0s autopkgtest [22:01:17]: starting date and time: 2025-03-15 22:01:17+0000
  0s autopkgtest [22:01:17]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [22:01:17]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2uzc_r09/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-snpstats --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-20@lcy02-8.secgroup --name adt-plucky-amd64-r-bioc-snpstats-20250315-220117-juju-7f2275-prod-proposed-migration-environment-20-6187d2d1-ae3b-4ba7-82be-14007d5df21a --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/
 45s autopkgtest [22:02:02]: testbed dpkg architecture: amd64
 45s autopkgtest [22:02:02]: testbed apt version: 2.9.31ubuntu1
 45s autopkgtest [22:02:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 45s autopkgtest [22:02:02]: testbed release detected to be: None
 46s autopkgtest [22:02:03]: updating testbed package index (apt update)
 46s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
 46s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
 46s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
 46s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
 46s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB]
 46s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB]
 46s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB]
 46s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB]
 46s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB]
 46s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B]
 46s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B]
 46s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB]
 46s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB]
 46s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB]
 46s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB]
 46s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B]
 46s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B]
 47s Fetched 1265 kB in 0s (4294 kB/s)
 48s Reading package lists...
 48s Reading package lists...
 49s Building dependency tree...
 49s Reading state information...
 49s Calculating upgrade...
 50s Calculating upgrade...
 50s The following package was automatically installed and is no longer required:
 50s   libnl-genl-3-200
 50s Use 'sudo apt autoremove' to remove it.
 50s The following NEW packages will be installed:
 50s   bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10
 50s   linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic
 50s   linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic
 50s   linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids
 50s The following packages will be upgraded:
 50s   apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu
 50s   cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0
 50s   gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common
 50s   libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0
 50s   libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1
 50s   libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5
 50s   libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200
 50s   libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13
 50s   libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1
 50s   libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic
 50s   linux-headers-generic linux-headers-virtual linux-image-generic
 50s   linux-image-virtual linux-libc-dev linux-tools-common linux-virtual
 50s   media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils
 50s   pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend
 50s   python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe
 50s   python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm
 50s   python3.13-minimal rsync rsyslog strace xz-utils
 50s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded.
 50s Need to get 807 MB of archives.
 50s After this operation, 326 MB of additional disk space will be used.
 50s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB]
 50s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB]
 50s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB]
 50s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB]
 50s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB]
 50s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB]
 50s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB]
 50s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB]
 50s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB]
 50s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB]
 50s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB]
 50s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB]
 50s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB]
 50s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB]
 50s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB]
 50s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB]
 50s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB]
 50s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB]
 50s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB]
 51s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB]
 51s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB]
 51s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB]
 51s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB]
 51s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B]
 51s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB]
 51s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB]
 51s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB]
 51s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB]
 51s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB]
 51s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB]
 51s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB]
 51s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB]
 51s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B]
 51s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB]
 51s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB]
 51s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB]
 51s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB]
 51s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB]
 51s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB]
 51s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB]
 51s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB]
 51s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB]
 51s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB]
 51s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB]
 51s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB]
 51s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB]
 51s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB]
 51s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB]
 51s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB]
 51s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB]
 51s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB]
 51s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB]
 51s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB]
 51s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB]
 51s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB]
 51s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB]
 51s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB]
 51s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB]
 51s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB]
 51s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB]
 51s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B]
 51s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB]
 51s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB]
 51s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB]
 51s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB]
 51s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
 51s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB]
 51s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB]
 51s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB]
 51s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB]
 51s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB]
 51s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB]
 51s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB]
 51s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB]
 51s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB]
 51s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB]
 51s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB]
 51s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB]
 57s 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]
 58s 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]
 58s 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]
 59s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B]
 59s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB]
 59s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B]
 59s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB]
 59s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B]
 59s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB]
 59s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB]
 59s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB]
 59s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB]
 59s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB]
 59s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB]
 59s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B]
 59s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB]
 59s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB]
 59s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB]
 59s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB]
 59s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B]
 60s Preconfiguring packages ...
 60s Fetched 807 MB in 9s (91.4 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 ... 100%
(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 ... 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 ... 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) ...
 63s Setting up libapt-pkg7.0:amd64 (2.9.33) ...
 63s (Reading database ... 
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 89s Setting up apt-utils (2.9.33) ...
 89s Setting up libdebuginfod-common (0.192-4) ...
 89s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ...
 89s Setting up bpftool (7.6.0+6.14.0-10.10) ...
 89s Setting up libestr0:amd64 (0.1.11-2) ...
 89s Setting up libbrotli1:amd64 (1.1.0-2build4) ...
 89s Setting up libsqlite3-0:amd64 (3.46.1-2) ...
 89s Setting up dosfstools (4.2-1.2) ...
 89s Setting up rsyslog (8.2412.0-2ubuntu2) ...
 89s info: The user `syslog' is already a member of `adm'.
 90s Setting up binutils-common:amd64 (2.44-3ubuntu1) ...
 90s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ...
 90s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ...
 90s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ...
 90s Setting up linux-headers-generic (6.14.0-10.10) ...
 90s Setting up libjemalloc2:amd64 (5.3.0-3) ...
 90s Setting up libsframe1:amd64 (2.44-3ubuntu1) ...
 90s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ...
 90s Setting up apparmor (4.1.0~beta5-0ubuntu8) ...
 91s Installing new version of config file /etc/apparmor.d/openvpn ...
 92s Reloading AppArmor profiles 
 94s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ...
 94s No schema files found: doing nothing.
 94s Setting up libglib2.0-data (2.84.0-1) ...
 94s Setting up libncurses6:amd64 (6.5+20250216-2) ...
 94s Setting up strace (6.13+ds-1ubuntu1) ...
 94s Setting up xz-utils (5.6.4-1) ...
 94s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ...
 94s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ...
 98s Setting up libncursesw6:amd64 (6.5+20250216-2) ...
 98s Setting up libpci3:amd64 (1:3.13.0-2) ...
 98s Setting up python-apt-common (2.9.9build1) ...
 98s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ...
 98s Setting up pnp.ids (0.393-3) ...
 98s Setting up libnl-3-200:amd64 (3.7.0-1) ...
 98s Setting up python3.13-minimal (3.13.2-2) ...
 99s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ...
 99s Setting up libbinutils:amd64 (2.44-3ubuntu1) ...
 99s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ...
 99s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ...
 99s Setting up rsync (3.4.1+ds1-3) ...
100s rsync.service is a disabled or a static unit not running, not starting it.
100s Setting up python3.13-gdbm (3.13.2-2) ...
100s Setting up libpython3-stdlib:amd64 (3.13.2-2) ...
100s Setting up ncurses-term (6.5+20250216-2) ...
100s Setting up libctf0:amd64 (2.44-3ubuntu1) ...
100s Setting up libpython3.13:amd64 (3.13.2-2) ...
100s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
100s Setting up libdebuginfod1t64:amd64 (0.192-4) ...
100s Setting up linux-headers-virtual (6.14.0-10.10) ...
100s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ...
100s Setting up python3.13 (3.13.2-2) ...
101s Setting up htop (3.4.0-2) ...
101s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ...
105s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic
105s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic
105s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic
105s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic
105s Setting up libfwupd3:amd64 (2.0.6-4) ...
105s Setting up python3 (3.13.2-2) ...
105s Setting up python3-markupsafe (2.1.5-1build4) ...
105s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ...
109s Setting up libnl-route-3-200:amd64 (3.7.0-1) ...
109s Setting up hwdata (0.393-3) ...
109s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
109s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ...
109s Setting up linux-perf (6.14.0-10.10) ...
109s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ...
109s Setting up python3-gi (3.50.0-4build1) ...
109s Setting up pciutils (1:3.13.0-2) ...
109s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ...
109s Setting up curl (8.12.1-3ubuntu1) ...
109s Setting up linux-image-virtual (6.14.0-10.10) ...
109s Setting up linux-tools-common (6.14.0-10.10) ...
109s Setting up fwupd (2.0.6-4) ...
110s fwupd-refresh.service is a disabled or a static unit not running, not starting it.
110s fwupd.service is a disabled or a static unit not running, not starting it.
110s Setting up python3-systemd (235-1build6) ...
110s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ...
110s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ...
110s Setting up linux-image-generic (6.14.0-10.10) ...
110s Setting up python3-dbus (1.3.2-5build5) ...
110s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ...
110s Setting up linux-generic (6.14.0-10.10) ...
110s Setting up python3-apt (2.9.9build1) ...
111s Setting up python3-yaml (6.0.2-1build2) ...
111s Setting up python3-lazr.uri (1.0.6-6) ...
111s Setting up binutils (2.44-3ubuntu1) ...
111s Setting up cloud-init-base (25.1-0ubuntu3) ...
113s Setting up linux-virtual (6.14.0-10.10) ...
113s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ...
113s Setting up cloud-init (25.1-0ubuntu3) ...
113s Processing triggers for systemd (257.3-1ubuntu3) ...
113s Processing triggers for man-db (2.13.0-1) ...
116s Processing triggers for dbus (1.16.2-1ubuntu1) ...
116s Processing triggers for libc-bin (2.41-1ubuntu1) ...
116s Processing triggers for initramfs-tools (0.146ubuntu1) ...
116s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic
116s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
131s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ...
131s /etc/kernel/postinst.d/initramfs-tools:
131s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic
131s W: No lz4 in /usr/bin:/sbin:/bin, using gzip
146s /etc/kernel/postinst.d/zz-update-grub:
146s Sourcing file `/etc/default/grub'
146s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
146s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
146s Generating grub configuration file ...
146s Found linux image: /boot/vmlinuz-6.14.0-10-generic
146s Found initrd image: /boot/initrd.img-6.14.0-10-generic
147s Found linux image: /boot/vmlinuz-6.12.0-16-generic
147s Found initrd image: /boot/initrd.img-6.12.0-16-generic
147s Found linux image: /boot/vmlinuz-6.11.0-8-generic
147s Found initrd image: /boot/initrd.img-6.11.0-8-generic
147s Warning: os-prober will not be executed to detect other bootable partitions.
147s Systems on them will not be added to the GRUB boot configuration.
147s Check GRUB_DISABLE_OS_PROBER documentation entry.
147s Adding boot menu entry for UEFI Firmware Settings ...
147s done
149s Reading package lists...
150s Building dependency tree...
150s Reading state information...
151s Solving dependencies...
151s The following packages will be REMOVED:
151s   libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib*
151s   libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
151s   linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic*
151s   linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic*
151s   linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic*
151s   linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8*
151s   linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16*
151s   linux-tools-6.12.0-16-generic*
151s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded.
151s After this operation, 545 MB disk space will be freed.
151s (Reading database ... 
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(Reading database ... 148643 files and directories currently installed.)
151s Removing libnl-genl-3-200:amd64 (3.7.0-1) ...
151s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
151s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
151s Removing libpython3.12t64:amd64 (3.12.9-1) ...
151s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ...
151s Removing libnsl2:amd64 (1.3.0-3build3) ...
151s Removing libpython3.12-minimal:amd64 (3.12.9-1) ...
151s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
152s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
156s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ...
156s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ...
160s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ...
160s /etc/kernel/postrm.d/initramfs-tools:
160s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic
161s /etc/kernel/postrm.d/zz-update-grub:
161s Sourcing file `/etc/default/grub'
161s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
161s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
161s Generating grub configuration file ...
161s Found linux image: /boot/vmlinuz-6.14.0-10-generic
161s Found initrd image: /boot/initrd.img-6.14.0-10-generic
161s Found linux image: /boot/vmlinuz-6.12.0-16-generic
161s Found initrd image: /boot/initrd.img-6.12.0-16-generic
162s Warning: os-prober will not be executed to detect other bootable partitions.
162s Systems on them will not be added to the GRUB boot configuration.
162s Check GRUB_DISABLE_OS_PROBER documentation entry.
162s Adding boot menu entry for UEFI Firmware Settings ...
162s done
162s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ...
162s W: Removing the running kernel
162s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic
162s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic
162s /etc/kernel/postrm.d/initramfs-tools:
162s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic
162s /etc/kernel/postrm.d/zz-update-grub:
162s Sourcing file `/etc/default/grub'
162s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
162s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
162s Generating grub configuration file ...
163s Found linux image: /boot/vmlinuz-6.14.0-10-generic
163s Found initrd image: /boot/initrd.img-6.14.0-10-generic
163s Warning: os-prober will not be executed to detect other bootable partitions.
163s Systems on them will not be added to the GRUB boot configuration.
163s Check GRUB_DISABLE_OS_PROBER documentation entry.
163s Adding boot menu entry for UEFI Firmware Settings ...
163s done
163s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
164s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ...
166s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ...
166s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ...
166s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ...
166s Processing triggers for libc-bin (2.41-1ubuntu1) ...
166s (Reading database ... 
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(Reading database ... 76972 files and directories currently installed.)
166s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ...
166s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ...
166s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ...
166s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ...
166s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed
166s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
166s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ...
167s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty
167s autopkgtest [22:04:04]: upgrading testbed (apt dist-upgrade and autopurge)
167s Reading package lists...
167s Building dependency tree...
167s Reading state information...
168s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
168s Starting 2 pkgProblemResolver with broken count: 0
168s Done
169s Entering ResolveByKeep
169s 
170s Calculating upgrade...
170s The following packages will be upgraded:
170s   libc-bin libc-dev-bin libc6 libc6-dev locales
170s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
170s Need to get 10.5 MB of archives.
170s After this operation, 1024 B of additional disk space will be used.
170s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB]
170s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB]
170s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB]
170s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB]
170s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB]
171s Preconfiguring packages ...
171s Fetched 10.5 MB in 0s (32.2 MB/s)
171s (Reading database ... 
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(Reading database ... 76968 files and directories currently installed.)
171s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ...
171s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
171s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ...
171s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ...
172s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Setting up libc6:amd64 (2.41-1ubuntu2) ...
172s (Reading database ... 
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172s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ...
172s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
172s Setting up libc-bin (2.41-1ubuntu2) ...
172s (Reading database ... 
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(Reading database ... 76968 files and directories currently installed.)
172s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
172s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
173s Setting up locales (2.41-1ubuntu2) ...
174s Generating locales (this might take a while)...
176s   en_US.UTF-8... done
176s Generation complete.
176s Setting up libc-dev-bin (2.41-1ubuntu2) ...
176s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ...
176s Processing triggers for man-db (2.13.0-1) ...
177s Processing triggers for systemd (257.3-1ubuntu3) ...
178s Reading package lists...
179s Building dependency tree...
179s Reading state information...
179s Starting pkgProblemResolver with broken count: 0
179s Starting 2 pkgProblemResolver with broken count: 0
179s Done
180s Solving dependencies...
180s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
181s autopkgtest [22:04:18]: rebooting testbed after setup commands that affected boot
184s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds...
204s autopkgtest [22:04:41]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025
205s autopkgtest [22:04:42]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-snpstats
207s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-snpstats 1.56.0+dfsg-2 (dsc) [2203 B]
207s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-snpstats 1.56.0+dfsg-2 (tar) [7752 kB]
207s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-bioc-snpstats 1.56.0+dfsg-2 (diff) [4484 B]
207s gpgv: Signature made Sat Jan 11 21:16:46 2025 UTC
207s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
207s gpgv:                issuer "crusoe@debian.org"
207s gpgv: Can't check signature: No public key
207s dpkg-source: warning: cannot verify inline signature for ./r-bioc-snpstats_1.56.0+dfsg-2.dsc: no acceptable signature found
207s autopkgtest [22:04:44]: testing package r-bioc-snpstats version 1.56.0+dfsg-2
207s autopkgtest [22:04:44]: build not needed
209s autopkgtest [22:04:46]: test pkg-r-autopkgtest: preparing testbed
209s Reading package lists...
209s Building dependency tree...
209s Reading state information...
210s Starting pkgProblemResolver with broken count: 0
210s Starting 2 pkgProblemResolver with broken count: 0
210s Done
211s The following NEW packages will be installed:
211s   build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu
211s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
211s   g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
211s   gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14
211s   gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8
211s   libblas-dev libblas3 libbz2-dev libcairo2 libcc1-0 libdatrie1 libdeflate-dev
211s   libdeflate0 libfontconfig1 libgcc-14-dev libgfortran-14-dev libgfortran5
211s   libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6 libicu-dev libisl23
211s   libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
211s   libjpeg8-dev liblapack-dev liblapack3 liblerc4 liblsan0 liblzma-dev libmpc3
211s   libncurses-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
211s   libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
211s   libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev libquadmath0
211s   libreadline-dev libsharpyuv0 libsm6 libstdc++-14-dev libtcl8.6 libthai-data
211s   libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7
211s   libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
211s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
211s   r-bioc-biocgenerics r-bioc-snpstats r-bioc-zlibbioc r-cran-hexbin
211s   r-cran-lattice r-cran-matrix r-cran-survival unzip x11-common xdg-utils zip
211s   zlib1g-dev
211s 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded.
211s Need to get 169 MB of archives.
211s After this operation, 481 MB of additional disk space will be used.
211s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB]
211s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB]
211s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB]
211s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B]
211s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B]
211s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB]
211s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB]
211s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB]
211s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB]
211s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB]
211s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB]
211s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB]
211s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB]
211s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB]
211s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB]
211s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB]
211s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB]
211s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB]
211s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B]
211s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B]
211s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB]
211s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB]
212s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB]
212s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B]
212s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B]
212s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B]
212s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB]
212s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
212s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
212s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB]
212s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB]
212s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB]
212s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB]
212s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB]
212s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB]
212s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB]
212s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B]
212s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B]
212s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB]
212s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB]
212s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB]
212s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB]
212s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB]
212s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB]
212s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B]
212s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
212s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB]
212s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
212s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB]
212s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB]
212s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB]
212s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB]
212s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
212s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB]
212s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB]
212s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB]
212s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB]
212s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
212s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B]
212s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B]
212s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB]
212s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB]
212s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB]
212s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB]
212s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
212s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
212s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB]
212s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB]
212s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB]
212s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB]
212s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB]
212s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB]
212s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB]
212s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B]
212s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB]
212s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB]
212s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB]
212s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB]
212s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB]
212s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB]
212s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB]
212s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB]
212s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
212s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB]
212s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB]
212s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
212s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
212s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB]
212s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
212s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB]
212s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB]
212s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB]
212s Get:93 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB]
212s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB]
212s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB]
212s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB]
212s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB]
212s Get:98 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B]
212s Get:99 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B]
212s Get:100 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
212s Get:101 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB]
212s Get:102 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB]
212s Get:103 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-survival amd64 3.8-3-1 [8239 kB]
213s Get:104 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
213s Get:105 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-bioc-snpstats amd64 1.56.0+dfsg-2 [8473 kB]
213s Get:106 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-hexbin amd64 1.28.5-1 [1581 kB]
213s Preconfiguring packages ...
214s Fetched 169 MB in 2s (81.3 MB/s)
214s Selecting previously unselected package libisl23:amd64.
214s (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.)
214s Preparing to unpack .../000-libisl23_0.27-1_amd64.deb ...
214s Unpacking libisl23:amd64 (0.27-1) ...
214s Selecting previously unselected package libmpc3:amd64.
214s Preparing to unpack .../001-libmpc3_1.3.1-1build2_amd64.deb ...
214s Unpacking libmpc3:amd64 (1.3.1-1build2) ...
214s Selecting previously unselected package cpp-14-x86-64-linux-gnu.
214s Preparing to unpack .../002-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
214s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
214s Selecting previously unselected package cpp-14.
214s Preparing to unpack .../003-cpp-14_14.2.0-17ubuntu3_amd64.deb ...
214s Unpacking cpp-14 (14.2.0-17ubuntu3) ...
214s Selecting previously unselected package cpp-x86-64-linux-gnu.
214s Preparing to unpack .../004-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
214s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
214s Selecting previously unselected package cpp.
214s Preparing to unpack .../005-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ...
215s Unpacking cpp (4:14.2.0-1ubuntu1) ...
215s Selecting previously unselected package libcc1-0:amd64.
215s Preparing to unpack .../006-libcc1-0_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libgomp1:amd64.
215s Preparing to unpack .../007-libgomp1_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libitm1:amd64.
215s Preparing to unpack .../008-libitm1_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libasan8:amd64.
215s Preparing to unpack .../009-libasan8_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package liblsan0:amd64.
215s Preparing to unpack .../010-liblsan0_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libtsan2:amd64.
215s Preparing to unpack .../011-libtsan2_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libubsan1:amd64.
215s Preparing to unpack .../012-libubsan1_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libhwasan0:amd64.
215s Preparing to unpack .../013-libhwasan0_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libquadmath0:amd64.
215s Preparing to unpack .../014-libquadmath0_15-20250222-0ubuntu1_amd64.deb ...
215s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ...
215s Selecting previously unselected package libgcc-14-dev:amd64.
215s Preparing to unpack .../015-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ...
215s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ...
215s Selecting previously unselected package gcc-14-x86-64-linux-gnu.
215s Preparing to unpack .../016-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
215s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
216s Selecting previously unselected package gcc-14.
216s Preparing to unpack .../017-gcc-14_14.2.0-17ubuntu3_amd64.deb ...
216s Unpacking gcc-14 (14.2.0-17ubuntu3) ...
216s Selecting previously unselected package gcc-x86-64-linux-gnu.
216s Preparing to unpack .../018-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
216s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
216s Selecting previously unselected package gcc.
216s Preparing to unpack .../019-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ...
216s Unpacking gcc (4:14.2.0-1ubuntu1) ...
216s Selecting previously unselected package libstdc++-14-dev:amd64.
216s Preparing to unpack .../020-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ...
216s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
216s Selecting previously unselected package g++-14-x86-64-linux-gnu.
216s Preparing to unpack .../021-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
216s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
217s Selecting previously unselected package g++-14.
217s Preparing to unpack .../022-g++-14_14.2.0-17ubuntu3_amd64.deb ...
217s Unpacking g++-14 (14.2.0-17ubuntu3) ...
217s Selecting previously unselected package g++-x86-64-linux-gnu.
217s Preparing to unpack .../023-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
217s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
217s Selecting previously unselected package g++.
217s Preparing to unpack .../024-g++_4%3a14.2.0-1ubuntu1_amd64.deb ...
217s Unpacking g++ (4:14.2.0-1ubuntu1) ...
217s Selecting previously unselected package build-essential.
217s Preparing to unpack .../025-build-essential_12.10ubuntu1_amd64.deb ...
217s Unpacking build-essential (12.10ubuntu1) ...
217s Selecting previously unselected package dctrl-tools.
217s Preparing to unpack .../026-dctrl-tools_2.24-3build3_amd64.deb ...
217s Unpacking dctrl-tools (2.24-3build3) ...
217s Selecting previously unselected package fonts-dejavu-mono.
217s Preparing to unpack .../027-fonts-dejavu-mono_2.37-8_all.deb ...
217s Unpacking fonts-dejavu-mono (2.37-8) ...
217s Selecting previously unselected package fonts-dejavu-core.
217s Preparing to unpack .../028-fonts-dejavu-core_2.37-8_all.deb ...
217s Unpacking fonts-dejavu-core (2.37-8) ...
217s Selecting previously unselected package fontconfig-config.
217s Preparing to unpack .../029-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ...
217s Unpacking fontconfig-config (2.15.0-2ubuntu1) ...
217s Selecting previously unselected package libfontconfig1:amd64.
217s Preparing to unpack .../030-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ...
217s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
218s Selecting previously unselected package fontconfig.
218s Preparing to unpack .../031-fontconfig_2.15.0-2ubuntu1_amd64.deb ...
218s Unpacking fontconfig (2.15.0-2ubuntu1) ...
218s Selecting previously unselected package libgfortran5:amd64.
218s Preparing to unpack .../032-libgfortran5_15-20250222-0ubuntu1_amd64.deb ...
218s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ...
218s Selecting previously unselected package libgfortran-14-dev:amd64.
218s Preparing to unpack .../033-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ...
218s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ...
218s Selecting previously unselected package gfortran-14-x86-64-linux-gnu.
218s Preparing to unpack .../034-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ...
218s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
218s Selecting previously unselected package gfortran-14.
218s Preparing to unpack .../035-gfortran-14_14.2.0-17ubuntu3_amd64.deb ...
218s Unpacking gfortran-14 (14.2.0-17ubuntu3) ...
218s Selecting previously unselected package gfortran-x86-64-linux-gnu.
218s Preparing to unpack .../036-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ...
218s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
218s Selecting previously unselected package gfortran.
218s Preparing to unpack .../037-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ...
218s Unpacking gfortran (4:14.2.0-1ubuntu1) ...
218s Selecting previously unselected package icu-devtools.
218s Preparing to unpack .../038-icu-devtools_76.1-1ubuntu2_amd64.deb ...
218s Unpacking icu-devtools (76.1-1ubuntu2) ...
218s Selecting previously unselected package libblas3:amd64.
218s Preparing to unpack .../039-libblas3_3.12.1-2_amd64.deb ...
218s Unpacking libblas3:amd64 (3.12.1-2) ...
218s Selecting previously unselected package libblas-dev:amd64.
218s Preparing to unpack .../040-libblas-dev_3.12.1-2_amd64.deb ...
218s Unpacking libblas-dev:amd64 (3.12.1-2) ...
218s Selecting previously unselected package libbz2-dev:amd64.
218s Preparing to unpack .../041-libbz2-dev_1.0.8-6_amd64.deb ...
218s Unpacking libbz2-dev:amd64 (1.0.8-6) ...
219s Selecting previously unselected package libpixman-1-0:amd64.
219s Preparing to unpack .../042-libpixman-1-0_0.44.0-3_amd64.deb ...
219s Unpacking libpixman-1-0:amd64 (0.44.0-3) ...
219s Selecting previously unselected package libxcb-render0:amd64.
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219s Unpacking libxcb-render0:amd64 (1.17.0-2) ...
219s Selecting previously unselected package libxcb-shm0:amd64.
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219s Unpacking libxcb-shm0:amd64 (1.17.0-2) ...
219s Selecting previously unselected package libxrender1:amd64.
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219s Selecting previously unselected package libcairo2:amd64.
219s Preparing to unpack .../046-libcairo2_1.18.2-2_amd64.deb ...
219s Unpacking libcairo2:amd64 (1.18.2-2) ...
219s Selecting previously unselected package libdatrie1:amd64.
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219s Selecting previously unselected package libdeflate0:amd64.
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219s Selecting previously unselected package libdeflate-dev:amd64.
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219s Unpacking libdeflate-dev:amd64 (1.23-1) ...
219s Selecting previously unselected package libgraphite2-3:amd64.
219s Preparing to unpack .../050-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ...
219s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
219s Selecting previously unselected package libharfbuzz0b:amd64.
219s Preparing to unpack .../051-libharfbuzz0b_10.2.0-1_amd64.deb ...
219s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ...
219s Selecting previously unselected package x11-common.
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219s Selecting previously unselected package libice6:amd64.
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219s Unpacking libice6:amd64 (2:1.1.1-1) ...
219s Selecting previously unselected package libicu-dev:amd64.
219s Preparing to unpack .../054-libicu-dev_76.1-1ubuntu2_amd64.deb ...
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220s Selecting previously unselected package libjpeg-turbo8:amd64.
220s Preparing to unpack .../055-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ...
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220s Selecting previously unselected package libjpeg8:amd64.
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220s Selecting previously unselected package libjpeg8-dev:amd64.
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220s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ...
220s Selecting previously unselected package libjpeg-dev:amd64.
220s Preparing to unpack .../059-libjpeg-dev_8c-2ubuntu11_amd64.deb ...
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220s Selecting previously unselected package liblapack3:amd64.
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220s Selecting previously unselected package libncurses-dev:amd64.
220s Preparing to unpack .../063-libncurses-dev_6.5+20250216-2_amd64.deb ...
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220s Selecting previously unselected package libthai-data.
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220s Selecting previously unselected package libthai0:amd64.
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220s Selecting previously unselected package libpango-1.0-0:amd64.
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221s Selecting previously unselected package libpangoft2-1.0-0:amd64.
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221s Selecting previously unselected package libpangocairo-1.0-0:amd64.
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221s Selecting previously unselected package libpaper2:amd64.
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221s Selecting previously unselected package libpcre2-16-0:amd64.
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221s Selecting previously unselected package libpcre2-posix3:amd64.
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221s Selecting previously unselected package libpkgconf3:amd64.
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221s Selecting previously unselected package zlib1g-dev:amd64.
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221s Selecting previously unselected package libpng-dev:amd64.
221s Preparing to unpack .../077-libpng-dev_1.6.47-1_amd64.deb ...
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221s Selecting previously unselected package libreadline-dev:amd64.
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221s Selecting previously unselected package libsharpyuv0:amd64.
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221s Selecting previously unselected package libsm6:amd64.
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221s Selecting previously unselected package libjbig0:amd64.
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222s Selecting previously unselected package libwebp7:amd64.
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222s Selecting previously unselected package libtiff6:amd64.
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222s Selecting previously unselected package libxft2:amd64.
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222s Selecting previously unselected package libxss1:amd64.
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222s Selecting previously unselected package libtk8.6:amd64.
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224s Setting up libgraphite2-3:amd64 (1.3.14-2ubuntu1) ...
224s Setting up libpixman-1-0:amd64 (0.44.0-3) ...
224s Setting up libsharpyuv0:amd64 (1.5.0-0.1) ...
224s Setting up libncurses-dev:amd64 (6.5+20250216-2) ...
224s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu1) ...
224s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
224s Setting up libdatrie1:amd64 (0.2.13-3build1) ...
224s Setting up libxcb-render0:amd64 (1.17.0-2) ...
224s Setting up unzip (6.0-28ubuntu6) ...
224s Setting up x11-common (1:7.7+23ubuntu3) ...
224s Setting up libdeflate0:amd64 (1.23-1) ...
224s Setting up libxcb-shm0:amd64 (1.17.0-2) ...
224s Setting up libreadline-dev:amd64 (8.2-6) ...
224s Setting up libgomp1:amd64 (15-20250222-0ubuntu1) ...
224s Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
224s Setting up libpcre2-16-0:amd64 (10.45-1) ...
224s Setting up zip (3.0-14ubuntu2) ...
224s Setting up libpcre2-32-0:amd64 (10.45-1) ...
224s Setting up libblas3:amd64 (3.12.1-2) ...
225s 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
225s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ...
225s Setting up libpkgconf3:amd64 (1.8.1-4) ...
225s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ...
225s Setting up fonts-dejavu-mono (2.37-8) ...
225s Setting up libmpc3:amd64 (1.3.1-1build2) ...
225s Setting up libtcl8.6:amd64 (8.6.16+dfsg-1) ...
225s Setting up icu-devtools (76.1-1ubuntu2) ...
225s Setting up fonts-dejavu-core (2.37-8) ...
225s Setting up pkgconf-bin (1.8.1-4) ...
225s Setting up libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ...
225s Setting up libgfortran5:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libwebp7:amd64 (1.5.0-0.1) ...
225s Setting up liblzma-dev:amd64 (5.6.4-1) ...
225s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ...
225s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
225s Setting up libpcre2-posix3:amd64 (10.45-1) ...
225s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
225s Setting up libthai-data (0.1.29-2build1) ...
225s Setting up libxss1:amd64 (1:1.2.3-1build3) ...
225s Setting up libpaper2:amd64 (2.2.5-0.3) ...
225s Setting up libtsan2:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libisl23:amd64 (0.27-1) ...
225s Setting up libdeflate-dev:amd64 (1.23-1) ...
225s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ...
225s Setting up xdg-utils (1.2.1-2ubuntu1) ...
225s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
225s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ...
225s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libblas-dev:amd64 (3.12.1-2) ...
225s 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
225s Setting up dctrl-tools (2.24-3build3) ...
225s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ...
225s Setting up libbz2-dev:amd64 (1.0.8-6) ...
225s Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
225s Setting up libice6:amd64 (2:1.1.1-1) ...
225s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ...
225s Setting up liblapack3:amd64 (3.12.1-2) ...
225s 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
225s Setting up libpcre2-dev:amd64 (10.45-1) ...
225s Setting up fontconfig-config (2.15.0-2ubuntu1) ...
225s Setting up libpng-dev:amd64 (1.6.47-1) ...
225s Setting up libpaper-utils (2.2.5-0.3) ...
225s Setting up pkgconf:amd64 (1.8.1-4) ...
225s Setting up libthai0:amd64 (0.1.29-2build1) ...
225s Setting up liblapack-dev:amd64 (3.12.1-2) ...
225s 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
225s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
225s Setting up cpp-14 (14.2.0-17ubuntu3) ...
225s Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ...
225s Setting up libfontconfig1:amd64 (2.15.0-2ubuntu1) ...
225s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ...
225s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ...
225s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ...
225s Setting up libsm6:amd64 (2:1.2.4-1) ...
225s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
225s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ...
225s Setting up fontconfig (2.15.0-2ubuntu1) ...
227s Regenerating fonts cache... done.
227s Setting up libxft2:amd64 (2.3.6-1build1) ...
227s Setting up libtk8.6:amd64 (8.6.16-1) ...
227s Setting up libpango-1.0-0:amd64 (1.56.2-1) ...
227s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ...
227s Setting up libcairo2:amd64 (1.18.2-2) ...
227s Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
227s Setting up cpp (4:14.2.0-1ubuntu1) ...
227s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
227s Setting up libpangoft2-1.0-0:amd64 (1.56.2-1) ...
227s Setting up libpangocairo-1.0-0:amd64 (1.56.2-1) ...
227s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
227s Setting up gcc-14 (14.2.0-17ubuntu3) ...
227s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
227s Setting up r-base-core (4.4.3-1) ...
228s Creating config file /etc/R/Renviron with new version
228s Setting up r-cran-lattice (0.22-6-1) ...
228s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ...
228s Setting up r-cran-hexbin (1.28.5-1) ...
228s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
228s Setting up g++-14 (14.2.0-17ubuntu3) ...
228s Setting up gfortran-14 (14.2.0-17ubuntu3) ...
228s Setting up r-bioc-biocgenerics (0.52.0-2) ...
228s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ...
228s Setting up gcc (4:14.2.0-1ubuntu1) ...
228s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
228s Setting up r-cran-matrix (1.7-3-1) ...
228s Setting up g++ (4:14.2.0-1ubuntu1) ...
228s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
228s Setting up build-essential (12.10ubuntu1) ...
228s Setting up r-cran-survival (3.8-3-1) ...
228s Setting up gfortran (4:14.2.0-1ubuntu1) ...
228s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
228s 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
228s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
228s 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
228s Setting up r-bioc-snpstats (1.56.0+dfsg-2) ...
228s Setting up r-base-dev (4.4.3-1) ...
228s Setting up pkg-r-autopkgtest (20231212ubuntu1) ...
228s Processing triggers for libc-bin (2.41-1ubuntu2) ...
228s Processing triggers for man-db (2.13.0-1) ...
231s Processing triggers for install-info (7.1.1-1) ...
232s autopkgtest [22:05:09]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
232s autopkgtest [22:05:09]: test pkg-r-autopkgtest: [-----------------------
232s Test: Try to load the R library snpStats
232s 
232s R version 4.4.3 (2025-02-28) -- "Trophy Case"
232s Copyright (C) 2025 The R Foundation for Statistical Computing
232s Platform: x86_64-pc-linux-gnu
232s 
232s R is free software and comes with ABSOLUTELY NO WARRANTY.
232s You are welcome to redistribute it under certain conditions.
232s Type 'license()' or 'licence()' for distribution details.
232s 
232s R is a collaborative project with many contributors.
232s Type 'contributors()' for more information and
232s 'citation()' on how to cite R or R packages in publications.
232s 
232s Type 'demo()' for some demos, 'help()' for on-line help, or
232s 'help.start()' for an HTML browser interface to help.
232s Type 'q()' to quit R.
232s 
232s > library('snpStats')
232s Loading required package: survival
233s Loading required package: Matrix
234s > 
234s > 
234s Other tests are currently unsupported!
234s They will be progressively added.
234s autopkgtest [22:05:11]: test pkg-r-autopkgtest: -----------------------]
234s autopkgtest [22:05:11]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
234s pkg-r-autopkgtest    PASS
235s autopkgtest [22:05:12]: @@@@@@@@@@@@@@@@@@@@ summary
235s pkg-r-autopkgtest    PASS
251s nova [W] Skipping flock for amd64
251s Creating nova instance adt-plucky-amd64-r-bioc-snpstats-20250315-220117-juju-7f2275-prod-proposed-migration-environment-20-6187d2d1-ae3b-4ba7-82be-14007d5df21a from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)...
251s nova [W] Timed out waiting for 3fc5e759-e7bc-4529-b249-a130a2bc6387 to get deleted.