0s autopkgtest [04:16:01]: starting date and time: 2026-02-10 04:16:01+0000
  0s autopkgtest [04:16:01]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [04:16:01]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zg7xs9vn/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-bioc-mutationalpatterns --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-8.secgroup --name adt-resolute-amd64-r-bioc-mutationalpatterns-20260210-041601-juju-7f2275-prod-proposed-migration-environment-2-dc0cb2de-245a-4dfc-83c9-9a325add1f88 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  4s Creating nova instance adt-resolute-amd64-r-bioc-mutationalpatterns-20260210-041601-juju-7f2275-prod-proposed-migration-environment-2-dc0cb2de-245a-4dfc-83c9-9a325add1f88 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 74s autopkgtest [04:17:15]: testbed dpkg architecture: amd64
 74s autopkgtest [04:17:15]: testbed apt version: 3.1.14
 74s autopkgtest [04:17:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 75s autopkgtest [04:17:16]: testbed release detected to be: None
 75s autopkgtest [04:17:16]: updating testbed package index (apt update)
 75s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 75s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 75s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB]
 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB]
 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB]
 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB]
 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB]
 76s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B]
 76s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B]
 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB]
 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB]
 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB]
 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB]
 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B]
 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 78s Fetched 5189 kB in 2s (2955 kB/s)
 78s Reading package lists...
 79s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 79s Reading package lists...
 79s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 80s Calculating upgrade...
 80s The following package was automatically installed and is no longer required:
 80s   libpython3.13
 80s Use 'sudo apt autoremove' to remove it.
 80s The following NEW packages will be installed:
 80s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 80s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 80s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 80s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 80s The following packages will be upgraded:
 80s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 80s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 80s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 80s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 80s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
 80s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 80s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 80s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 80s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 80s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 80s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 80s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 80s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 80s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 80s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 80s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 80s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 80s Need to get 237 MB of archives.
 80s After this operation, 339 MB of additional disk space will be used.
 80s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 80s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 80s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 80s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 80s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 80s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 80s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 80s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 80s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 80s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 80s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 80s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 80s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 80s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 80s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 80s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 80s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 80s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 80s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 81s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 81s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 81s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 81s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 81s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 81s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 81s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 81s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 81s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 81s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 81s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 81s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 81s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 81s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 81s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 81s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 81s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 81s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 81s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 81s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 81s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 81s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 81s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 81s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 81s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 81s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
 81s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
 81s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
 81s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
 81s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
 81s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
 81s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
 81s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
 81s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
 81s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
 81s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
 81s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
 81s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
 81s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
 81s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
 81s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
 81s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
 81s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
 81s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
 81s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
 81s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
 81s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
 84s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB]
 84s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
 84s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
 84s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
 84s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
 84s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
 84s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
 84s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
 85s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
 85s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
 85s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
 85s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
 85s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
 85s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
 85s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
 85s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
 85s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 85s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
 85s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 85s Fetched 237 MB in 5s (47.0 MB/s)
 85s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 85s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
 85s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
 85s Setting up debianutils (5.23.2build1) ...
 85s (Reading database ... 
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 85s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
 86s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
 86s Setting up dash (0.5.12-12ubuntu3) ...
 86s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 86s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
 86s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
 86s Setting up findutils (4.10.0-3build2) ...
 86s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 86s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
 86s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 86s Setting up sed (4.9-2build3) ...
 86s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 86s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
 86s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
 86s Setting up tar (1.35+dfsg-3.1build2) ...
 86s (Reading database ... 
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 95s man-db.service is a disabled or a static unit not running, not starting it.
 95s Setting up libjansson4:amd64 (2.14-2build4) ...
 95s Setting up libglib2.0-data (2.87.2-2) ...
 95s Setting up pollinate (4.33-4ubuntu5) ...
106s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
106s Setting up libwrap0:amd64 (7.6.q-36build2) ...
106s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
107s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
107s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
107s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
107s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
107s Setting up patch (2.8-2build1) ...
107s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
107s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
107s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
107s Setting up lsof (4.99.4+dfsg-2build2) ...
107s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
107s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
107s Setting up dracut-install (109-11ubuntu1) ...
107s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
107s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
107s Setting up pnp.ids (0.394-1build1) ...
107s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
107s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
107s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
107s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
107s Setting up mawk (1.3.4.20260129-1) ...
107s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
107s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
107s Setting up linux-image-virtual (6.19.0-3.3) ...
107s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
107s Setting up libbsd0:amd64 (0.12.2-2build2) ...
107s Setting up libdrm-common (2.4.131-1) ...
107s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
107s Setting up dbus-bin (1.16.2-2ubuntu3) ...
107s Setting up libonig5:amd64 (6.9.10-1build1) ...
107s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
107s Setting up ethtool (1:6.15-3build1) ...
107s Setting up python3-referencing (0.36.2-1ubuntu2) ...
107s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
107s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
107s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
107s Setting up tcpdump (4.99.5-2ubuntu3) ...
107s Setting up linux-image-generic (6.19.0-3.3) ...
107s Setting up wget (1.25.0-2ubuntu4) ...
107s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
107s Setting up iptables (1.8.11-2ubuntu3) ...
107s Setting up iproute2 (6.18.0-1ubuntu1) ...
108s Setting up linux-headers-generic (6.19.0-3.3) ...
108s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
108s Setting up hwdata (0.394-1build1) ...
108s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
108s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
108s No schema files found: doing nothing.
108s Setting up dbus (1.16.2-2ubuntu3) ...
108s A reboot is required to replace the running dbus-daemon.
108s Please reboot the system when convenient.
108s Setting up shared-mime-info (2.4-5build3) ...
108s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
108s Setting up pciutils (1:3.14.0-1build2) ...
108s Setting up python3-markdown-it (3.0.0-3build1) ...
109s Setting up libdrm2:amd64 (2.4.131-1) ...
109s Setting up libpython3.14:amd64 (3.14.2-1) ...
109s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
109s Setting up linux-tools-common (6.19.0-3.3) ...
109s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
109s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
109s Setting up apt (3.1.15) ...
109s Setting up linux-headers-virtual (6.19.0-3.3) ...
109s Setting up linux-generic (6.19.0-3.3) ...
109s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
109s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
109s Setting up ubuntu-standard (1.564) ...
109s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
109s Setting up linux-virtual (6.19.0-3.3) ...
109s Setting up linux-perf (6.19.0-3.3) ...
109s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
109s Processing triggers for debianutils (5.23.2build1) ...
109s Processing triggers for install-info (7.2-5) ...
109s Processing triggers for initramfs-tools (0.150ubuntu7) ...
109s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
114s Processing triggers for libc-bin (2.42-2ubuntu4) ...
114s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
114s /etc/kernel/postinst.d/initramfs-tools:
114s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
118s /etc/kernel/postinst.d/zz-update-grub:
118s Sourcing file `/etc/default/grub'
118s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
118s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
118s Generating grub configuration file ...
118s Found linux image: /boot/vmlinuz-6.19.0-3-generic
119s Found initrd image: /boot/initrd.img-6.19.0-3-generic
119s Found linux image: /boot/vmlinuz-6.18.0-9-generic
119s Found initrd image: /boot/initrd.img-6.18.0-9-generic
119s Warning: os-prober will not be executed to detect other bootable partitions.
119s Systems on them will not be added to the GRUB boot configuration.
119s Check GRUB_DISABLE_OS_PROBER documentation entry.
119s Adding boot menu entry for UEFI Firmware Settings ...
119s done
119s autopkgtest [04:18:00]: upgrading testbed (apt dist-upgrade and autopurge)
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
120s Calculating upgrade...
120s The following package was automatically installed and is no longer required:
120s   libpython3.13
120s Use 'sudo apt autoremove' to remove it.
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
120s Solving dependencies...
121s The following packages will be REMOVED:
121s   libpython3.13*
121s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
121s After this operation, 7599 kB disk space will be freed.
121s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
121s Removing libpython3.13:amd64 (3.13.11-1) ...
121s Processing triggers for libc-bin (2.42-2ubuntu4) ...
121s autopkgtest [04:18:02]: rebooting testbed after setup commands that affected boot
150s autopkgtest [04:18:31]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
152s autopkgtest [04:18:33]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-mutationalpatterns
153s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mutationalpatterns 3.16.0+dfsg-2 (dsc) [2595 B]
153s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mutationalpatterns 3.16.0+dfsg-2 (tar) [1925 kB]
153s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-mutationalpatterns 3.16.0+dfsg-2 (diff) [3564 B]
153s gpgv: Signature made Tue Jan 14 07:53:19 2025 UTC
153s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
153s gpgv:                issuer "crusoe@debian.org"
153s gpgv: Can't check signature: No public key
153s dpkg-source: warning: cannot verify inline signature for ./r-bioc-mutationalpatterns_3.16.0+dfsg-2.dsc: no acceptable signature found
154s autopkgtest [04:18:35]: testing package r-bioc-mutationalpatterns version 3.16.0+dfsg-2
154s autopkgtest [04:18:35]: build not needed
156s autopkgtest [04:18:37]: test pkg-r-autopkgtest: preparing testbed
156s Reading package lists...
156s Building dependency tree...
156s Reading state information...
156s Solving dependencies...
157s The following NEW packages will be installed:
157s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
157s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
157s   fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax
157s   g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15
157s   gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15
157s   gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools
157s   javascript-common libasan8 libbibtex-parser-perl libblas-dev libblas3
157s   libboost-dev libboost1.90-dev libbz2-dev libc-dev-bin libc6-dev libcairo2
157s   libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1
157s   libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 libgraphite2-3
157s   libharfbuzz0b libhwasan0 libice6 libicu-dev libio-string-perl libisl23
157s   libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
157s   libjpeg8-dev libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim
157s   libjs-highlight.js libjs-jquery libjs-jquery-datatables
157s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr
157s   libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js
157s   libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker
157s   libkpathsea6 liblapack-dev liblapack3 liblatex-tounicode-perl liblerc4
157s   liblsan0 liblua5.4-0 liblzma-dev libmpc3 libmpfi0 libncurses-dev
157s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
157s   libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
157s   libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libptexenc1 libquadmath0
157s   libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libsynctex2 libtcl8.6
157s   libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev
157s   libtk8.6 libtsan2 libubsan1 libwebp7 libxaw7 libxcb-render0 libxcb-shm0
157s   libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libzstd-dev
157s   libzzip-0-13t64 linux-libc-dev node-bootstrap-sass node-html5shiv
157s   node-normalize.css pandoc pandoc-data pkg-r-autopkgtest pkgconf pkgconf-bin
157s   r-base-core r-base-dev r-bioc-annotationdbi r-bioc-biobase
157s   r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
157s   r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart r-bioc-biostrings
157s   r-bioc-bsgenome r-bioc-delayedarray r-bioc-genomeinfodb
157s   r-bioc-genomeinfodbdata r-bioc-genomicalignments r-bioc-genomicfeatures
157s   r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics
157s   r-bioc-mutationalpatterns r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer
157s   r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray
157s   r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation
157s   r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc
157s   r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops
157s   r-cran-blob r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem
157s   r-cran-callr r-cran-cli r-cran-cluster r-cran-codetools r-cran-colorspace
157s   r-cran-commonmark r-cran-cowplot r-cran-cpp11 r-cran-crayon r-cran-curl
157s   r-cran-dbi r-cran-dbplyr r-cran-desc r-cran-diffobj r-cran-digest
157s   r-cran-doparallel r-cran-dplyr r-cran-evaluate r-cran-fansi r-cran-farver
157s   r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-foreach
157s   r-cran-formatr r-cran-fs r-cran-futile.logger r-cran-futile.options
157s   r-cran-generics r-cran-ggalluvial r-cran-ggdendro r-cran-ggplot2 r-cran-glue
157s   r-cran-gridbase r-cran-gridextra r-cran-gtable r-cran-highr r-cran-hms
157s   r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-httr2 r-cran-isoband
157s   r-cran-iterators r-cran-jquerylib r-cran-jsonlite r-cran-knitr
157s   r-cran-labeling r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval
157s   r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
157s   r-cran-matrixstats r-cran-memoise r-cran-mime r-cran-nmf r-cran-openssl
157s   r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten
157s   r-cran-pkgload r-cran-plogr r-cran-plyr r-cran-png r-cran-pracma
157s   r-cran-praise r-cran-prettyunits r-cran-processx r-cran-progress
157s   r-cran-promises r-cran-ps r-cran-purrr r-cran-r6 r-cran-rappdirs
157s   r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-registry r-cran-reshape2
157s   r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rngtools
157s   r-cran-rprojroot r-cran-rsqlite r-cran-s7 r-cran-sass r-cran-scales
157s   r-cran-shiny r-cran-snow r-cran-sourcetools r-cran-stringi r-cran-stringr
157s   r-cran-sys r-cran-testthat r-cran-tibble r-cran-tidyr r-cran-tidyselect
157s   r-cran-tinytex r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-waldo
157s   r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml
157s   rpcsvc-proto t1utils tex-common texlive-base texlive-bibtex-extra
157s   texlive-binaries texlive-latex-base unzip x11-common xdg-utils zip
157s   zlib1g-dev
157s 0 upgraded, 318 newly installed, 0 to remove and 0 not upgraded.
157s Need to get 481 MB of archives.
157s After this operation, 1451 MB of additional disk space will be used.
157s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
157s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
157s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
157s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
157s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
157s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
157s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
157s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
157s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
157s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
157s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
157s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
157s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
157s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
158s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
158s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
158s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
158s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
158s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
158s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
158s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
158s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
159s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
159s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
159s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
159s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
159s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
160s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
160s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
160s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
160s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
160s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
160s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
160s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
160s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
160s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
160s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
160s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB]
160s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
160s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lmodern all 2.005-1build1 [4788 kB]
160s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
160s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
160s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
160s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
161s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
161s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
161s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
161s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
161s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B]
161s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-string-perl all 1.08-4 [11.1 kB]
161s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblatex-tounicode-perl all 1.93-1 [29.2 kB]
161s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB]
161s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
161s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
161s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB]
161s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B]
161s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
161s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
161s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
161s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
161s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
161s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
161s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
161s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
161s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
161s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
161s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
161s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
161s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
161s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
161s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
161s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
161s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
161s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
161s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
161s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
161s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB]
162s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
162s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB]
162s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
162s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
162s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
162s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
162s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
162s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B]
162s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
162s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB]
162s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB]
162s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
162s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB]
162s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5build1 [66.0 kB]
162s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
162s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
162s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
162s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
162s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpfi0 amd64 1.5.4+ds-4build1 [36.6 kB]
162s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
162s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
162s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
162s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
162s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
162s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
162s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
162s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
162s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
162s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
162s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
162s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
162s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
162s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
162s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
162s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpotrace0 amd64 1.16-2build2 [17.9 kB]
162s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 libptexenc1 amd64 2025.20250727.75242+ds-5build1 [46.4 kB]
162s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
162s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
162s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
162s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsynctex2 amd64 2025.20250727.75242+ds-5build1 [62.1 kB]
162s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
162s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 libteckit0 amd64 2.5.13+ds-1 [431 kB]
162s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5build1 [125 kB]
162s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
162s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
162s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
162s Get:124 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
162s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
162s Get:126 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
162s Get:127 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
162s Get:128 http://ftpmaster.internal/ubuntu resolute/main amd64 libxmu6 amd64 2:1.1.3-4 [48.9 kB]
162s Get:129 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB]
162s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 libxaw7 amd64 2:1.0.16-1build1 [190 kB]
162s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB]
162s Get:132 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
162s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [30.1 kB]
162s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
162s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
162s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
162s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
162s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
163s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
163s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
163s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
163s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
164s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
164s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
164s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
164s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
164s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
164s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
164s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
164s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
164s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
164s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
164s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB]
164s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
164s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB]
164s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
164s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
164s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
164s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
164s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
164s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB]
164s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
164s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
164s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
164s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
164s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB]
164s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
164s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
164s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
164s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
164s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
164s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
164s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
164s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
164s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
164s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
164s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
164s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
164s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
164s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
164s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
164s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
165s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
165s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
165s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB]
165s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
165s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB]
165s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
165s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
165s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB]
165s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB]
165s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
165s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
165s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
165s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB]
165s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB]
165s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB]
165s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
165s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
165s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbplyr all 2.5.1+dfsg-1 [1237 kB]
165s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB]
165s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocfilecache all 2.14.0+dfsg-2 [300 kB]
165s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB]
165s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
165s Get:205 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lambda.r all 1.2.4-2build2 [118 kB]
165s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.options all 1.0.1-3build2 [20.5 kB]
165s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.logger all 1.4.3-4build2 [98.4 kB]
165s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-snow all 1:0.4.4-2build1 [98.7 kB]
165s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB]
165s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
165s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
165s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
165s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
165s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
165s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
165s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
165s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
165s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
165s Get:219 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
165s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
165s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB]
165s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
165s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB]
165s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
165s Get:225 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
166s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
166s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB]
166s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB]
166s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB]
166s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
166s Get:231 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
166s Get:232 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
166s Get:233 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
166s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
166s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
166s Get:236 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
166s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
166s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
166s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
166s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB]
166s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bookdown all 0.42+dfsg-1 [1409 kB]
166s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB]
166s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 tex-common all 6.20 [30.0 kB]
166s Get:244 http://ftpmaster.internal/ubuntu resolute/main amd64 t1utils amd64 1.41-4build4 [62.7 kB]
166s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-binaries amd64 2025.20250727.75242+ds-5build1 [8747 kB]
166s Get:246 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-base all 2025.20260124-1 [22.8 MB]
167s Get:247 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-base all 2025.20260124-1 [1321 kB]
167s Get:248 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-bibtex-extra all 2025.20260124-1 [80.6 MB]
168s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocversion all 3.20.0-2 [11.1 kB]
168s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB]
168s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hms all 1.1.4-1 [102 kB]
168s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
168s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
168s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr2 all 1.1.1-2 [752 kB]
168s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml2 amd64 1.4.1-1 [329 kB]
168s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biomart all 2.62.1+dfsg-1 [444 kB]
168s Get:257 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
168s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
168s Get:259 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
168s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB]
168s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB]
169s Get:262 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
169s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
169s Get:264 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB]
169s Get:265 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
169s Get:266 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB]
169s Get:267 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
169s Get:268 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1391 kB]
169s Get:269 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
169s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
169s Get:271 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB]
169s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
169s Get:273 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB]
169s Get:274 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
169s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rtracklayer amd64 1.66.0-3 [5225 kB]
169s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-bsgenome all 1.74.0-2 [7001 kB]
169s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB]
169s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-registry all 0.5-1-2build2 [202 kB]
169s Get:279 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rngtools all 1.5.2-1build1 [84.4 kB]
169s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cluster amd64 2.1.8.2-1 [570 kB]
170s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gridbase all 0.4-7-5build2 [162 kB]
170s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-colorspace amd64 2.1-1+dfsg-1 [1563 kB]
170s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
170s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB]
170s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB]
170s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-doparallel all 1.0.17-1build1 [189 kB]
170s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
170s Get:288 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
170s Get:289 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB]
170s Get:290 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
170s Get:291 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
170s Get:292 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB]
170s Get:293 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB]
170s Get:294 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB]
170s Get:295 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
170s Get:296 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reshape2 amd64 1.4.4-2build2 [123 kB]
170s Get:297 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nmf amd64 0.28-1 [3027 kB]
170s Get:298 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-variantannotation amd64 1.52.0-2 [3642 kB]
170s Get:299 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pracma all 2.4.6-1 [1720 kB]
170s Get:300 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
170s Get:301 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggdendro all 0.2.0+dfsg-1 [173 kB]
170s Get:302 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cowplot all 1.1.3+dfsg-1 [614 kB]
170s Get:303 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lazyeval amd64 0.2.2-1build2 [146 kB]
171s Get:304 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ggalluvial all 0.12.5-2 [1982 kB]
171s Get:305 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-mutationalpatterns all 3.16.0+dfsg-2 [2523 kB]
171s Get:306 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB]
171s Get:307 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
171s Get:308 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
171s Get:309 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
171s Get:310 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
171s Get:311 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diffobj amd64 0.3.5-1build1 [1156 kB]
171s Get:312 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gridextra all 2.3-3build2 [1032 kB]
171s Get:313 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgbuild all 1.4.8-1 [219 kB]
171s Get:314 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rprojroot all 2.1.1-1 [131 kB]
171s Get:315 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgload all 1.4.1-1 [252 kB]
171s Get:316 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-praise all 1.0.0-4build2 [20.9 kB]
171s Get:317 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-waldo all 0.6.2-1 [153 kB]
171s Get:318 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB]
171s Preconfiguring packages ...
171s Fetched 481 MB in 14s (33.6 MB/s)
171s Selecting previously unselected package libc-dev-bin.
172s (Reading database ... 
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(Reading database ... 125269 files and directories currently installed.)
172s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
172s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
172s Selecting previously unselected package linux-libc-dev:amd64.
172s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
172s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
172s Selecting previously unselected package libcrypt-dev:amd64.
172s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
172s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
172s Selecting previously unselected package rpcsvc-proto.
172s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
172s Unpacking rpcsvc-proto (1.4.3-1build1) ...
172s Selecting previously unselected package libc6-dev:amd64.
172s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
172s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
172s Selecting previously unselected package libisl23:amd64.
172s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
172s Unpacking libisl23:amd64 (0.27-1build1) ...
172s Selecting previously unselected package libmpc3:amd64.
172s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
172s Unpacking libmpc3:amd64 (1.3.1-2) ...
172s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
172s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
172s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
172s Selecting previously unselected package cpp-15.
172s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
172s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
172s Selecting previously unselected package cpp-x86-64-linux-gnu.
172s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
172s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
172s Selecting previously unselected package cpp.
172s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
172s Unpacking cpp (4:15.2.0-4ubuntu1) ...
172s Selecting previously unselected package libcc1-0:amd64.
172s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libgomp1:amd64.
172s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libitm1:amd64.
172s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libasan8:amd64.
172s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package liblsan0:amd64.
172s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libtsan2:amd64.
172s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libubsan1:amd64.
172s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libhwasan0:amd64.
172s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libquadmath0:amd64.
172s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ...
172s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ...
172s Selecting previously unselected package libgcc-15-dev:amd64.
172s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ...
172s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
172s Selecting previously unselected package gcc-15-x86-64-linux-gnu.
172s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
172s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package gcc-15.
173s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking gcc-15 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package gcc-x86-64-linux-gnu.
173s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package gcc.
173s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking gcc (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package libstdc++-15-dev:amd64.
173s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package g++-15-x86-64-linux-gnu.
173s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package g++-15.
173s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking g++-15 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package g++-x86-64-linux-gnu.
173s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package g++.
173s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking g++ (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package build-essential.
173s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ...
173s Unpacking build-essential (12.12ubuntu2) ...
173s Selecting previously unselected package dctrl-tools.
173s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ...
173s Unpacking dctrl-tools (2.24-3build4) ...
173s Selecting previously unselected package fonts-dejavu-mono.
173s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ...
173s Unpacking fonts-dejavu-mono (2.37-8build1) ...
173s Selecting previously unselected package fonts-dejavu-core.
173s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ...
173s Unpacking fonts-dejavu-core (2.37-8build1) ...
173s Selecting previously unselected package fontconfig-config.
173s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ...
173s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
173s Selecting previously unselected package libfontconfig1:amd64.
173s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ...
173s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
173s Selecting previously unselected package fontconfig.
173s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ...
173s Unpacking fontconfig (2.17.1-3ubuntu1) ...
173s Selecting previously unselected package fonts-font-awesome.
173s Preparing to unpack .../037-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ...
173s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ...
173s Selecting previously unselected package fonts-glyphicons-halflings.
173s Preparing to unpack .../038-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ...
173s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
173s Selecting previously unselected package fonts-lmodern.
173s Preparing to unpack .../039-fonts-lmodern_2.005-1build1_all.deb ...
173s Unpacking fonts-lmodern (2.005-1build1) ...
173s Selecting previously unselected package fonts-mathjax.
173s Preparing to unpack .../040-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
173s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ...
173s Selecting previously unselected package libgfortran5:amd64.
173s Preparing to unpack .../041-libgfortran5_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libgfortran-15-dev:amd64.
173s Preparing to unpack .../042-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package gfortran-15-x86-64-linux-gnu.
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175s Selecting previously unselected package libjs-sifter.js.
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175s Selecting previously unselected package libjs-microplugin.js.
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175s Selecting previously unselected package libjs-jquery-selectize.js.
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175s Selecting previously unselected package libjs-prettify.
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175s Selecting previously unselected package libkpathsea6:amd64.
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175s Selecting previously unselected package liblapack3:amd64.
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175s Selecting previously unselected package liblerc4:amd64.
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175s Selecting previously unselected package liblua5.4-0:amd64.
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175s Selecting previously unselected package libmpfi0:amd64.
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175s Selecting previously unselected package libncurses-dev:amd64.
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175s Selecting previously unselected package libthai-data.
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176s Selecting previously unselected package libpango-1.0-0:amd64.
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176s Selecting previously unselected package libpangocairo-1.0-0:amd64.
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176s Selecting previously unselected package libpng-dev:amd64.
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176s Selecting previously unselected package libtcl8.6:amd64.
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176s Selecting previously unselected package libxpm4:amd64.
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176s Selecting previously unselected package libzzip-0-13t64:amd64.
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176s Selecting previously unselected package pandoc-data.
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177s Selecting previously unselected package xdg-utils.
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177s Selecting previously unselected package r-base-core.
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177s Selecting previously unselected package liblzma-dev:amd64.
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177s Selecting previously unselected package pkgconf-bin.
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177s Selecting previously unselected package pkgconf:amd64.
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177s Selecting previously unselected package libtirpc-dev:amd64.
177s Preparing to unpack .../145-libtirpc-dev_1.3.6+ds-1_amd64.deb ...
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177s Selecting previously unselected package r-base-dev.
177s Preparing to unpack .../146-r-base-dev_4.5.2-1ubuntu2_all.deb ...
177s Unpacking r-base-dev (4.5.2-1ubuntu2) ...
177s Selecting previously unselected package pkg-r-autopkgtest.
177s Preparing to unpack .../147-pkg-r-autopkgtest_20250812_all.deb ...
177s Unpacking pkg-r-autopkgtest (20250812) ...
177s Selecting previously unselected package r-bioc-biocgenerics.
177s Preparing to unpack .../148-r-bioc-biocgenerics_0.52.0-2_all.deb ...
177s Unpacking r-bioc-biocgenerics (0.52.0-2) ...
177s Selecting previously unselected package r-bioc-biobase.
177s Preparing to unpack .../149-r-bioc-biobase_2.66.0-2_amd64.deb ...
177s Unpacking r-bioc-biobase (2.66.0-2) ...
177s Selecting previously unselected package r-bioc-s4vectors.
177s Preparing to unpack .../150-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ...
177s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ...
177s Selecting previously unselected package r-bioc-iranges.
177s Preparing to unpack .../151-r-bioc-iranges_2.40.1-3_amd64.deb ...
177s Unpacking r-bioc-iranges (2.40.1-3) ...
177s Selecting previously unselected package r-cran-dbi.
177s Preparing to unpack .../152-r-cran-dbi_1.2.3-1build1_all.deb ...
177s Unpacking r-cran-dbi (1.2.3-1build1) ...
177s Selecting previously unselected package r-cran-bit.
177s Preparing to unpack .../153-r-cran-bit_4.6.0+dfsg-1_amd64.deb ...
177s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
177s Selecting previously unselected package r-cran-bit64.
177s Preparing to unpack .../154-r-cran-bit64_4.6.0-1-4_amd64.deb ...
177s Unpacking r-cran-bit64 (4.6.0-1-4) ...
177s Selecting previously unselected package r-cran-rlang.
177s Preparing to unpack .../155-r-cran-rlang_1.1.5-3_amd64.deb ...
177s Unpacking r-cran-rlang (1.1.5-3) ...
177s Selecting previously unselected package r-cran-cli.
177s Preparing to unpack .../156-r-cran-cli_3.6.4-1_amd64.deb ...
177s Unpacking r-cran-cli (3.6.4-1) ...
177s Selecting previously unselected package r-cran-glue.
177s Preparing to unpack .../157-r-cran-glue_1.8.0-1_amd64.deb ...
177s Unpacking r-cran-glue (1.8.0-1) ...
177s Selecting previously unselected package r-cran-lifecycle.
177s Preparing to unpack .../158-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ...
177s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ...
177s Selecting previously unselected package r-cran-vctrs.
177s Preparing to unpack .../159-r-cran-vctrs_0.6.5-1_amd64.deb ...
177s Unpacking r-cran-vctrs (0.6.5-1) ...
177s Selecting previously unselected package r-cran-blob.
177s Preparing to unpack .../160-r-cran-blob_1.3.0-1_all.deb ...
177s Unpacking r-cran-blob (1.3.0-1) ...
177s Selecting previously unselected package r-cran-fastmap.
177s Preparing to unpack .../161-r-cran-fastmap_1.2.0-1_amd64.deb ...
177s Unpacking r-cran-fastmap (1.2.0-1) ...
177s Selecting previously unselected package r-cran-cachem.
177s Preparing to unpack .../162-r-cran-cachem_1.1.0-1_amd64.deb ...
177s Unpacking r-cran-cachem (1.1.0-1) ...
177s Selecting previously unselected package r-cran-memoise.
177s Preparing to unpack .../163-r-cran-memoise_2.0.1-1build1_all.deb ...
177s Unpacking r-cran-memoise (2.0.1-1build1) ...
177s Selecting previously unselected package r-cran-pkgconfig.
177s Preparing to unpack .../164-r-cran-pkgconfig_2.0.3-2build2_all.deb ...
177s Unpacking r-cran-pkgconfig (2.0.3-2build2) ...
177s Selecting previously unselected package r-cran-plogr.
177s Preparing to unpack .../165-r-cran-plogr_0.2.0-3build2_all.deb ...
177s Unpacking r-cran-plogr (0.2.0-3build2) ...
177s Selecting previously unselected package r-cran-cpp11.
177s Preparing to unpack .../166-r-cran-cpp11_0.5.3-1_all.deb ...
177s Unpacking r-cran-cpp11 (0.5.3-1) ...
177s Selecting previously unselected package r-cran-rsqlite.
177s Preparing to unpack .../167-r-cran-rsqlite_2.3.9-1_amd64.deb ...
177s Unpacking r-cran-rsqlite (2.3.9-1) ...
177s Selecting previously unselected package r-cran-curl.
177s Preparing to unpack .../168-r-cran-curl_7.0.0+dfsg-1_amd64.deb ...
177s Unpacking r-cran-curl (7.0.0+dfsg-1) ...
177s Selecting previously unselected package r-cran-jsonlite.
177s Preparing to unpack .../169-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ...
177s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ...
177s Selecting previously unselected package r-cran-mime.
177s Preparing to unpack .../170-r-cran-mime_0.12-2_amd64.deb ...
177s Unpacking r-cran-mime (0.12-2) ...
178s Selecting previously unselected package r-cran-sys.
178s Preparing to unpack .../171-r-cran-sys_3.4.3-1_amd64.deb ...
178s Unpacking r-cran-sys (3.4.3-1) ...
178s Selecting previously unselected package r-cran-askpass.
178s Preparing to unpack .../172-r-cran-askpass_1.2.1-1_amd64.deb ...
178s Unpacking r-cran-askpass (1.2.1-1) ...
178s Selecting previously unselected package r-cran-openssl.
178s Preparing to unpack .../173-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ...
178s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
178s Selecting previously unselected package r-cran-r6.
178s Preparing to unpack .../174-r-cran-r6_2.6.1-1_all.deb ...
178s Unpacking r-cran-r6 (2.6.1-1) ...
178s Selecting previously unselected package r-cran-httr.
178s Preparing to unpack .../175-r-cran-httr_1.4.7+dfsg-1_all.deb ...
178s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
178s Selecting previously unselected package r-cran-png.
178s Preparing to unpack .../176-r-cran-png_0.1-8-1build2_amd64.deb ...
178s Unpacking r-cran-png (0.1-8-1build2) ...
178s Selecting previously unselected package r-bioc-zlibbioc.
178s Preparing to unpack .../177-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ...
178s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ...
178s Selecting previously unselected package r-bioc-xvector.
178s Preparing to unpack .../178-r-bioc-xvector_0.46.0-2_amd64.deb ...
178s Unpacking r-bioc-xvector (0.46.0-2) ...
178s Selecting previously unselected package r-bioc-ucsc.utils.
178s Preparing to unpack .../179-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ...
178s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ...
178s Selecting previously unselected package r-bioc-genomeinfodbdata.
178s Preparing to unpack .../180-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ...
178s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ...
178s Selecting previously unselected package r-bioc-genomeinfodb.
178s Preparing to unpack .../181-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ...
178s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
178s Selecting previously unselected package r-cran-crayon.
178s Preparing to unpack .../182-r-cran-crayon_1.5.3-1_all.deb ...
178s Unpacking r-cran-crayon (1.5.3-1) ...
178s Selecting previously unselected package r-bioc-biostrings.
178s Preparing to unpack .../183-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ...
178s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ...
178s Selecting previously unselected package r-bioc-keggrest.
178s Preparing to unpack .../184-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ...
178s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ...
178s Selecting previously unselected package r-bioc-annotationdbi.
178s Preparing to unpack .../185-r-bioc-annotationdbi_1.68.0-2_all.deb ...
178s Unpacking r-bioc-annotationdbi (1.68.0-2) ...
178s Selecting previously unselected package r-cran-generics.
178s Preparing to unpack .../186-r-cran-generics_0.1.4-1_all.deb ...
178s Unpacking r-cran-generics (0.1.4-1) ...
178s Selecting previously unselected package r-cran-magrittr.
178s Preparing to unpack .../187-r-cran-magrittr_2.0.3-1_amd64.deb ...
178s Unpacking r-cran-magrittr (2.0.3-1) ...
178s Selecting previously unselected package r-cran-utf8.
178s Preparing to unpack .../188-r-cran-utf8_1.2.4-1_amd64.deb ...
178s Unpacking r-cran-utf8 (1.2.4-1) ...
178s Selecting previously unselected package r-cran-pillar.
178s Preparing to unpack .../189-r-cran-pillar_1.11.1+dfsg-1_all.deb ...
178s Unpacking r-cran-pillar (1.11.1+dfsg-1) ...
178s Selecting previously unselected package r-cran-fansi.
178s Preparing to unpack .../190-r-cran-fansi_1.0.6-2_amd64.deb ...
178s Unpacking r-cran-fansi (1.0.6-2) ...
178s Selecting previously unselected package r-cran-tibble.
178s Preparing to unpack .../191-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ...
178s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
178s Selecting previously unselected package r-cran-withr.
178s Preparing to unpack .../192-r-cran-withr_3.0.2+dfsg-1_all.deb ...
178s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
178s Selecting previously unselected package r-cran-tidyselect.
178s Preparing to unpack .../193-r-cran-tidyselect_1.2.1+dfsg-1_amd64.deb ...
178s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
178s Selecting previously unselected package r-cran-dplyr.
178s Preparing to unpack .../194-r-cran-dplyr_1.1.4-4_amd64.deb ...
178s Unpacking r-cran-dplyr (1.1.4-4) ...
178s Selecting previously unselected package r-cran-purrr.
178s Preparing to unpack .../195-r-cran-purrr_1.0.4-1_amd64.deb ...
178s Unpacking r-cran-purrr (1.0.4-1) ...
178s Selecting previously unselected package r-cran-stringi.
178s Preparing to unpack .../196-r-cran-stringi_1.8.4-1build2_amd64.deb ...
178s Unpacking r-cran-stringi (1.8.4-1build2) ...
178s Selecting previously unselected package r-cran-stringr.
178s Preparing to unpack .../197-r-cran-stringr_1.5.1-1_all.deb ...
178s Unpacking r-cran-stringr (1.5.1-1) ...
178s Selecting previously unselected package r-cran-tidyr.
178s Preparing to unpack .../198-r-cran-tidyr_1.3.1-1_amd64.deb ...
178s Unpacking r-cran-tidyr (1.3.1-1) ...
178s Selecting previously unselected package r-cran-dbplyr.
178s Preparing to unpack .../199-r-cran-dbplyr_2.5.1+dfsg-1_all.deb ...
178s Unpacking r-cran-dbplyr (2.5.1+dfsg-1) ...
178s Selecting previously unselected package r-cran-filelock.
178s Preparing to unpack .../200-r-cran-filelock_1.0.3-1_amd64.deb ...
178s Unpacking r-cran-filelock (1.0.3-1) ...
178s Selecting previously unselected package r-bioc-biocfilecache.
178s Preparing to unpack .../201-r-bioc-biocfilecache_2.14.0+dfsg-2_all.deb ...
178s Unpacking r-bioc-biocfilecache (2.14.0+dfsg-2) ...
178s Selecting previously unselected package r-bioc-biocio.
178s Preparing to unpack .../202-r-bioc-biocio_1.16.0+dfsg-2_all.deb ...
178s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ...
178s Selecting previously unselected package r-cran-formatr.
178s Preparing to unpack .../203-r-cran-formatr_1.14-2_all.deb ...
178s Unpacking r-cran-formatr (1.14-2) ...
178s Selecting previously unselected package r-cran-lambda.r.
178s Preparing to unpack .../204-r-cran-lambda.r_1.2.4-2build2_all.deb ...
178s Unpacking r-cran-lambda.r (1.2.4-2build2) ...
178s Selecting previously unselected package r-cran-futile.options.
178s Preparing to unpack .../205-r-cran-futile.options_1.0.1-3build2_all.deb ...
178s Unpacking r-cran-futile.options (1.0.1-3build2) ...
178s Selecting previously unselected package r-cran-futile.logger.
178s Preparing to unpack .../206-r-cran-futile.logger_1.4.3-4build2_all.deb ...
178s Unpacking r-cran-futile.logger (1.4.3-4build2) ...
178s Selecting previously unselected package r-cran-snow.
178s Preparing to unpack .../207-r-cran-snow_1%3a0.4.4-2build1_all.deb ...
178s Unpacking r-cran-snow (1:0.4.4-2build1) ...
178s Selecting previously unselected package r-cran-codetools.
178s Preparing to unpack .../208-r-cran-codetools_0.2-20-1build1_all.deb ...
178s Unpacking r-cran-codetools (0.2-20-1build1) ...
178s Selecting previously unselected package r-cran-bh.
178s Preparing to unpack .../209-r-cran-bh_1.84.0-1_all.deb ...
178s Unpacking r-cran-bh (1.84.0-1) ...
178s Selecting previously unselected package r-bioc-biocparallel.
178s Preparing to unpack .../210-r-bioc-biocparallel_1.40.0-2_amd64.deb ...
178s Unpacking r-bioc-biocparallel (1.40.0-2) ...
178s Selecting previously unselected package r-cran-base64enc.
179s Preparing to unpack .../211-r-cran-base64enc_0.1-3-3build1_amd64.deb ...
179s Unpacking r-cran-base64enc (0.1-3-3build1) ...
179s Selecting previously unselected package r-cran-digest.
179s Preparing to unpack .../212-r-cran-digest_0.6.39-1_amd64.deb ...
179s Unpacking r-cran-digest (0.6.39-1) ...
179s Selecting previously unselected package r-cran-htmltools.
179s Preparing to unpack .../213-r-cran-htmltools_0.5.8.1-1_amd64.deb ...
179s Unpacking r-cran-htmltools (0.5.8.1-1) ...
179s Selecting previously unselected package r-cran-evaluate.
179s Preparing to unpack .../214-r-cran-evaluate_1.0.5-1_all.deb ...
179s Unpacking r-cran-evaluate (1.0.5-1) ...
179s Selecting previously unselected package r-cran-xfun.
179s Preparing to unpack .../215-r-cran-xfun_0.55+dfsg-1_amd64.deb ...
179s Unpacking r-cran-xfun (0.55+dfsg-1) ...
179s Selecting previously unselected package r-cran-highr.
179s Preparing to unpack .../216-r-cran-highr_0.11+dfsg-1_all.deb ...
179s Unpacking r-cran-highr (0.11+dfsg-1) ...
179s Selecting previously unselected package r-cran-yaml.
179s Preparing to unpack .../217-r-cran-yaml_2.3.10-1_amd64.deb ...
179s Unpacking r-cran-yaml (2.3.10-1) ...
179s Selecting previously unselected package libjs-mathjax.
179s Preparing to unpack .../218-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ...
179s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ...
179s Selecting previously unselected package r-cran-knitr.
179s Preparing to unpack .../219-r-cran-knitr_1.51+dfsg-1_all.deb ...
179s Unpacking r-cran-knitr (1.51+dfsg-1) ...
179s Selecting previously unselected package r-cran-jquerylib.
179s Preparing to unpack .../220-r-cran-jquerylib_0.1.4+dfsg-5_all.deb ...
179s Unpacking r-cran-jquerylib (0.1.4+dfsg-5) ...
179s Selecting previously unselected package r-cran-fs.
179s Preparing to unpack .../221-r-cran-fs_1.6.5+dfsg-1_amd64.deb ...
179s Unpacking r-cran-fs (1.6.5+dfsg-1) ...
179s Selecting previously unselected package r-cran-rappdirs.
179s Preparing to unpack .../222-r-cran-rappdirs_0.3.3-1build1_amd64.deb ...
179s Unpacking r-cran-rappdirs (0.3.3-1build1) ...
179s Selecting previously unselected package r-cran-sass.
179s Preparing to unpack .../223-r-cran-sass_0.4.9+dfsg-1_amd64.deb ...
179s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
179s Selecting previously unselected package r-cran-bslib.
179s Preparing to unpack .../224-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ...
179s Unpacking r-cran-bslib (0.9.0+dfsg-3build1) ...
179s Selecting previously unselected package r-cran-fontawesome.
179s Preparing to unpack .../225-r-cran-fontawesome_0.5.3-1_all.deb ...
179s Unpacking r-cran-fontawesome (0.5.3-1) ...
179s Selecting previously unselected package r-cran-tinytex.
179s Preparing to unpack .../226-r-cran-tinytex_0.58-1_all.deb ...
179s Unpacking r-cran-tinytex (0.58-1) ...
179s Selecting previously unselected package libjs-modernizr.
179s Preparing to unpack .../227-libjs-modernizr_3.13.0-0.1build1_all.deb ...
179s Unpacking libjs-modernizr (3.13.0-0.1build1) ...
179s Selecting previously unselected package r-cran-littler.
179s Preparing to unpack .../228-r-cran-littler_0.3.22-1_amd64.deb ...
179s Unpacking r-cran-littler (0.3.22-1) ...
179s Selecting previously unselected package r-cran-pkgkitten.
179s Preparing to unpack .../229-r-cran-pkgkitten_0.2.4-1_all.deb ...
179s Unpacking r-cran-pkgkitten (0.2.4-1) ...
179s Selecting previously unselected package r-cran-rcpp.
179s Preparing to unpack .../230-r-cran-rcpp_1.1.0-1_amd64.deb ...
179s Unpacking r-cran-rcpp (1.1.0-1) ...
179s Selecting previously unselected package r-cran-later.
179s Preparing to unpack .../231-r-cran-later_1.4.1+dfsg-1_amd64.deb ...
179s Unpacking r-cran-later (1.4.1+dfsg-1) ...
179s Selecting previously unselected package r-cran-promises.
179s Preparing to unpack .../232-r-cran-promises_1.3.2+dfsg-1_amd64.deb ...
179s Unpacking r-cran-promises (1.3.2+dfsg-1) ...
179s Selecting previously unselected package r-cran-httpuv.
179s Preparing to unpack .../233-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ...
179s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ...
179s Selecting previously unselected package r-cran-xtable.
179s Preparing to unpack .../234-r-cran-xtable_1%3a1.8-4-2build1_all.deb ...
179s Unpacking r-cran-xtable (1:1.8-4-2build1) ...
179s Selecting previously unselected package r-cran-sourcetools.
179s Preparing to unpack .../235-r-cran-sourcetools_0.1.7-1-1_amd64.deb ...
179s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
179s Selecting previously unselected package r-cran-commonmark.
179s Preparing to unpack .../236-r-cran-commonmark_1.9.5-1_amd64.deb ...
179s Unpacking r-cran-commonmark (1.9.5-1) ...
179s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
179s Preparing to unpack .../237-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ...
179s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
179s Selecting previously unselected package r-cran-shiny.
179s Preparing to unpack .../238-r-cran-shiny_1.10.0+dfsg-2_all.deb ...
179s Unpacking r-cran-shiny (1.10.0+dfsg-2) ...
179s Selecting previously unselected package r-cran-rmarkdown.
179s Preparing to unpack .../239-r-cran-rmarkdown_2.30+dfsg-1_all.deb ...
179s Unpacking r-cran-rmarkdown (2.30+dfsg-1) ...
180s Selecting previously unselected package r-cran-bookdown.
180s Preparing to unpack .../240-r-cran-bookdown_0.42+dfsg-1_all.deb ...
180s Unpacking r-cran-bookdown (0.42+dfsg-1) ...
180s Selecting previously unselected package r-cran-biocmanager.
180s Preparing to unpack .../241-r-cran-biocmanager_1.30.25+dfsg-1_all.deb ...
180s Unpacking r-cran-biocmanager (1.30.25+dfsg-1) ...
180s Selecting previously unselected package tex-common.
180s Preparing to unpack .../242-tex-common_6.20_all.deb ...
180s Unpacking tex-common (6.20) ...
180s Selecting previously unselected package t1utils.
180s Preparing to unpack .../243-t1utils_1.41-4build4_amd64.deb ...
180s Unpacking t1utils (1.41-4build4) ...
180s Selecting previously unselected package texlive-binaries.
180s Preparing to unpack .../244-texlive-binaries_2025.20250727.75242+ds-5build1_amd64.deb ...
180s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ...
180s Selecting previously unselected package texlive-base.
180s Preparing to unpack .../245-texlive-base_2025.20260124-1_all.deb ...
180s Unpacking texlive-base (2025.20260124-1) ...
180s Selecting previously unselected package texlive-latex-base.
180s Preparing to unpack .../246-texlive-latex-base_2025.20260124-1_all.deb ...
180s Unpacking texlive-latex-base (2025.20260124-1) ...
180s Selecting previously unselected package texlive-bibtex-extra.
180s Preparing to unpack .../247-texlive-bibtex-extra_2025.20260124-1_all.deb ...
180s Unpacking texlive-bibtex-extra (2025.20260124-1) ...
181s Selecting previously unselected package r-bioc-biocversion.
181s Preparing to unpack .../248-r-bioc-biocversion_3.20.0-2_all.deb ...
181s Unpacking r-bioc-biocversion (3.20.0-2) ...
181s Selecting previously unselected package r-bioc-biocstyle.
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186s Setting up r-base-core (4.5.2-1ubuntu2) ...
186s Creating config file /etc/R/Renviron with new version
186s Setting up r-cran-crayon (1.5.3-1) ...
186s Setting up r-cran-labeling (0.4.3-1) ...
186s Setting up r-cran-sourcetools (0.1.7-1-1) ...
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186s Setting up r-cran-viridislite (0.4.3-1) ...
186s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ...
186s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
186s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
186s Setting up r-cran-cluster (2.1.8.2-1) ...
186s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
186s Setting up r-cran-lazyeval (0.2.2-1build2) ...
186s Setting up r-cran-commonmark (1.9.5-1) ...
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186s Setting up r-cran-pkgkitten (0.2.4-1) ...
186s Setting up texlive-base (2025.20260124-1) ...
187s tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
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187s Setting up r-cran-gridbase (0.4-7-5build2) ...
187s Setting up r-cran-pracma (2.4.6-1) ...
187s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
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187s Setting up r-cran-mime (0.12-2) ...
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187s Setting up r-cran-generics (0.1.4-1) ...
187s Setting up r-cran-base64enc (0.1-3-3build1) ...
187s Setting up r-cran-iterators (1.0.14-1build1) ...
187s Setting up r-cran-abind (1.4-8-1build1) ...
187s Setting up r-cran-digest (0.6.39-1) ...
187s Setting up r-cran-yaml (2.3.10-1) ...
187s Setting up r-cran-lambda.r (1.2.4-2build2) ...
187s Setting up r-cran-evaluate (1.0.5-1) ...
187s Setting up r-cran-dbi (1.2.3-1build1) ...
187s Setting up r-cran-highr (0.11+dfsg-1) ...
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187s Setting up r-cran-prettyunits (1.2.0-1) ...
187s Setting up r-cran-fansi (1.0.6-2) ...
187s Setting up r-cran-mass (7.3-65-1) ...
187s Setting up r-cran-snow (1:0.4.4-2build1) ...
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187s Setting up r-cran-xtable (1:1.8-4-2build1) ...
187s Setting up r-cran-cli (3.6.4-1) ...
187s Setting up gfortran (4:15.2.0-4ubuntu1) ...
187s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
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187s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
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187s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
187s Setting up r-cran-bitops (1.0-9-1) ...
187s Setting up r-bioc-biocversion (3.20.0-2) ...
187s Setting up r-cran-rprojroot (2.1.1-1) ...
187s Setting up r-cran-bit64 (4.6.0-1-4) ...
187s Setting up r-cran-biocmanager (1.30.25+dfsg-1) ...
187s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
187s Setting up r-cran-askpass (1.2.1-1) ...
187s Setting up r-cran-fastmap (1.2.0-1) ...
187s Setting up r-cran-png (0.1-8-1build2) ...
187s Setting up r-bioc-biobase (2.66.0-2) ...
187s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
187s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
187s Setting up r-cran-utf8 (1.2.4-1) ...
187s Setting up r-cran-colorspace (2.1-1+dfsg-1) ...
187s Setting up r-cran-stringi (1.8.4-1build2) ...
187s Setting up texlive-latex-base (2025.20260124-1) ...
187s Setting up r-cran-s7 (0.2.0-1) ...
187s Setting up r-cran-cpp11 (0.5.3-1) ...
187s Setting up r-cran-plyr (1.8.9-1) ...
187s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
187s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
187s Setting up r-cran-isoband (0.2.7-1) ...
187s Setting up r-cran-futile.logger (1.4.3-4build2) ...
187s Setting up r-cran-waldo (0.6.2-1) ...
187s Setting up r-cran-scales (1.4.0-1) ...
187s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
187s Setting up r-cran-later (1.4.1+dfsg-1) ...
187s Setting up r-cran-matrix (1.7-4-1) ...
187s Setting up r-cran-doparallel (1.0.17-1build1) ...
187s Setting up r-cran-htmltools (0.5.8.1-1) ...
187s Setting up r-cran-tinytex (0.58-1) ...
187s Setting up r-cran-knitr (1.51+dfsg-1) ...
187s Setting up g++ (4:15.2.0-4ubuntu1) ...
187s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
187s Setting up r-cran-cachem (1.1.0-1) ...
187s Setting up r-cran-sass (0.4.9+dfsg-1) ...
187s Setting up build-essential (12.12ubuntu2) ...
187s Setting up r-bioc-iranges (2.40.1-3) ...
187s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
187s Setting up r-cran-restfulr (0.0.15-1) ...
187s Setting up r-cran-vctrs (0.6.5-1) ...
187s Setting up r-cran-pillar (1.11.1+dfsg-1) ...
187s Setting up r-cran-rngtools (1.5.2-1build1) ...
187s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
187s Setting up r-base-dev (4.5.2-1ubuntu2) ...
187s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
187s Setting up r-cran-stringr (1.5.1-1) ...
187s Setting up r-bioc-biocparallel (1.40.0-2) ...
187s Setting up r-cran-callr (3.7.6-1) ...
187s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ...
187s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
187s Setting up r-cran-desc (1.4.3-1) ...
187s Setting up r-cran-xml2 (1.4.1-1) ...
187s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
187s Setting up r-cran-fontawesome (0.5.3-1) ...
187s Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
187s Setting up r-cran-jquerylib (0.1.4+dfsg-5) ...
187s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
187s Setting up texlive-bibtex-extra (2025.20260124-1) ...
187s Setting up r-cran-reshape2 (1.4.4-2build2) ...
187s Setting up r-cran-httr2 (1.1.1-2) ...
187s Setting up r-cran-httr (1.4.7+dfsg-1) ...
187s Setting up r-cran-nmf (0.28-1) ...
187s Setting up r-cran-gridextra (2.3-3build2) ...
187s Setting up r-cran-hms (1.1.4-1) ...
187s Setting up r-cran-memoise (2.0.1-1build1) ...
187s Setting up r-cran-promises (1.3.2+dfsg-1) ...
187s Setting up r-cran-purrr (1.0.4-1) ...
187s Setting up r-cran-ggdendro (0.2.0+dfsg-1) ...
187s Setting up r-cran-blob (1.3.0-1) ...
187s Setting up pkg-r-autopkgtest (20250812) ...
187s Setting up r-bioc-xvector (0.46.0-2) ...
187s Setting up r-cran-pkgbuild (1.4.8-1) ...
187s Setting up r-cran-dplyr (1.1.4-4) ...
187s Setting up r-cran-rsqlite (2.3.9-1) ...
187s Setting up r-cran-progress (1.2.3-1) ...
187s Setting up r-cran-cowplot (1.1.3+dfsg-1) ...
187s Setting up r-cran-pkgload (1.4.1-1) ...
187s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
187s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ...
187s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
187s Setting up r-cran-testthat (3.2.3-1) ...
187s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
187s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
187s Setting up r-cran-tidyr (1.3.1-1) ...
187s Setting up r-cran-ggalluvial (0.12.5-2) ...
187s Setting up r-cran-dbplyr (2.5.1+dfsg-1) ...
187s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
187s Setting up r-bioc-biocfilecache (2.14.0+dfsg-2) ...
187s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
187s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
187s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
187s Setting up r-cran-rmarkdown (2.30+dfsg-1) ...
187s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
187s Setting up r-cran-bookdown (0.42+dfsg-1) ...
187s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
187s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ...
187s Setting up r-bioc-annotationdbi (1.68.0-2) ...
187s Setting up r-bioc-biomart (2.62.1+dfsg-1) ...
187s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ...
187s Setting up r-bioc-genomicalignments (1.42.0-2) ...
187s Setting up r-bioc-rtracklayer (1.66.0-3) ...
187s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
187s Setting up r-bioc-bsgenome (1.74.0-2) ...
187s Setting up r-bioc-variantannotation (1.52.0-2) ...
187s Setting up r-bioc-mutationalpatterns (3.16.0+dfsg-2) ...
187s Processing triggers for libc-bin (2.42-2ubuntu4) ...
187s Processing triggers for man-db (2.13.1-1build1) ...
189s Processing triggers for install-info (7.2-5) ...
189s Processing triggers for tex-common (6.20) ...
189s Running updmap-sys. This may take some time... done.
189s Running mktexlsr /var/lib/texmf ... done.
189s Building format(s) --all.
203s 	This may take some time... done.
204s autopkgtest [04:19:25]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
204s autopkgtest [04:19:25]: test pkg-r-autopkgtest: [-----------------------
204s Test: Try to load the R library MutationalPatterns
204s 
204s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
204s Copyright (C) 2025 The R Foundation for Statistical Computing
204s Platform: x86_64-pc-linux-gnu
204s 
204s R is free software and comes with ABSOLUTELY NO WARRANTY.
204s You are welcome to redistribute it under certain conditions.
204s Type 'license()' or 'licence()' for distribution details.
204s 
204s R is a collaborative project with many contributors.
204s Type 'contributors()' for more information and
204s 'citation()' on how to cite R or R packages in publications.
204s 
204s Type 'demo()' for some demos, 'help()' for on-line help, or
204s 'help.start()' for an HTML browser interface to help.
204s Type 'q()' to quit R.
204s 
204s > library('MutationalPatterns')
204s Loading required package: GenomicRanges
204s Loading required package: stats4
204s Loading required package: BiocGenerics
204s 
204s Attaching package: ‘BiocGenerics’
204s 
204s The following objects are masked from ‘package:stats’:
204s 
204s     IQR, mad, sd, var, xtabs
204s 
204s The following objects are masked from ‘package:base’:
204s 
204s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
204s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
204s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
204s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
204s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
204s     table, tapply, union, unique, unsplit, which.max, which.min
204s 
204s Loading required package: S4Vectors
205s 
205s Attaching package: ‘S4Vectors’
205s 
205s The following object is masked from ‘package:utils’:
205s 
205s     findMatches
205s 
205s The following objects are masked from ‘package:base’:
205s 
205s     expand.grid, I, unname
205s 
205s Loading required package: IRanges
205s Loading required package: GenomeInfoDb
206s Loading required package: NMF
206s Loading required package: registry
206s Loading required package: rngtools
206s Loading required package: cluster
207s NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2
207s   To enable shared memory capabilities, try: install.extras('
207s NMF
207s ')
207s 
207s Attaching package: ‘NMF’
207s 
207s The following object is masked from ‘package:S4Vectors’:
207s 
207s     nrun
207s 
207s > 
207s + grep -Rl BSgenome.Hsapiens.UCSC.hg19 tests/testthat tests/testthat.R
207s + rm tests/testthat/test-plot_spectrum.R tests/testthat/test-read_vcfs_as_granges.R tests/testthat/test-determine_regional_similarity.R tests/testthat/test-type_context.R tests/testthat/test-strand_occurrences.R tests/testthat/test-plot_spectrum_region.R tests/testthat/test-mut_matrix_stranded.R tests/testthat/test-plot_strand.R tests/testthat/test-bin_mutation_density.R tests/testthat/test-get_indel_context.R tests/testthat/test-mut_matrix.R tests/testthat/test-mut_context.R tests/testthat/test-calculate_lesion_segretation.R tests/testthat/test-context_potential_damage_analysis.R tests/testthat/test-mut_type_occurrences.R
207s FIXME: Do not delete tests requiring bipartite once r-bioc-ccfindr is available
207s + echo FIXME: Do not delete tests requiring bipartite once r-bioc-ccfindr is available
207s + apt-cache show r-bioc-ccfindr
207s + rm tests/testthat/test-extract_signatures.R
207s + find tests -type f -iname *.R
207s + wc -l
207s Test: Run tests for MutationalPatterns
207s + NBTEST=51
207s + [ 51 -gt 0 ]
207s + echo Test: Run tests for MutationalPatterns
207s Start: testthat.R
207s + cd tests
207s + echo Start: testthat.R
207s + R --no-save
207s 
207s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
207s Copyright (C) 2025 The R Foundation for Statistical Computing
207s Platform: x86_64-pc-linux-gnu
207s 
207s R is free software and comes with ABSOLUTELY NO WARRANTY.
207s You are welcome to redistribute it under certain conditions.
207s Type 'license()' or 'licence()' for distribution details.
207s 
207s R is a collaborative project with many contributors.
207s Type 'contributors()' for more information and
207s 'citation()' on how to cite R or R packages in publications.
207s 
207s Type 'demo()' for some demos, 'help()' for on-line help, or
207s 'help.start()' for an HTML browser interface to help.
207s Type 'q()' to quit R.
207s 
207s > library(testthat)
207s Loading required package: GenomicRanges
207s Loading required package: stats4
207s > library(MutationalPatterns)
207s Loading required package: BiocGenerics
207s 
207s Attaching package: ‘BiocGenerics’
207s 
207s The following objects are masked from ‘package:stats’:
207s 
207s     IQR, mad, sd, var, xtabs
207s 
207s The following objects are masked from ‘package:base’:
207s 
207s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
207s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
207s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
207s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
207s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
207s     table, tapply, union, unique, unsplit, which.max, which.min
207s 
207s Loading required package: S4Vectors
207s 
207s Attaching package: ‘S4Vectors’
207s 
207s The following object is masked from ‘package:utils’:
207s 
207s     findMatches
207s 
207s The following objects are masked from ‘package:base’:
207s 
207s     expand.grid, I, unname
207s 
207s Loading required package: IRanges
208s Loading required package: GenomeInfoDb
208s Loading required package: NMF
208s Loading required package: registry
208s Loading required package: rngtools
208s Loading required package: cluster
209s NMF - BioConductor layer [OK] | Shared memory capabilities [NO: bigmemory] | Cores 2/2
209s   To enable shared memory capabilities, try: install.extras('
209s NMF
209s ')
209s 
209s Attaching package: ‘NMF’
209s 
209s The following object is masked from ‘package:S4Vectors’:
209s 
209s     nrun
209s 
209s The following object is masked from ‘package:testthat’:
209s 
209s     compare
209s 
209s > 
209s > test_check("MutationalPatterns")
254s [ FAIL 0 | WARN 28 | SKIP 0 | PASS 305 ]
254s 
254s [ FAIL 0 | WARN 28 | SKIP 0 | PASS 305 ]
254s > 
254s + exit 0
254s autopkgtest [04:20:15]: test pkg-r-autopkgtest: -----------------------]
255s autopkgtest [04:20:16]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
255s pkg-r-autopkgtest    PASS
255s autopkgtest [04:20:16]: @@@@@@@@@@@@@@@@@@@@ summary
255s pkg-r-autopkgtest    PASS