 752s Preparing to unpack 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libwebpdemux2:amd64 (1.5.0-0.1) ... 752s Selecting previously unselected package libwebpmux3:amd64. 752s Preparing to unpack .../072-libwebpmux3_1.5.0-0.1_amd64.deb ... 752s Unpacking libwebpmux3:amd64 (1.5.0-0.1) ... 752s Selecting previously unselected package python3-pil:amd64. 752s Preparing to unpack .../073-python3-pil_11.1.0-5build1_amd64.deb ... 752s Unpacking python3-pil:amd64 (11.1.0-5build1) ... 752s Selecting previously unselected package libpixman-1-0:amd64. 752s Preparing to unpack .../074-libpixman-1-0_0.44.0-3_amd64.deb ... 752s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 753s Selecting previously unselected package libxcb-render0:amd64. 753s Preparing to unpack .../075-libxcb-render0_1.17.0-2_amd64.deb ... 753s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 753s Selecting previously unselected package libxcb-shm0:amd64. 753s Preparing to unpack .../076-libxcb-shm0_1.17.0-2_amd64.deb ... 753s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 753s Selecting previously unselected package libcairo2:amd64. 753s Preparing to unpack .../077-libcairo2_1.18.2-2_amd64.deb ... 753s Unpacking libcairo2:amd64 (1.18.2-2) ... 753s Selecting previously unselected package python3-cairo. 753s Preparing to unpack .../078-python3-cairo_1.26.1-2build2_amd64.deb ... 753s Unpacking python3-cairo (1.26.1-2build2) ... 753s Selecting previously unselected package python3-freetype. 753s Preparing to unpack .../079-python3-freetype_2.5.1-1_all.deb ... 753s Unpacking python3-freetype (2.5.1-1) ... 753s Selecting previously unselected package python3-rlpycairo. 753s Preparing to unpack .../080-python3-rlpycairo_0.3.0-3_all.deb ... 753s Unpacking python3-rlpycairo (0.3.0-3) ... 753s Selecting previously unselected package python3-reportlab. 753s Preparing to unpack .../081-python3-reportlab_4.3.1-1_all.deb ... 753s Unpacking python3-reportlab (4.3.1-1) ... 753s Selecting previously unselected package xml-core. 753s Preparing to unpack .../082-xml-core_0.19_all.deb ... 753s Unpacking xml-core (0.19) ... 753s Selecting previously unselected package w3c-sgml-lib. 753s Preparing to unpack .../083-w3c-sgml-lib_1.3-3_all.deb ... 753s Unpacking w3c-sgml-lib (1.3-3) ... 753s Selecting previously unselected package python3-biopython. 753s Preparing to unpack .../084-python3-biopython_1.85+dfsg-2build1_amd64.deb ... 753s Unpacking python3-biopython (1.85+dfsg-2build1) ... 753s Selecting previously unselected package libjs-jquery. 753s Preparing to unpack .../085-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 753s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 753s Selecting previously unselected package libjs-jquery-ui. 753s Preparing to unpack .../086-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 753s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 753s Selecting previously unselected package fonts-lyx. 753s Preparing to unpack .../087-fonts-lyx_2.4.3-1_all.deb ... 753s Unpacking fonts-lyx (2.4.3-1) ... 753s Selecting previously unselected package python-matplotlib-data. 753s Preparing to unpack .../088-python-matplotlib-data_3.8.3-7build1_all.deb ... 753s Unpacking python-matplotlib-data (3.8.3-7build1) ... 753s Selecting previously unselected package python3-dateutil. 753s Preparing to unpack .../089-python3-dateutil_2.9.0-3_all.deb ... 753s Unpacking python3-dateutil (2.9.0-3) ... 753s Selecting previously unselected package python3-contourpy. 753s Preparing to unpack .../090-python3-contourpy_1.3.1-1build1_amd64.deb ... 753s Unpacking python3-contourpy (1.3.1-1build1) ... 753s Selecting previously unselected package python3-cycler. 753s Preparing to unpack .../091-python3-cycler_0.12.1-1_all.deb ... 753s Unpacking python3-cycler (0.12.1-1) ... 753s Selecting previously unselected package python3-brotli. 753s Preparing to unpack .../092-python3-brotli_1.1.0-2build4_amd64.deb ... 753s Unpacking python3-brotli (1.1.0-2build4) ... 753s Selecting previously unselected package python3-platformdirs. 753s Preparing to unpack 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python3-decorator (5.1.1-5) ... 754s Selecting previously unselected package liblbfgsb0:amd64. 754s Preparing to unpack .../099-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 754s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 754s Selecting previously unselected package python3-scipy. 754s Preparing to unpack .../100-python3-scipy_1.14.1-4ubuntu2_amd64.deb ... 754s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 754s Selecting previously unselected package python3-mpmath. 754s Preparing to unpack .../101-python3-mpmath_1.3.0-1_all.deb ... 754s Unpacking python3-mpmath (1.3.0-1) ... 754s Selecting previously unselected package python3-sympy. 754s Preparing to unpack .../102-python3-sympy_1.13.3-5_all.deb ... 754s Unpacking python3-sympy (1.13.3-5) ... 754s Selecting previously unselected package python3-ufolib2. 754s Preparing to unpack .../103-python3-ufolib2_0.17.0+dfsg1-1_all.deb ... 754s Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ... 755s Selecting previously unselected package python3-unicodedata2. 755s Preparing to unpack .../104-python3-unicodedata2_15.1.0+ds-1build3_amd64.deb ... 755s Unpacking python3-unicodedata2 (15.1.0+ds-1build3) ... 755s Selecting previously unselected package python3-all. 755s Preparing to unpack .../105-python3-all_3.13.2-2_amd64.deb ... 755s Unpacking python3-all (3.13.2-2) ... 755s Selecting previously unselected package unicode-data. 755s Preparing to unpack .../106-unicode-data_15.1.0-1_all.deb ... 755s Unpacking unicode-data (15.1.0-1) ... 755s Selecting previously unselected package python3-fonttools. 755s Preparing to unpack .../107-python3-fonttools_4.55.3-2build1_amd64.deb ... 755s Unpacking python3-fonttools (4.55.3-2build1) ... 755s Selecting previously unselected package python3-kiwisolver. 755s Preparing to unpack .../108-python3-kiwisolver_1.4.7-3build1_amd64.deb ... 755s Unpacking python3-kiwisolver (1.4.7-3build1) ... 755s Selecting previously unselected package python3-packaging. 755s Preparing to unpack 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python3-pandas-lib:amd64 (2.2.3+dfsg-8build1) ... 756s Selecting previously unselected package python3-pandas. 756s Preparing to unpack .../115-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 756s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 756s Selecting previously unselected package cython3. 756s Preparing to unpack .../116-cython3_3.0.11+dfsg-2ubuntu2_amd64.deb ... 756s Unpacking cython3 (3.0.11+dfsg-2ubuntu2) ... 756s Selecting previously unselected package python3-joblib. 756s Preparing to unpack .../117-python3-joblib_1.4.2-3_all.deb ... 756s Unpacking python3-joblib (1.4.2-3) ... 756s Selecting previously unselected package python3-networkx. 756s Preparing to unpack .../118-python3-networkx_3.2.1-4ubuntu1_all.deb ... 756s Unpacking python3-networkx (3.2.1-4ubuntu1) ... 757s Selecting previously unselected package python3-pomegranate. 757s Preparing to unpack .../119-python3-pomegranate_0.15.0-1build1_amd64.deb ... 757s Unpacking python3-pomegranate (0.15.0-1build1) ... 757s Selecting previously unselected package python3-importlib-metadata. 757s Preparing to unpack .../120-python3-importlib-metadata_8.6.1-1_all.deb ... 757s Unpacking python3-importlib-metadata (8.6.1-1) ... 757s Selecting previously unselected package python3-pyfaidx. 757s Preparing to unpack .../121-python3-pyfaidx_0.8.1.3-1_all.deb ... 757s Unpacking python3-pyfaidx (0.8.1.3-1) ... 757s Selecting previously unselected package libhtscodecs2:amd64. 757s Preparing to unpack .../122-libhtscodecs2_1.6.1-2_amd64.deb ... 757s Unpacking libhtscodecs2:amd64 (1.6.1-2) ... 757s Selecting previously unselected package libhts3t64:amd64. 757s Preparing to unpack .../123-libhts3t64_1.21+ds-1_amd64.deb ... 757s Unpacking libhts3t64:amd64 (1.21+ds-1) ... 757s Selecting previously unselected package python3-pysam. 757s Preparing to unpack .../124-python3-pysam_0.23.0+ds-1build1_amd64.deb ... 757s Unpacking python3-pysam (0.23.0+ds-1build1) ... 757s Selecting previously unselected package python3-threadpoolctl. 757s Preparing to unpack .../125-python3-threadpoolctl_3.1.0-1_all.deb ... 757s Unpacking python3-threadpoolctl (3.1.0-1) ... 757s Selecting previously unselected package python3-sklearn-lib:amd64. 757s Preparing to unpack .../126-python3-sklearn-lib_1.4.2+dfsg-8_amd64.deb ... 757s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 758s Selecting previously unselected package python3-sklearn. 758s Preparing to unpack .../127-python3-sklearn_1.4.2+dfsg-8_all.deb ... 758s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 758s Selecting previously unselected package zip. 758s Preparing to unpack .../128-zip_3.0-14ubuntu2_amd64.deb ... 758s Unpacking zip (3.0-14ubuntu2) ... 758s Selecting previously unselected package unzip. 758s Preparing to unpack .../129-unzip_6.0-28ubuntu6_amd64.deb ... 758s Unpacking unzip (6.0-28ubuntu6) ... 758s Selecting previously unselected package libpaper2:amd64. 758s Preparing to unpack .../130-libpaper2_2.2.5-0.3_amd64.deb ... 758s 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libthai0:amd64. 758s Preparing to unpack .../136-libthai0_0.1.29-2build1_amd64.deb ... 758s Unpacking libthai0:amd64 (0.1.29-2build1) ... 758s Selecting previously unselected package libpango-1.0-0:amd64. 758s Preparing to unpack .../137-libpango-1.0-0_1.56.2-1_amd64.deb ... 758s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 758s Selecting previously unselected package libpangoft2-1.0-0:amd64. 758s Preparing to unpack .../138-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 758s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 758s Selecting previously unselected package libpangocairo-1.0-0:amd64. 758s Preparing to unpack .../139-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 758s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 758s Selecting previously unselected package libice6:amd64. 758s Preparing to unpack .../140-libice6_2%3a1.1.1-1_amd64.deb ... 758s Unpacking libice6:amd64 (2:1.1.1-1) ... 758s Selecting previously unselected package libsm6:amd64. 758s Preparing to unpack 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package libdebhelper-perl. 760s Preparing to unpack .../147-libdebhelper-perl_13.24.1ubuntu2_all.deb ... 760s Unpacking libdebhelper-perl (13.24.1ubuntu2) ... 760s Selecting previously unselected package libtool. 760s Preparing to unpack .../148-libtool_2.5.4-4_all.deb ... 760s Unpacking libtool (2.5.4-4) ... 760s Selecting previously unselected package dh-autoreconf. 760s Preparing to unpack .../149-dh-autoreconf_20_all.deb ... 760s Unpacking dh-autoreconf (20) ... 760s Selecting previously unselected package libarchive-zip-perl. 760s Preparing to unpack .../150-libarchive-zip-perl_1.68-1_all.deb ... 760s Unpacking libarchive-zip-perl (1.68-1) ... 760s Selecting previously unselected package libfile-stripnondeterminism-perl. 760s Preparing to unpack .../151-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... 760s Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... 760s Selecting previously unselected package dh-strip-nondeterminism. 760s Preparing to unpack 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760s Preparing to unpack .../158-debhelper_13.24.1ubuntu2_all.deb ... 760s Unpacking debhelper (13.24.1ubuntu2) ... 760s Selecting previously unselected package dh-python. 760s Preparing to unpack .../159-dh-python_6.20250308_all.deb ... 760s Unpacking dh-python (6.20250308) ... 760s Selecting previously unselected package libgpgmepp6t64:amd64. 760s Preparing to unpack .../160-libgpgmepp6t64_1.24.2-1ubuntu2_amd64.deb ... 760s Unpacking libgpgmepp6t64:amd64 (1.24.2-1ubuntu2) ... 760s Selecting previously unselected package libpoppler147:amd64. 760s Preparing to unpack .../161-libpoppler147_25.03.0-2_amd64.deb ... 760s Unpacking libpoppler147:amd64 (25.03.0-2) ... 760s Selecting previously unselected package poppler-utils. 760s Preparing to unpack .../162-poppler-utils_25.03.0-2_amd64.deb ... 760s Unpacking poppler-utils (25.03.0-2) ... 760s Selecting previously unselected package pybuild-plugin-autopkgtest. 760s Preparing to unpack .../163-pybuild-plugin-autopkgtest_6.20250308_all.deb 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up python3-all (3.13.2-2) ... 762s Setting up python3-pytz (2025.1-3) ... 762s Setting up libxcb-shm0:amd64 (1.17.0-2) ... 762s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ... 762s Setting up python3-freetype (2.5.1-1) ... 762s Setting up python3-networkx (3.2.1-4ubuntu1) ... 763s Setting up python3-wheel (0.45.1-1) ... 763s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ... 763s Setting up python3-platformdirs (4.3.6-1) ... 763s Setting up python3-tz (2025.1-3) ... 763s Setting up python3-fs (2.4.16-7) ... 764s Setting up unicode-data (15.1.0-1) ... 764s Setting up python3-decorator (5.1.1-5) ... 764s Setting up zip (3.0-14ubuntu2) ... 764s Setting up libfontenc1:amd64 (1:1.1.8-1build1) ... 764s Setting up autotools-dev (20220109.1) ... 764s Setting up libblas3:amd64 (3.12.1-2) ... 764s 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 764s Setting up python3-packaging (24.2-1) ... 764s Setting up python3-pyproject-hooks (1.2.0-1) ... 764s Setting up python3-brotli (1.1.0-2build4) ... 764s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... 764s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ... 764s Setting up python3-cycler (0.12.1-1) ... 765s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 765s Setting up fonts-dejavu-mono (2.37-8) ... 765s Setting up python3-kiwisolver (1.4.7-3build1) ... 765s Setting up libmpc3:amd64 (1.3.1-1build2) ... 765s Setting up python3-numpy-dev:amd64 (1:2.2.3+ds-5) ... 765s Setting up cython3 (3.0.11+dfsg-2ubuntu2) ... 765s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ... 765s Setting up autopoint (0.23.1-1) ... 765s Setting up fonts-dejavu-core (2.37-8) ... 765s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 765s Setting up python3-toml (0.10.2-1) ... 765s Setting up python3-installer (0.7.0+dfsg1-3) ... 765s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ... 765s Setting up autoconf (2.72-3ubuntu1) 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766s Setting up python3-build (1.2.2-1) ... 766s Setting up python-matplotlib-data (3.8.3-7build1) ... 766s Setting up libwebpmux3:amd64 (1.5.0-0.1) ... 766s Setting up xdg-utils (1.2.1-2ubuntu1) ... 766s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 766s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ... 766s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ... 766s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ... 766s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 766s Setting up automake (1:1.17-3ubuntu1) ... 766s update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode 766s Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... 766s Setting up python3-pyfaidx (0.8.1.3-1) ... 766s Setting up python3-sympy (1.13.3-5) ... 772s Setting up libice6:amd64 (2:1.1.1-1) ... 772s Setting up liblapack3:amd64 (3.12.1-2) ... 772s update-alternatives: using 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libpango-1.0-0:amd64 (1.56.2-1) ... 779s Setting up python3.12-tk (3.12.9-1) ... 779s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-8) ... 779s Setting up fonts-urw-base35 (20200910-8) ... 780s Setting up libcairo2:amd64 (1.18.2-2) ... 780s Setting up python3.13-tk (3.13.2-2) ... 780s Setting up python3-pil:amd64 (11.1.0-5build1) ... 780s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 784s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... 784s Setting up python3-sklearn (1.4.2+dfsg-8) ... 785s Setting up cpp (4:14.2.0-1ubuntu1) ... 785s Setting up poppler-utils (25.03.0-2) ... 785s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 785s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ... 785s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ... 785s Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... 785s Setting up python3-cairo (1.26.1-2build2) ... 786s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 786s Setting up blt (2.5.3+dfsg-8) ... 786s Setting up python3-tk:amd64 (3.13.1-1) ... 786s Setting up gcc-14 (14.2.0-17ubuntu3) ... 786s Setting up python3-pil.imagetk:amd64 (11.1.0-5build1) ... 786s Setting up python3-rlpycairo (0.3.0-3) ... 786s Setting up r-base-core (4.4.3-1) ... 786s Creating config file /etc/R/Renviron with new version 786s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 786s Setting up python3-reportlab (4.3.1-1) ... 787s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 787s Setting up g++-14 (14.2.0-17ubuntu3) ... 787s Setting up r-bioc-biocgenerics (0.52.0-2) ... 787s Setting up libtool (2.5.4-4) ... 787s Setting up gcc (4:14.2.0-1ubuntu1) ... 787s Setting up dh-autoreconf (20) ... 787s Setting up g++ (4:14.2.0-1ubuntu1) ... 787s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 787s Setting up r-bioc-dnacopy (1.80.0-2) ... 787s Setting up build-essential (12.10ubuntu1) ... 787s Setting up debhelper (13.24.1ubuntu2) ... 787s Setting up pybuild-plugin-autopkgtest (6.20250308) ... 787s Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... 787s Setting up python3-fonttools (4.55.3-2build1) ... 788s Setting up python3-matplotlib (3.8.3-7build1) ... 789s Processing triggers for libc-bin (2.41-1ubuntu1) ... 789s Processing triggers for man-db (2.13.0-1) ... 790s Processing triggers for install-info (7.1.1-1) ... 791s Processing triggers for sgml-base (1.31) ... 791s Setting up w3c-sgml-lib (1.3-3) ... 818s Setting up python3-biopython (1.85+dfsg-2build1) ... 818s Setting up cnvkit (0.9.12-1) ... 822s autopkgtest [01:57:44]: test pybuild-autopkgtest: pybuild-autopkgtest 822s autopkgtest [01:57:44]: test pybuild-autopkgtest: [----------------------- 822s pybuild-autopkgtest 823s I: pybuild base:311: cd /tmp/autopkgtest.DR9FGQ/autopkgtest_tmp/build; python3.13 -m pytest test 825s ============================= test session starts ============================== 825s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 825s rootdir: /tmp/autopkgtest.DR9FGQ/autopkgtest_tmp/build 825s configfile: pyproject.toml 825s plugins: typeguard-4.4.2 825s collected 70 items 825s 829s test/test_cnvlib.py ........... [ 15%] 945s test/test_commands.py ............................. [ 57%] 948s test/test_genome.py ................... [ 84%] 949s test/test_io.py .......... [ 98%] 961s test/test_r.py .autopkgtest [02:00:02]: test pybuild-autopkgtest: -----------------------] 961s [100%] 961s 961s ======================== 70 passed in 136.44s (0:02:16) ======================== 961s pybuild-autopkgtest PASS 961s autopkgtest [02:00:03]: test pybuild-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 961s autopkgtest [02:00:03]: @@@@@@@@@@@@@@@@@@@@ summary 961s run-unit-test PASS 961s pybuild-autopkgtest PASS 977s nova [W] Skipping flock for amd64 977s Creating nova instance adt-plucky-amd64-cnvkit-20250316-012924-juju-7f2275-prod-proposed-migration-environment-20-4b327b99-8874-485a-9860-3780c48cf5ea from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 977s nova [W] Timed out waiting for 530856ad-f471-4984-8b34-0434e7a4a65e to get deleted. 977s nova [W] Skipping flock for amd64 977s Creating nova instance adt-plucky-amd64-cnvkit-20250316-012924-juju-7f2275-prod-proposed-migration-environment-20-4b327b99-8874-485a-9860-3780c48cf5ea from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 977s nova [W] Timed out waiting for 7d8926b1-2472-46cf-858d-51bd576c6ed2 to get deleted.