0s autopkgtest [22:00:52]: starting date and time: 2025-03-15 22:00:52+0000
  0s autopkgtest [22:00:52]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [22:00:52]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9czvtvn3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-bioc-rtracklayer --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-7.secgroup --name adt-plucky-amd64-r-bioc-rtracklayer-20250315-220051-juju-7f2275-prod-proposed-migration-environment-15-21f12f32-e930-4452-944c-b079c8351525 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 51s autopkgtest [22:01:43]: testbed dpkg architecture: amd64
 51s autopkgtest [22:01:43]: testbed apt version: 2.9.31ubuntu1
 51s autopkgtest [22:01:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 51s autopkgtest [22:01:43]: testbed release detected to be: None
 51s autopkgtest [22:01:43]: updating testbed package index (apt update)
 52s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
 52s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 52s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 52s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 52s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB]
 52s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB]
 52s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB]
 52s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB]
 52s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB]
 52s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B]
 52s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B]
 52s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB]
 52s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB]
 52s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB]
 52s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B]
 52s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB]
 52s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B]
 52s Fetched 1265 kB in 0s (5581 kB/s)
 53s Reading package lists...
 53s + lsb_release --codename --short
 53s + RELEASE=plucky
 53s + cat
 53s + [ plucky != trusty ]
 53s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y --allow-downgrades -o Dpkg::Options::=--force-confnew dist-upgrade
 53s Reading package lists...
 54s Building dependency tree...
 54s Reading state information...
 54s Calculating upgrade...
 54s Calculating upgrade...
 54s The following package was automatically installed and is no longer required:
 54s   libnl-genl-3-200
 54s 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]
 59s 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]
 59s 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]
 59s 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]
 60s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B]
 60s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB]
 60s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B]
 60s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB]
 60s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B]
 60s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB]
 60s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB]
 60s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB]
 60s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB]
 60s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB]
 60s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB]
 60s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B]
 60s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB]
 60s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB]
 60s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB]
 60s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB]
 60s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B]
 61s Preconfiguring packages ...
 61s Fetched 807 MB in 6s (141 MB/s)
 61s (Reading database ... 
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(Reading database ... 100%
(Reading database ... 109138 files and directories currently installed.)
 61s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ...
 61s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ...
 61s Setting up ncurses-bin (6.5+20250216-2) ...
 61s (Reading database ... 
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(Reading database ... 109138 files and directories currently installed.)
 61s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ...
 61s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ...
 61s Setting up ncurses-base (6.5+20250216-2) ...
 61s (Reading database ... 
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(Reading database ... 109138 files and directories currently installed.)
 61s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ...
 61s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ...
 62s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ...
 62s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ...
 62s Setting up liblz4-1:amd64 (1.10.0-4) ...
 62s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109138 files and directories currently installed.)
 62s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ...
 62s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ...
 62s Setting up liblzma5:amd64 (5.6.4-1) ...
 62s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 109138 files and directories currently installed.)
 62s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ...
 62s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ...
 62s Setting up libapt-pkg7.0:amd64 (2.9.33) ...
 63s (Reading database ... 
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 81s Installing new version of config file /etc/mime.types ...
 81s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ...
 81s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ...
 81s Setting up pci.ids (0.0~2025.03.09-1) ...
 81s Setting up apt-utils (2.9.33) ...
 81s Setting up libdebuginfod-common (0.192-4) ...
 81s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ...
 81s Setting up bpftool (7.6.0+6.14.0-10.10) ...
 81s Setting up libestr0:amd64 (0.1.11-2) ...
 81s Setting up libbrotli1:amd64 (1.1.0-2build4) ...
 81s Setting up libsqlite3-0:amd64 (3.46.1-2) ...
 81s Setting up dosfstools (4.2-1.2) ...
 81s Setting up rsyslog (8.2412.0-2ubuntu2) ...
 81s info: The user `syslog' is already a member of `adm'.
 82s Setting up binutils-common:amd64 (2.44-3ubuntu1) ...
 82s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ...
 82s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ...
 82s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ...
 82s Setting up linux-headers-generic (6.14.0-10.10) ...
 82s Setting up libjemalloc2:amd64 (5.3.0-3) ...
 82s Setting up libsframe1:amd64 (2.44-3ubuntu1) ...
 82s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ...
 82s Setting up apparmor (4.1.0~beta5-0ubuntu8) ...
 82s Installing new version of config file /etc/apparmor.d/openvpn ...
 83s Reloading AppArmor profiles 
 85s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ...
 85s No schema files found: doing nothing.
 85s Setting up libglib2.0-data (2.84.0-1) ...
 85s Setting up libncurses6:amd64 (6.5+20250216-2) ...
 85s Setting up strace (6.13+ds-1ubuntu1) ...
 85s Setting up xz-utils (5.6.4-1) ...
 85s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ...
 85s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ...
 87s Setting up libncursesw6:amd64 (6.5+20250216-2) ...
 87s Setting up libpci3:amd64 (1:3.13.0-2) ...
 87s Setting up python-apt-common (2.9.9build1) ...
 87s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ...
 87s Setting up pnp.ids (0.393-3) ...
 87s Setting up libnl-3-200:amd64 (3.7.0-1) ...
 87s Setting up python3.13-minimal (3.13.2-2) ...
 88s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ...
 88s Setting up libbinutils:amd64 (2.44-3ubuntu1) ...
 88s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ...
 88s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ...
 88s Setting up rsync (3.4.1+ds1-3) ...
 89s rsync.service is a disabled or a static unit not running, not starting it.
 89s Setting up python3.13-gdbm (3.13.2-2) ...
 89s Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
 89s Setting up ncurses-term (6.5+20250216-2) ...
 89s Setting up libctf0:amd64 (2.44-3ubuntu1) ...
 89s Setting up libpython3.13:amd64 (3.13.2-2) ...
 89s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
 89s Setting up libdebuginfod1t64:amd64 (0.192-4) ...
 89s Setting up linux-headers-virtual (6.14.0-10.10) ...
 89s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ...
 89s Setting up python3.13 (3.13.2-2) ...
 90s Setting up htop (3.4.0-2) ...
 90s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ...
 92s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic
 92s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic
 92s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic
 92s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic
 92s Setting up libfwupd3:amd64 (2.0.6-4) ...
 92s Setting up python3 (3.13.2-2) ...
 93s Setting up python3-markupsafe (2.1.5-1build4) ...
 93s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ...
 95s Setting up libnl-route-3-200:amd64 (3.7.0-1) ...
 95s Setting up hwdata (0.393-3) ...
 95s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
 95s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ...
 95s Setting up linux-perf (6.14.0-10.10) ...
 95s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ...
 95s Setting up python3-gi (3.50.0-4build1) ...
 95s Setting up pciutils (1:3.13.0-2) ...
 95s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ...
 95s Setting up curl (8.12.1-3ubuntu1) ...
 95s Setting up linux-image-virtual (6.14.0-10.10) ...
 95s Setting up linux-tools-common (6.14.0-10.10) ...
 95s Setting up fwupd (2.0.6-4) ...
 96s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
 96s fwupd.service is a disabled or a static unit not running, not starting it.
 96s Setting up python3-systemd (235-1build6) ...
 96s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ...
 96s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ...
 96s Setting up linux-image-generic (6.14.0-10.10) ...
 96s Setting up python3-dbus (1.3.2-5build5) ...
 96s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ...
 96s Setting up linux-generic (6.14.0-10.10) ...
 96s Setting up python3-apt (2.9.9build1) ...
 96s Setting up python3-yaml (6.0.2-1build2) ...
 96s Setting up python3-lazr.uri (1.0.6-6) ...
 97s Setting up binutils (2.44-3ubuntu1) ...
 97s Setting up cloud-init-base (25.1-0ubuntu3) ...
 98s Setting up linux-virtual (6.14.0-10.10) ...
 98s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ...
 98s Setting up cloud-init (25.1-0ubuntu3) ...
 98s Processing triggers for systemd (257.3-1ubuntu3) ...
 98s Processing triggers for man-db (2.13.0-1) ...
100s Processing triggers for dbus (1.16.2-1ubuntu1) ...
100s Processing triggers for libc-bin (2.41-1ubuntu1) ...
100s Processing triggers for initramfs-tools (0.146ubuntu1) ...
100s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic
100s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
112s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ...
112s /etc/kernel/postinst.d/initramfs-tools:
112s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic
112s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
124s /etc/kernel/postinst.d/zz-update-grub:
124s Sourcing file `/etc/default/grub'
124s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
124s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
124s Generating grub configuration file ...
124s Found linux image: /boot/vmlinuz-6.14.0-10-generic
124s Found initrd image: /boot/initrd.img-6.14.0-10-generic
124s Found linux image: /boot/vmlinuz-6.12.0-16-generic
124s Found initrd image: /boot/initrd.img-6.12.0-16-generic
124s Found linux image: /boot/vmlinuz-6.11.0-8-generic
124s Found initrd image: /boot/initrd.img-6.11.0-8-generic
125s Warning: os-prober will not be executed to detect other bootable partitions.
125s Systems on them will not be added to the GRUB boot configuration.
125s Check GRUB_DISABLE_OS_PROBER documentation entry.
125s Adding boot menu entry for UEFI Firmware Settings ...
125s done
125s + rm /etc/apt/preferences.d/force-downgrade-to-release.pref
125s + /usr/lib/apt/apt-helper analyze-pattern ?true
125s + uname -r
125s + sed s/\./\\./g
125s + running_kernel_pattern=^linux-.*6\.12\.0-16-generic.*
125s + apt list ?obsolete
125s + tail -n+2
125s + cut -d/ -f1
125s + grep -v ^linux-.*6\.12\.0-16-generic.*
126s + obsolete_pkgs=linux-headers-6.11.0-8-generic
126s linux-headers-6.11.0-8
126s linux-headers-6.12.0-16
126s linux-image-6.11.0-8-generic
126s linux-modules-6.11.0-8-generic
126s linux-tools-6.11.0-8-generic
126s linux-tools-6.11.0-8
126s linux-tools-6.12.0-16
126s + DEBIAN_FRONTEND=noninteractive eatmydata apt-get -y purge --autoremove linux-headers-6.11.0-8-generic linux-headers-6.11.0-8 linux-headers-6.12.0-16 linux-image-6.11.0-8-generic linux-modules-6.11.0-8-generic linux-tools-6.11.0-8-generic linux-tools-6.11.0-8 linux-tools-6.12.0-16
126s Reading package lists...
127s Building dependency tree...
127s Reading state information...
127s Solving dependencies...
127s The following packages will be REMOVED:
127s   libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib*
127s   libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
127s   linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic*
127s   linux-image-6.11.0-8-generic* linux-modules-6.11.0-8-generic*
127s   linux-tools-6.11.0-8* linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16*
127s   linux-tools-6.12.0-16-generic*
128s 0 upgraded, 0 newly installed, 15 to remove and 5 not upgraded.
128s After this operation, 371 MB disk space will be freed.
128s (Reading database ... 
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(Reading database ... 148643 files and directories currently installed.)
128s Removing libnl-genl-3-200:amd64 (3.7.0-1) ...
128s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
128s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
128s Removing libpython3.12t64:amd64 (3.12.9-1) ...
128s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ...
128s Removing libnsl2:amd64 (1.3.0-3build3) ...
128s Removing libpython3.12-minimal:amd64 (3.12.9-1) ...
128s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
129s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
131s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ...
131s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ...
134s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
134s /etc/kernel/postrm.d/initramfs-tools:
134s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
134s /etc/kernel/postrm.d/zz-update-grub:
134s Sourcing file `/etc/default/grub'
134s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
134s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
134s Generating grub configuration file ...
134s Found linux image: /boot/vmlinuz-6.14.0-10-generic
134s Found initrd image: /boot/initrd.img-6.14.0-10-generic
134s Found linux image: /boot/vmlinuz-6.12.0-16-generic
134s Found initrd image: /boot/initrd.img-6.12.0-16-generic
135s Warning: os-prober will not be executed to detect other bootable partitions.
135s Systems on them will not be added to the GRUB boot configuration.
135s Check GRUB_DISABLE_OS_PROBER documentation entry.
135s Adding boot menu entry for UEFI Firmware Settings ...
135s done
135s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
135s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ...
135s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ...
135s Processing triggers for libc-bin (2.41-1ubuntu1) ...
135s (Reading database ... 
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(Reading database ... 84830 files and directories currently installed.)
135s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
135s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ...
135s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
135s + grep -q trusty /etc/lsb-release
135s + [ ! -d /usr/share/doc/unattended-upgrades ]
135s + [ ! -d /usr/share/doc/lxd ]
135s + [ ! -d /usr/share/doc/lxd-client ]
135s + [ ! -d /usr/share/doc/snapd ]
135s + type iptables
135s + cat
135s + chmod 755 /etc/rc.local
135s + . /etc/rc.local
135s + iptables -w -t mangle -A FORWARD -p tcp --tcp-flags SYN,RST SYN -j TCPMSS --clamp-mss-to-pmtu
135s + iptables -A OUTPUT -d 10.255.255.1/32 -p tcp -j DROP
135s + iptables -A OUTPUT -d 10.255.255.2/32 -p tcp -j DROP
135s + uname -m
135s + [ x86_64 = ppc64le ]
135s + [ -d /run/systemd/system ]
135s + systemd-detect-virt --quiet --vm
135s + mkdir -p /etc/systemd/system/systemd-random-seed.service.d/
135s + cat
135s + grep -q lz4 /etc/initramfs-tools/initramfs.conf
135s + echo COMPRESS=lz4
135s autopkgtest [22:03:07]: upgrading testbed (apt dist-upgrade and autopurge)
135s Reading package lists...
136s Building dependency tree...
136s Reading state information...
136s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
136s Starting 2 pkgProblemResolver with broken count: 0
136s Done
137s Entering ResolveByKeep
137s 
137s Calculating upgrade...
137s The following packages will be upgraded:
137s   libc-bin libc-dev-bin libc6 libc6-dev locales
137s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
137s Need to get 10.5 MB of archives.
137s After this operation, 1024 B of additional disk space will be used.
137s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB]
138s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB]
138s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB]
138s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB]
138s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB]
138s Preconfiguring packages ...
138s Fetched 10.5 MB in 1s (19.3 MB/s)
138s (Reading database ... 
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(Reading database ... 84827 files and directories currently installed.)
138s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ...
138s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
139s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ...
139s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
139s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ...
139s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
139s Setting up libc6:amd64 (2.41-1ubuntu2) ...
139s (Reading database ... 
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(Reading database ... 84827 files and directories currently installed.)
139s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ...
139s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
139s Setting up libc-bin (2.41-1ubuntu2) ...
139s (Reading database ... 
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139s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
139s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
140s Setting up locales (2.41-1ubuntu2) ...
141s Generating locales (this might take a while)...
142s   en_US.UTF-8... done
142s Generation complete.
142s Setting up libc-dev-bin (2.41-1ubuntu2) ...
142s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ...
142s Processing triggers for man-db (2.13.0-1) ...
143s Processing triggers for systemd (257.3-1ubuntu3) ...
144s Reading package lists...
144s Building dependency tree...
144s Reading state information...
144s Starting pkgProblemResolver with broken count: 0
144s Starting 2 pkgProblemResolver with broken count: 0
144s Done
145s Solving dependencies...
145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
145s autopkgtest [22:03:17]: rebooting testbed after setup commands that affected boot
149s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
161s autopkgtest [22:03:33]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025
162s autopkgtest [22:03:34]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-rtracklayer
164s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-rtracklayer 1.66.0-2 (dsc) [2459 B]
164s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-rtracklayer 1.66.0-2 (tar) [4113 kB]
164s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-rtracklayer 1.66.0-2 (diff) [27.5 kB]
164s gpgv: Signature made Mon Jan 13 14:23:45 2025 UTC
164s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
164s gpgv:                issuer "crusoe@debian.org"
164s gpgv: Can't check signature: No public key
164s dpkg-source: warning: cannot verify inline signature for ./r-bioc-rtracklayer_1.66.0-2.dsc: no acceptable signature found
164s autopkgtest [22:03:35]: testing package r-bioc-rtracklayer version 1.66.0-2
164s autopkgtest [22:03:36]: build not needed
166s autopkgtest [22:03:38]: test pkg-r-autopkgtest: preparing testbed
166s Reading package lists...
166s Building dependency tree...
166s Reading state information...
166s Starting pkgProblemResolver with broken count: 0
166s Starting 2 pkgProblemResolver with broken count: 0
166s Done
167s The following NEW packages will be installed:
167s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
167s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
167s   g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
167s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14
167s   gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
167s   libblas-dev libblas3 libboost-dev libboost1.83-dev libbz2-dev libcairo2
167s   libcc1-0 libdatrie1 libdeflate-dev libdeflate0 libfontconfig1 libgcc-14-dev
167s   libgfortran-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
167s   libhwasan0 libice6 libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev
167s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev
167s   liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3 libncurses-dev
167s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
167s   libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
167s   libpixman-1-0 libpkgconf3 libpng-dev libquadmath0 libreadline-dev
167s   libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 libthai-data libthai0
167s   libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0
167s   libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64 pkg-r-autopkgtest pkgconf
167s   pkgconf-bin r-base-core r-base-dev r-bioc-annotate r-bioc-annotationdbi
167s   r-bioc-biobase r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
167s   r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-genefilter
167s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
167s   r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest
167s   r-bioc-limma r-bioc-matrixgenerics r-bioc-org.hs.eg.db r-bioc-rhtslib
167s   r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors
167s   r-bioc-sparsearray r-bioc-summarizedexperiment r-bioc-ucsc.utils
167s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-bh
167s   r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-cachem r-cran-cli
167s   r-cran-codetools r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi
167s   r-cran-fastmap r-cran-formatr r-cran-futile.logger r-cran-futile.options
167s   r-cran-glue r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice
167s   r-cran-lifecycle r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime
167s   r-cran-openssl r-cran-pkgconfig r-cran-plogr r-cran-png r-cran-r6
167s   r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rsqlite
167s   r-cran-runit r-cran-snow r-cran-statmod r-cran-survival r-cran-sys
167s   r-cran-vctrs r-cran-xml r-cran-xtable r-cran-yaml unzip x11-common xdg-utils
167s   zip zlib1g-dev
167s 0 upgraded, 178 newly installed, 0 to remove and 0 not upgraded.
167s Need to get 326 MB of archives.
167s After this operation, 1157 MB of additional disk space will be used.
167s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
167s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
167s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB]
167s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B]
167s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B]
167s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB]
167s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB]
167s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB]
167s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB]
167s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB]
167s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB]
167s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB]
167s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB]
167s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB]
168s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB]
168s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB]
168s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB]
168s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB]
168s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B]
168s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B]
168s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB]
168s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB]
168s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB]
168s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B]
168s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B]
168s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
168s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB]
168s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
168s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
168s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB]
168s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB]
168s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB]
168s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB]
168s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB]
168s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB]
169s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB]
169s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B]
169s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B]
169s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB]
169s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB]
169s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB]
169s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost1.83-dev amd64 1.83.0-4.1ubuntu2 [10.7 MB]
169s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libboost-dev amd64 1.83.0.2ubuntu1 [4468 B]
169s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB]
169s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
169s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
169s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
169s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
169s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
169s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
169s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB]
169s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB]
169s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
169s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
169s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
169s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
169s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB]
169s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
169s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB]
169s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
169s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
169s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
169s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB]
169s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB]
169s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
169s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB]
169s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
169s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
169s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB]
169s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB]
169s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB]
169s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
169s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
169s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB]
169s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB]
169s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B]
169s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB]
169s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB]
169s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
169s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB]
169s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB]
169s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
169s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
169s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB]
169s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
169s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
169s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
169s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
169s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
169s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB]
169s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
169s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB]
169s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
169s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
169s Get:95 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB]
169s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB]
169s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB]
169s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB]
169s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB]
169s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B]
169s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
169s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
170s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
170s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
170s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-iranges amd64 2.40.1-2 [2310 kB]
170s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-dbi all 1.2.3-1 [853 kB]
170s Get:107 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
170s Get:108 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bit64 amd64 4.6.0-1-1ubuntu2 [501 kB]
170s Get:109 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB]
170s Get:110 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
170s Get:111 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
170s Get:112 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB]
170s Get:113 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
170s Get:114 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-blob all 1.2.4-1 [49.8 kB]
170s Get:115 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
170s Get:116 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
170s Get:117 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-memoise all 2.0.1-1 [53.9 kB]
170s Get:118 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB]
170s Get:119 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-plogr all 0.2.0-3build1 [15.1 kB]
170s Get:120 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB]
170s Get:121 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
170s Get:122 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-curl amd64 6.2.1+dfsg-1ubuntu1 [197 kB]
170s Get:123 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
170s Get:124 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
170s Get:125 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
170s Get:126 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
170s Get:127 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
170s Get:128 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
170s Get:129 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
170s Get:130 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
170s Get:131 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
170s Get:132 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
170s Get:133 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
170s Get:134 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
170s Get:135 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
170s Get:136 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
170s Get:137 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
170s Get:138 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-2 [183 kB]
170s Get:139 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
170s Get:140 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml amd64 3.99-0.18-1 [1748 kB]
170s Get:141 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xtable all 1:1.8-4-2 [689 kB]
170s Get:142 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB]
170s Get:143 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB]
170s Get:144 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
170s Get:145 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lambda.r all 1.2.4-2build1 [119 kB]
170s Get:146 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.options all 1.0.1-3build1 [20.2 kB]
170s Get:147 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-futile.logger all 1.4.3-4build1 [99.3 kB]
170s Get:148 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-snow all 1:0.4.4-2 [97.6 kB]
170s Get:149 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-codetools all 0.2-20-1 [90.5 kB]
170s Get:150 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
170s Get:151 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
170s Get:152 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
170s Get:153 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
170s Get:154 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB]
170s Get:155 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB]
170s Get:156 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
170s Get:157 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
170s Get:158 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
170s Get:159 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB]
170s Get:160 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-abind all 1.4-8-1 [66.9 kB]
170s Get:161 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
170s Get:162 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-1 [1392 kB]
171s Get:163 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
171s Get:164 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
171s Get:165 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB]
171s Get:166 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
171s Get:167 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB]
171s Get:168 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
171s Get:169 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
171s Get:170 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-rtracklayer amd64 1.66.0-2 [5227 kB]
171s Get:171 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-bsgenome all 1.74.0-2 [7001 kB]
171s Get:172 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB]
171s Get:173 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genefilter amd64 1.88.0-2 [1243 kB]
171s Get:174 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB]
171s Get:175 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
171s Get:176 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-limma amd64 3.62.2+dfsg-1 [1969 kB]
171s Get:177 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-org.hs.eg.db all 3.20.0-3 [63.1 MB]
171s Get:178 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-runit all 0.4.33-1 [377 kB]
172s Preconfiguring packages ...
172s Fetched 326 MB in 4s (75.7 MB/s)
172s Selecting previously unselected package libisl23:amd64.
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172s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ...
172s Unpacking libisl23:amd64 (0.27-1) ...
172s Selecting previously unselected package libmpc3:amd64.
172s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ...
172s Unpacking libmpc3:amd64 (1.3.1-1build2) ...
172s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
172s Preparing to unpack .../002-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
172s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
173s Selecting previously unselected package cpp-14.
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173s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
173s Selecting previously unselected package cpp-x86-64-linux-gnu.
173s Preparing to unpack .../004-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
173s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
173s Selecting previously unselected package cpp.
173s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ...
173s Unpacking cpp (4:14.2.0-1ubuntu1) ...
173s Selecting previously unselected package libcc1-0:amd64.
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173s Selecting previously unselected package libgomp1:amd64.
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173s Selecting previously unselected package libitm1:amd64.
173s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_amd64.deb ...
173s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ...
173s Selecting previously unselected package libasan8:amd64.
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173s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ...
173s Selecting previously unselected package liblsan0:amd64.
173s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_amd64.deb ...
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173s Selecting previously unselected package libtsan2:amd64.
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173s Selecting previously unselected package libubsan1:amd64.
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173s Selecting previously unselected package libhwasan0:amd64.
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173s Selecting previously unselected package libquadmath0:amd64.
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173s Selecting previously unselected package libgcc-14-dev:amd64.
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173s Selecting previously unselected package gcc-14-x86-64-linux-gnu.
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174s Selecting previously unselected package gcc-14.
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174s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
174s Selecting previously unselected package gcc-x86-64-linux-gnu.
174s Preparing to unpack .../018-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
174s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
174s Selecting previously unselected package gcc.
174s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ...
174s Unpacking gcc (4:14.2.0-1ubuntu1) ...
174s Selecting previously unselected package libstdc++-14-dev:amd64.
174s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ...
174s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
174s Selecting previously unselected package g++-14-x86-64-linux-gnu.
174s Preparing to unpack .../021-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
174s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
174s Selecting previously unselected package g++-14.
174s Preparing to unpack .../022-g++-14_14.2.0-17ubuntu3_amd64.deb ...
174s Unpacking g++-14 (14.2.0-17ubuntu3) ...
174s Selecting previously unselected package g++-x86-64-linux-gnu.
174s Preparing to unpack .../023-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
174s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
174s Selecting previously unselected package g++.
174s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_amd64.deb ...
174s Unpacking g++ (4:14.2.0-1ubuntu1) ...
174s Selecting previously unselected package build-essential.
174s Preparing to unpack .../025-build-essential_12.10ubuntu1_amd64.deb ...
174s Unpacking build-essential (12.10ubuntu1) ...
174s Selecting previously unselected package dctrl-tools.
174s Preparing to unpack .../026-dctrl-tools_2.24-3build3_amd64.deb ...
174s Unpacking dctrl-tools (2.24-3build3) ...
174s Selecting previously unselected package fonts-dejavu-mono.
174s Preparing to unpack .../027-fonts-dejavu-mono_2.37-8_all.deb ...
174s Unpacking fonts-dejavu-mono (2.37-8) ...
175s Selecting previously unselected package fonts-dejavu-core.
175s Preparing to unpack .../028-fonts-dejavu-core_2.37-8_all.deb ...
175s Unpacking fonts-dejavu-core (2.37-8) ...
175s Selecting previously unselected package fontconfig-config.
175s Preparing to unpack .../029-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ...
175s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
175s Selecting previously unselected package libfontconfig1:amd64.
175s Preparing to unpack .../030-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ...
175s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
175s Selecting previously unselected package fontconfig.
175s Preparing to unpack .../031-fontconfig_2.15.0-2ubuntu1_amd64.deb ...
175s Unpacking fontconfig (2.15.0-2ubuntu1) ...
175s Selecting previously unselected package libgfortran5:amd64.
175s Preparing to unpack .../032-libgfortran5_15-20250222-0ubuntu1_amd64.deb ...
175s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ...
175s Selecting previously unselected package libgfortran-14-dev:amd64.
175s Preparing to unpack .../033-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ...
175s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ...
175s Selecting previously unselected package gfortran-14-x86-64-linux-gnu.
175s Preparing to unpack .../034-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
175s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
175s Selecting previously unselected package gfortran-14.
175s Preparing to unpack .../035-gfortran-14_14.2.0-17ubuntu3_amd64.deb ...
175s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
175s Selecting previously unselected package gfortran-x86-64-linux-gnu.
175s Preparing to unpack .../036-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
175s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
175s Selecting previously unselected package gfortran.
175s Preparing to unpack .../037-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ...
175s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
175s Selecting previously unselected package icu-devtools.
175s Preparing to unpack .../038-icu-devtools_76.1-1ubuntu2_amd64.deb ...
175s Unpacking icu-devtools (76.1-1ubuntu2) ...
175s Selecting previously unselected package libblas3:amd64.
175s Preparing to unpack .../039-libblas3_3.12.1-2_amd64.deb ...
175s Unpacking libblas3:amd64 (3.12.1-2) ...
175s Selecting previously unselected package libblas-dev:amd64.
175s Preparing to unpack .../040-libblas-dev_3.12.1-2_amd64.deb ...
175s Unpacking libblas-dev:amd64 (3.12.1-2) ...
176s Selecting previously unselected package libboost1.83-dev:amd64.
176s Preparing to unpack .../041-libboost1.83-dev_1.83.0-4.1ubuntu2_amd64.deb ...
176s Unpacking libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ...
178s Selecting previously unselected package libboost-dev:amd64.
178s Preparing to unpack .../042-libboost-dev_1.83.0.2ubuntu1_amd64.deb ...
178s Unpacking libboost-dev:amd64 (1.83.0.2ubuntu1) ...
178s Selecting previously unselected package libbz2-dev:amd64.
178s Preparing to unpack .../043-libbz2-dev_1.0.8-6_amd64.deb ...
178s Unpacking libbz2-dev:amd64 (1.0.8-6) ...
178s Selecting previously unselected package libpixman-1-0:amd64.
178s Preparing to unpack .../044-libpixman-1-0_0.44.0-3_amd64.deb ...
178s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
178s Selecting previously unselected package libxcb-render0:amd64.
178s Preparing to unpack .../045-libxcb-render0_1.17.0-2_amd64.deb ...
178s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
178s Selecting previously unselected package libxcb-shm0:amd64.
178s Preparing to unpack .../046-libxcb-shm0_1.17.0-2_amd64.deb ...
178s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
178s Selecting previously unselected package libxrender1:amd64.
178s Preparing to unpack .../047-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
178s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
178s Selecting previously unselected package libcairo2:amd64.
178s Preparing to unpack .../048-libcairo2_1.18.2-2_amd64.deb ...
178s Unpacking libcairo2:amd64 (1.18.2-2) ...
178s Selecting previously unselected package libdatrie1:amd64.
178s Preparing to unpack .../049-libdatrie1_0.2.13-3build1_amd64.deb ...
178s Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
178s Selecting previously unselected package libdeflate0:amd64.
178s Preparing to unpack .../050-libdeflate0_1.23-1_amd64.deb ...
178s Unpacking libdeflate0:amd64 (1.23-1) ...
178s Selecting previously unselected package libdeflate-dev:amd64.
178s Preparing to unpack .../051-libdeflate-dev_1.23-1_amd64.deb ...
178s Unpacking libdeflate-dev:amd64 (1.23-1) ...
178s Selecting previously unselected package libgraphite2-3:amd64.
178s Preparing to unpack .../052-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
178s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
178s Selecting previously unselected package libharfbuzz0b:amd64.
178s Preparing to unpack .../053-libharfbuzz0b_10.2.0-1_amd64.deb ...
178s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ...
178s Selecting previously unselected package x11-common.
178s Preparing to unpack .../054-x11-common_1%3a7.7+23ubuntu3_all.deb ...
178s Unpacking x11-common (1:7.7+23ubuntu3) ...
178s Selecting previously unselected package libice6:amd64.
178s Preparing to unpack .../055-libice6_2%3a1.1.1-1_amd64.deb ...
178s Unpacking libice6:amd64 (2:1.1.1-1) ...
178s Selecting previously unselected package libicu-dev:amd64.
178s Preparing to unpack .../056-libicu-dev_76.1-1ubuntu2_amd64.deb ...
178s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ...
179s Selecting previously unselected package libjpeg-turbo8:amd64.
179s Preparing to unpack .../057-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ...
179s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
179s Selecting previously unselected package libjpeg-turbo8-dev:amd64.
179s Preparing to unpack .../058-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ...
179s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ...
179s Selecting previously unselected package libjpeg8:amd64.
179s Preparing to unpack .../059-libjpeg8_8c-2ubuntu11_amd64.deb ...
179s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
179s Selecting previously unselected package libjpeg8-dev:amd64.
179s Preparing to unpack .../060-libjpeg8-dev_8c-2ubuntu11_amd64.deb ...
179s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ...
179s Selecting previously unselected package libjpeg-dev:amd64.
179s Preparing to unpack .../061-libjpeg-dev_8c-2ubuntu11_amd64.deb ...
179s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ...
179s Selecting previously unselected package liblapack3:amd64.
179s Preparing to unpack .../062-liblapack3_3.12.1-2_amd64.deb ...
179s Unpacking liblapack3:amd64 (3.12.1-2) ...
179s Selecting previously unselected package liblapack-dev:amd64.
179s Preparing to unpack .../063-liblapack-dev_3.12.1-2_amd64.deb ...
179s Unpacking liblapack-dev:amd64 (3.12.1-2) ...
179s Selecting previously unselected package liblerc4:amd64.
179s Preparing to unpack .../064-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ...
179s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
179s Selecting previously unselected package libncurses-dev:amd64.
179s Preparing to unpack .../065-libncurses-dev_6.5+20250216-2_amd64.deb ...
179s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ...
179s Selecting previously unselected package libthai-data.
179s Preparing to unpack .../066-libthai-data_0.1.29-2build1_all.deb ...
179s Unpacking libthai-data (0.1.29-2build1) ...
179s Selecting previously unselected package libthai0:amd64.
179s Preparing to unpack .../067-libthai0_0.1.29-2build1_amd64.deb ...
179s Unpacking libthai0:amd64 (0.1.29-2build1) ...
179s Selecting previously unselected package libpango-1.0-0:amd64.
179s Preparing to unpack .../068-libpango-1.0-0_1.56.2-1_amd64.deb ...
179s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ...
179s Selecting previously unselected package libpangoft2-1.0-0:amd64.
179s Preparing to unpack .../069-libpangoft2-1.0-0_1.56.2-1_amd64.deb ...
179s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ...
179s Selecting previously unselected package libpangocairo-1.0-0:amd64.
179s Preparing to unpack .../070-libpangocairo-1.0-0_1.56.2-1_amd64.deb ...
179s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ...
179s Selecting previously unselected package libpaper2:amd64.
180s Preparing to unpack .../071-libpaper2_2.2.5-0.3_amd64.deb ...
180s Unpacking libpaper2:amd64 (2.2.5-0.3) ...
180s Selecting previously unselected package libpaper-utils.
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180s Unpacking libpaper-utils (2.2.5-0.3) ...
180s Selecting previously unselected package libpcre2-16-0:amd64.
180s Preparing to unpack .../073-libpcre2-16-0_10.45-1_amd64.deb ...
180s Unpacking libpcre2-16-0:amd64 (10.45-1) ...
180s Selecting previously unselected package libpcre2-32-0:amd64.
180s Preparing to unpack .../074-libpcre2-32-0_10.45-1_amd64.deb ...
180s Unpacking libpcre2-32-0:amd64 (10.45-1) ...
180s Selecting previously unselected package libpcre2-posix3:amd64.
180s Preparing to unpack .../075-libpcre2-posix3_10.45-1_amd64.deb ...
180s Unpacking libpcre2-posix3:amd64 (10.45-1) ...
180s Selecting previously unselected package libpcre2-dev:amd64.
180s Preparing to unpack .../076-libpcre2-dev_10.45-1_amd64.deb ...
180s Unpacking libpcre2-dev:amd64 (10.45-1) ...
180s Selecting previously unselected package libpkgconf3:amd64.
180s Preparing to unpack .../077-libpkgconf3_1.8.1-4_amd64.deb ...
180s Unpacking libpkgconf3:amd64 (1.8.1-4) ...
180s Selecting previously unselected package zlib1g-dev:amd64.
180s Preparing to unpack .../078-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ...
180s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
180s Selecting previously unselected package libpng-dev:amd64.
180s Preparing to unpack .../079-libpng-dev_1.6.47-1_amd64.deb ...
180s Unpacking libpng-dev:amd64 (1.6.47-1) ...
180s Selecting previously unselected package libreadline-dev:amd64.
180s Preparing to unpack .../080-libreadline-dev_8.2-6_amd64.deb ...
180s Unpacking libreadline-dev:amd64 (8.2-6) ...
180s Selecting previously unselected package libsharpyuv0:amd64.
180s Preparing to unpack .../081-libsharpyuv0_1.5.0-0.1_amd64.deb ...
180s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ...
180s Selecting previously unselected package libsm6:amd64.
180s Preparing to unpack .../082-libsm6_2%3a1.2.4-1_amd64.deb ...
180s Unpacking libsm6:amd64 (2:1.2.4-1) ...
180s Selecting previously unselected package libtcl8.6:amd64.
180s Preparing to unpack .../083-libtcl8.6_8.6.16+dfsg-1_amd64.deb ...
180s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ...
180s Selecting previously unselected package libjbig0:amd64.
180s Preparing to unpack .../084-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
180s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
180s Selecting previously unselected package libwebp7:amd64.
180s Preparing to unpack .../085-libwebp7_1.5.0-0.1_amd64.deb ...
180s Unpacking libwebp7:amd64 (1.5.0-0.1) ...
180s Selecting previously unselected package libtiff6:amd64.
180s Preparing to unpack .../086-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ...
180s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
180s Selecting previously unselected package libxft2:amd64.
180s Preparing to unpack .../087-libxft2_2.3.6-1build1_amd64.deb ...
180s Unpacking libxft2:amd64 (2.3.6-1build1) ...
180s Selecting previously unselected package libxss1:amd64.
180s Preparing to unpack .../088-libxss1_1%3a1.2.3-1build3_amd64.deb ...
180s Unpacking libxss1:amd64 (1:1.2.3-1build3) ...
180s Selecting previously unselected package libtk8.6:amd64.
180s Preparing to unpack .../089-libtk8.6_8.6.16-1_amd64.deb ...
180s Unpacking libtk8.6:amd64 (8.6.16-1) ...
180s Selecting previously unselected package libxt6t64:amd64.
180s Preparing to unpack .../090-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ...
180s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ...
180s Selecting previously unselected package zip.
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181s Selecting previously unselected package liblzma-dev:amd64.
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181s Selecting previously unselected package libtirpc-dev:amd64.
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181s Selecting previously unselected package r-bioc-biocgenerics.
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181s Selecting previously unselected package r-bioc-biobase.
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181s Selecting previously unselected package r-bioc-s4vectors.
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181s Selecting previously unselected package r-bioc-iranges.
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181s Selecting previously unselected package r-cran-dbi.
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181s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
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182s Selecting previously unselected package r-cran-rlang.
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182s Selecting previously unselected package r-cran-cli.
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182s Selecting previously unselected package r-cran-glue.
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182s Selecting previously unselected package r-cran-lifecycle.
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182s Selecting previously unselected package r-cran-vctrs.
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182s Selecting previously unselected package r-cran-blob.
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182s Selecting previously unselected package r-cran-fastmap.
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182s Selecting previously unselected package r-cran-cachem.
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182s Selecting previously unselected package r-cran-memoise.
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182s Selecting previously unselected package r-cran-plogr.
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182s Selecting previously unselected package r-cran-cpp11.
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182s Selecting previously unselected package r-cran-rsqlite.
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182s Selecting previously unselected package r-cran-jsonlite.
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182s Selecting previously unselected package r-cran-mime.
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182s Selecting previously unselected package r-cran-sys.
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182s Selecting previously unselected package r-cran-askpass.
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182s Selecting previously unselected package r-cran-openssl.
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182s Selecting previously unselected package r-cran-r6.
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182s Selecting previously unselected package r-cran-httr.
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182s Selecting previously unselected package r-cran-png.
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183s Selecting previously unselected package r-bioc-zlibbioc.
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183s Selecting previously unselected package r-bioc-xvector.
183s Preparing to unpack .../131-r-bioc-xvector_0.46.0-2_amd64.deb ...
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183s Selecting previously unselected package r-bioc-ucsc.utils.
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183s Selecting previously unselected package r-bioc-genomeinfodbdata.
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183s Selecting previously unselected package r-cran-crayon.
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183s Selecting previously unselected package r-bioc-biostrings.
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183s Selecting previously unselected package r-bioc-keggrest.
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183s Selecting previously unselected package r-bioc-annotationdbi.
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183s Selecting previously unselected package r-cran-xml.
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183s Selecting previously unselected package r-cran-xtable.
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183s Selecting previously unselected package r-bioc-annotate.
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183s Selecting previously unselected package r-bioc-biocio.
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183s Selecting previously unselected package r-cran-formatr.
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183s Selecting previously unselected package r-cran-lambda.r.
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184s Selecting previously unselected package r-bioc-biocparallel.
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184s Selecting previously unselected package r-cran-bitops.
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184s Selecting previously unselected package r-cran-matrixstats.
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184s Selecting previously unselected package r-bioc-matrixgenerics.
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184s Selecting previously unselected package r-cran-lattice.
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184s Selecting previously unselected package r-bioc-s4arrays.
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187s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
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187s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
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187s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
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187s Setting up unzip (6.0-28ubuntu6) ...
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187s Setting up libreadline-dev:amd64 (8.2-6) ...
187s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ...
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187s Setting up libpcre2-16-0:amd64 (10.45-1) ...
187s Setting up zip (3.0-14ubuntu2) ...
187s Setting up libpcre2-32-0:amd64 (10.45-1) ...
187s Setting up libblas3:amd64 (3.12.1-2) ...
187s 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
187s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ...
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187s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ...
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187s Setting up libmpc3:amd64 (1.3.1-1build2) ...
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187s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ...
187s Setting up libwebp7:amd64 (1.5.0-0.1) ...
187s Setting up liblzma-dev:amd64 (5.6.4-1) ...
187s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ...
187s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
187s Setting up libpcre2-posix3:amd64 (10.45-1) ...
187s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ...
187s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ...
187s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
187s Setting up libthai-data (0.1.29-2build1) ...
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188s Setting up libisl23:amd64 (0.27-1) ...
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188s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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188s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ...
188s Setting up libblas-dev:amd64 (3.12.1-2) ...
188s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
188s Setting up dctrl-tools (2.24-3build3) ...
188s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ...
188s Setting up libbz2-dev:amd64 (1.0.8-6) ...
188s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
188s Setting up libice6:amd64 (2:1.1.1-1) ...
188s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ...
188s Setting up liblapack3:amd64 (3.12.1-2) ...
188s 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
188s Setting up libpcre2-dev:amd64 (10.45-1) ...
188s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
188s Setting up libpng-dev:amd64 (1.6.47-1) ...
188s Setting up libpaper-utils (2.2.5-0.3) ...
188s Setting up pkgconf:amd64 (1.8.1-4) ...
188s Setting up libthai0:amd64 (0.1.29-2build1) ...
188s Setting up liblapack-dev:amd64 (3.12.1-2) ...
188s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
188s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
188s Setting up cpp-14 (14.2.0-17ubuntu3) ...
188s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
188s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
188s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ...
188s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
188s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
188s Setting up libsm6:amd64 (2:1.2.4-1) ...
188s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
188s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ...
188s Setting up fontconfig (2.15.0-2ubuntu1) ...
190s Regenerating fonts cache... done.
190s Setting up libxft2:amd64 (2.3.6-1build1) ...
190s Setting up libboost1.83-dev:amd64 (1.83.0-4.1ubuntu2) ...
190s Setting up libtk8.6:amd64 (8.6.16-1) ...
190s Setting up libpango-1.0-0:amd64 (1.56.2-1) ...
190s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
190s Setting up libcairo2:amd64 (1.18.2-2) ...
190s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
190s Setting up cpp (4:14.2.0-1ubuntu1) ...
190s Setting up libboost-dev:amd64 (1.83.0.2ubuntu1) ...
190s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
190s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ...
190s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ...
190s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
190s Setting up gcc-14 (14.2.0-17ubuntu3) ...
190s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
190s Setting up r-base-core (4.4.3-1) ...
190s Creating config file /etc/R/Renviron with new version
190s Setting up r-cran-crayon (1.5.3-1) ...
190s Setting up r-cran-futile.options (1.0.1-3build1) ...
190s Setting up r-cran-lattice (0.22-6-1) ...
190s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
190s Setting up r-cran-formatr (1.14-2) ...
190s Setting up r-cran-xml (3.99-0.18-1) ...
190s Setting up r-cran-statmod (1.5.0-1) ...
190s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
190s Setting up g++-14 (14.2.0-17ubuntu3) ...
190s Setting up r-cran-rjson (0.2.23-1) ...
190s Setting up r-cran-r6 (2.6.1-1) ...
190s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
190s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
190s Setting up r-cran-bh (1.84.0-1) ...
190s Setting up r-cran-curl (6.2.1+dfsg-1ubuntu1) ...
190s Setting up r-cran-codetools (0.2-20-1) ...
190s Setting up r-bioc-biocgenerics (0.52.0-2) ...
190s Setting up r-cran-rlang (1.1.5-1) ...
190s Setting up r-cran-matrixstats (1.5.0-1) ...
190s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
190s Setting up r-cran-sys (3.4.3-1) ...
190s Setting up r-cran-plogr (0.2.0-3build1) ...
190s Setting up r-cran-mime (0.12-2) ...
190s Setting up r-cran-abind (1.4-8-1) ...
190s Setting up r-cran-yaml (2.3.10-1) ...
190s Setting up r-cran-lambda.r (1.2.4-2build1) ...
190s Setting up r-cran-dbi (1.2.3-1) ...
190s Setting up r-cran-snow (1:0.4.4-2) ...
190s Setting up r-cran-glue (1.8.0-1) ...
190s Setting up r-cran-bit (4.6.0+dfsg-1) ...
190s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
190s Setting up r-cran-xtable (1:1.8-4-2) ...
190s Setting up r-cran-cli (3.6.4-1) ...
190s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ...
190s Setting up r-cran-bitops (1.0-9-1) ...
190s Setting up r-cran-bit64 (4.6.0-1-1ubuntu2) ...
190s Setting up gcc (4:14.2.0-1ubuntu1) ...
190s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
190s Setting up r-cran-askpass (1.2.1-1) ...
190s Setting up r-cran-fastmap (1.2.0-1) ...
190s Setting up r-cran-png (0.1-8-1build2) ...
190s Setting up r-bioc-biobase (2.66.0-2) ...
190s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
190s Setting up r-cran-pkgconfig (2.0.3-2build1) ...
190s Setting up r-cran-cpp11 (0.5.2-1) ...
190s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
190s Setting up r-cran-runit (0.4.33-1) ...
190s Setting up r-cran-futile.logger (1.4.3-4build1) ...
190s Setting up r-bioc-limma (3.62.2+dfsg-1) ...
190s Setting up r-cran-matrix (1.7-3-1) ...
190s Setting up g++ (4:14.2.0-1ubuntu1) ...
190s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
190s Setting up r-cran-cachem (1.1.0-1) ...
190s Setting up build-essential (12.10ubuntu1) ...
190s Setting up r-bioc-iranges (2.40.1-2) ...
190s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
190s Setting up r-cran-restfulr (0.0.15-1) ...
190s Setting up r-cran-vctrs (0.6.5-1) ...
190s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
190s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
190s Setting up r-bioc-biocparallel (1.40.0-2) ...
190s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
190s Setting up r-cran-survival (3.8-3-1) ...
190s Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
190s Setting up gfortran (4:14.2.0-1ubuntu1) ...
190s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
190s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
190s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
190s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
190s Setting up r-cran-httr (1.4.7+dfsg-1) ...
190s Setting up r-cran-memoise (2.0.1-1) ...
190s Setting up r-cran-blob (1.2.4-1) ...
190s Setting up r-bioc-xvector (0.46.0-2) ...
190s Setting up r-cran-rsqlite (2.3.9-1) ...
190s Setting up r-base-dev (4.4.3-1) ...
190s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
190s Setting up r-bioc-sparsearray (1.6.2+dfsg-1) ...
190s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
190s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
190s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
190s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
190s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
190s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
190s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
190s Setting up r-bioc-keggrest (1.46.0+dfsg-2) ...
190s Setting up r-bioc-annotationdbi (1.68.0-2) ...
190s Setting up r-bioc-annotate (1.84.0+dfsg-2) ...
190s Setting up r-bioc-genefilter (1.88.0-2) ...
190s Setting up r-bioc-genomicalignments (1.42.0-2) ...
190s Setting up r-bioc-org.hs.eg.db (3.20.0-3) ...
190s Setting up r-bioc-rtracklayer (1.66.0-2) ...
190s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
190s Setting up r-bioc-bsgenome (1.74.0-2) ...
190s Processing triggers for libc-bin (2.41-1ubuntu2) ...
190s Processing triggers for man-db (2.13.0-1) ...
192s Processing triggers for install-info (7.1.1-1) ...
193s autopkgtest [22:04:05]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
193s autopkgtest [22:04:05]: test pkg-r-autopkgtest: [-----------------------
193s Test: Try to load the R library rtracklayer
193s 
193s R version 4.4.3 (2025-02-28) -- "Trophy Case"
193s Copyright (C) 2025 The R Foundation for Statistical Computing
193s Platform: x86_64-pc-linux-gnu
193s 
193s R is free software and comes with ABSOLUTELY NO WARRANTY.
193s You are welcome to redistribute it under certain conditions.
193s Type 'license()' or 'licence()' for distribution details.
193s 
193s R is a collaborative project with many contributors.
193s Type 'contributors()' for more information and
193s 'citation()' on how to cite R or R packages in publications.
193s 
193s Type 'demo()' for some demos, 'help()' for on-line help, or
193s 'help.start()' for an HTML browser interface to help.
193s Type 'q()' to quit R.
193s 
193s > library('rtracklayer')
193s Loading required package: GenomicRanges
193s Loading required package: stats4
193s Loading required package: BiocGenerics
193s 
193s Attaching package: ‘BiocGenerics’
193s 
193s The following objects are masked from ‘package:stats’:
193s 
193s     IQR, mad, sd, var, xtabs
193s 
193s The following objects are masked from ‘package:base’:
193s 
193s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
193s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
193s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
193s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
193s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
193s     table, tapply, union, unique, unsplit, which.max, which.min
193s 
193s Loading required package: S4Vectors
194s 
194s Attaching package: ‘S4Vectors’
194s 
194s The following object is masked from ‘package:utils’:
194s 
194s     findMatches
194s 
194s The following objects are masked from ‘package:base’:
194s 
194s     expand.grid, I, unname
194s 
194s Loading required package: IRanges
195s Loading required package: GenomeInfoDb
202s > 
202s > 
202s Other tests are currently unsupported!
202s They will be progressively added.
202s autopkgtest [22:04:14]: test pkg-r-autopkgtest: -----------------------]
202s autopkgtest [22:04:14]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
202s pkg-r-autopkgtest    PASS
202s autopkgtest [22:04:14]: @@@@@@@@@@@@@@@@@@@@ summary
202s pkg-r-autopkgtest    PASS
219s nova [W] Skipping flock for amd64
219s Creating nova instance adt-plucky-amd64-r-bioc-rtracklayer-20250315-220051-juju-7f2275-prod-proposed-migration-environment-15-21f12f32-e930-4452-944c-b079c8351525 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)...
219s nova [W] Timed out waiting for cc6e74f2-c7e1-4aaa-8b90-f9bd1e1a266f to get deleted.