0s autopkgtest [04:16:11]: starting date and time: 2026-02-10 04:16:11+0000
  0s autopkgtest [04:16:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [04:16:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.d6il1_o1/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-phyloseq --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-15@sto01-19.secgroup --name adt-resolute-amd64-r-bioc-phyloseq-20260210-041611-juju-7f2275-prod-proposed-migration-environment-15-5dc57f90-e23f-49bd-9272-8436b775c899 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  3s Creating nova instance adt-resolute-amd64-r-bioc-phyloseq-20260210-041611-juju-7f2275-prod-proposed-migration-environment-15-5dc57f90-e23f-49bd-9272-8436b775c899 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 73s autopkgtest [04:17:24]: testbed dpkg architecture: amd64
 73s autopkgtest [04:17:24]: testbed apt version: 3.1.14
 73s autopkgtest [04:17:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 73s autopkgtest [04:17:24]: testbed release detected to be: None
 74s autopkgtest [04:17:25]: updating testbed package index (apt update)
 74s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 74s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 74s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 74s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 74s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB]
 75s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB]
 75s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [31.1 kB]
 75s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB]
 75s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB]
 75s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B]
 75s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B]
 75s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB]
 75s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB]
 75s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB]
 75s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B]
 75s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB]
 75s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 76s Fetched 5189 kB in 1s (5039 kB/s)
 76s Reading package lists...
 77s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 77s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 77s Reading package lists...
 77s Reading package lists...
 78s Building dependency tree...
 78s Reading state information...
 78s Calculating upgrade...
 78s The following package was automatically installed and is no longer required:
 78s   libpython3.13
 78s Use 'sudo apt autoremove' to remove it.
 78s The following NEW packages will be installed:
 78s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 78s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 78s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 78s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 78s The following packages will be upgraded:
 78s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 78s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 78s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 78s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 78s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
 78s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 78s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 78s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 78s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 78s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 78s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 78s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 78s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 78s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 78s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 78s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 78s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 78s Need to get 237 MB of archives.
 78s After this operation, 339 MB of additional disk space will be used.
 78s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 78s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 78s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 78s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 78s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 78s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 78s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 78s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 78s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 78s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 78s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 78s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 78s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 78s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 78s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 78s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 78s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 78s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 78s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 78s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 78s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 78s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 78s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 78s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 78s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 78s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 78s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 78s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 78s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 78s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 78s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 78s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 78s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 78s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 78s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 78s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 78s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 78s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 78s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 78s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 78s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 78s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 78s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 78s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 78s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 78s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 78s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 78s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 78s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 78s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 78s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 78s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 78s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 78s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 78s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 78s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 78s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 78s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 78s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 78s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 78s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
 78s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
 78s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
 78s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
 78s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
 78s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
 78s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
 78s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
 78s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
 78s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
 78s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
 78s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
 78s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
 78s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
 78s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
 78s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
 78s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
 78s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
 79s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
 79s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
 79s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
 79s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
 81s 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]
 81s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
 81s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
 81s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
 81s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
 81s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
 81s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
 81s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
 82s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
 82s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
 82s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
 82s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
 82s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
 82s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
 82s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
 82s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
 82s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 82s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
 82s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 82s Fetched 237 MB in 4s (58.2 MB/s)
 82s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 82s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
 82s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
 82s Setting up debianutils (5.23.2build1) ...
 82s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 82s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
 82s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
 82s Setting up dash (0.5.12-12ubuntu3) ...
 83s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 83s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
 83s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
 83s Setting up findutils (4.10.0-3build2) ...
 83s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 83s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
 83s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 83s Setting up sed (4.9-2build3) ...
 83s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 83s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
 83s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
 83s Setting up tar (1.35+dfsg-3.1build2) ...
 83s (Reading database ... 
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 92s Setting up libjansson4:amd64 (2.14-2build4) ...
 92s Setting up libglib2.0-data (2.87.2-2) ...
 92s Setting up pollinate (4.33-4ubuntu5) ...
103s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
103s Setting up libwrap0:amd64 (7.6.q-36build2) ...
103s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
104s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
104s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
104s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
104s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
104s Setting up patch (2.8-2build1) ...
104s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
104s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
104s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
104s Setting up lsof (4.99.4+dfsg-2build2) ...
104s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
104s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
104s Setting up dracut-install (109-11ubuntu1) ...
104s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
104s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
104s Setting up pnp.ids (0.394-1build1) ...
104s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
104s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
104s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
104s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
104s Setting up mawk (1.3.4.20260129-1) ...
104s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
104s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
104s Setting up linux-image-virtual (6.19.0-3.3) ...
104s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
104s Setting up libbsd0:amd64 (0.12.2-2build2) ...
104s Setting up libdrm-common (2.4.131-1) ...
104s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
104s Setting up dbus-bin (1.16.2-2ubuntu3) ...
104s Setting up libonig5:amd64 (6.9.10-1build1) ...
104s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
104s Setting up ethtool (1:6.15-3build1) ...
104s Setting up python3-referencing (0.36.2-1ubuntu2) ...
104s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
104s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
104s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
104s Setting up tcpdump (4.99.5-2ubuntu3) ...
104s Setting up linux-image-generic (6.19.0-3.3) ...
104s Setting up wget (1.25.0-2ubuntu4) ...
104s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
105s Setting up iptables (1.8.11-2ubuntu3) ...
105s Setting up iproute2 (6.18.0-1ubuntu1) ...
105s Setting up linux-headers-generic (6.19.0-3.3) ...
105s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
105s Setting up hwdata (0.394-1build1) ...
105s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
105s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
105s No schema files found: doing nothing.
105s Setting up dbus (1.16.2-2ubuntu3) ...
105s A reboot is required to replace the running dbus-daemon.
105s Please reboot the system when convenient.
105s Setting up shared-mime-info (2.4-5build3) ...
106s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
106s Setting up pciutils (1:3.14.0-1build2) ...
106s Setting up python3-markdown-it (3.0.0-3build1) ...
106s Setting up libdrm2:amd64 (2.4.131-1) ...
107s Setting up libpython3.14:amd64 (3.14.2-1) ...
107s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
107s Setting up linux-tools-common (6.19.0-3.3) ...
107s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
107s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
107s Setting up apt (3.1.15) ...
107s Setting up linux-headers-virtual (6.19.0-3.3) ...
107s Setting up linux-generic (6.19.0-3.3) ...
107s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
107s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
107s Setting up ubuntu-standard (1.564) ...
107s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
107s Setting up linux-virtual (6.19.0-3.3) ...
107s Setting up linux-perf (6.19.0-3.3) ...
107s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
107s Processing triggers for debianutils (5.23.2build1) ...
107s Processing triggers for install-info (7.2-5) ...
107s Processing triggers for initramfs-tools (0.150ubuntu7) ...
107s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
113s Processing triggers for libc-bin (2.42-2ubuntu4) ...
113s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
113s /etc/kernel/postinst.d/initramfs-tools:
113s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
117s /etc/kernel/postinst.d/zz-update-grub:
117s Sourcing file `/etc/default/grub'
117s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
117s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
117s Generating grub configuration file ...
118s Found linux image: /boot/vmlinuz-6.19.0-3-generic
118s Found initrd image: /boot/initrd.img-6.19.0-3-generic
118s Found linux image: /boot/vmlinuz-6.18.0-9-generic
118s Found initrd image: /boot/initrd.img-6.18.0-9-generic
118s Warning: os-prober will not be executed to detect other bootable partitions.
118s Systems on them will not be added to the GRUB boot configuration.
118s Check GRUB_DISABLE_OS_PROBER documentation entry.
118s Adding boot menu entry for UEFI Firmware Settings ...
118s done
118s autopkgtest [04:18:09]: upgrading testbed (apt dist-upgrade and autopurge)
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
119s Calculating upgrade...
119s The following package was automatically installed and is no longer required:
119s   libpython3.13
119s Use 'sudo apt autoremove' to remove it.
119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
119s Reading package lists...
119s Building dependency tree...
119s Reading state information...
120s Solving dependencies...
120s The following packages will be REMOVED:
120s   libpython3.13*
120s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
120s After this operation, 7599 kB disk space will be freed.
120s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
120s Removing libpython3.13:amd64 (3.13.11-1) ...
120s Processing triggers for libc-bin (2.42-2ubuntu4) ...
120s autopkgtest [04:18:11]: rebooting testbed after setup commands that affected boot
148s autopkgtest [04:18:39]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
150s autopkgtest [04:18:41]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-phyloseq
152s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-phyloseq 1.50.0+dfsg-2 (dsc) [2370 B]
152s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-phyloseq 1.50.0+dfsg-2 (tar) [1607 kB]
152s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-phyloseq 1.50.0+dfsg-2 (diff) [14.7 kB]
152s gpgv: Signature made Sun Jan 12 19:19:58 2025 UTC
152s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
152s gpgv:                issuer "crusoe@debian.org"
152s gpgv: Can't check signature: No public key
152s dpkg-source: warning: cannot verify inline signature for ./r-bioc-phyloseq_1.50.0+dfsg-2.dsc: no acceptable signature found
152s autopkgtest [04:18:43]: testing package r-bioc-phyloseq version 1.50.0+dfsg-2
152s autopkgtest [04:18:43]: build not needed
154s autopkgtest [04:18:45]: test pkg-r-autopkgtest: preparing testbed
155s Reading package lists...
155s Building dependency tree...
155s Reading state information...
155s Solving dependencies...
155s The following NEW packages will be installed:
155s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
155s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
155s   fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax
155s   g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15
155s   gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15
155s   gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools
155s   javascript-common libamd3 libasan8 libbibtex-parser-perl libblas-dev
155s   libblas3 libboost-dev libboost1.90-dev libbz2-dev libc-dev-bin libc6-dev
155s   libcairo2 libcc1-0 libcolamd3 libcrypt-dev libdatrie1 libdeflate-dev
155s   libdeflate0 libfontconfig1 libgcc-15-dev libgfortran-15-dev libgfortran5
155s   libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libhwasan0 libice6
155s   libicu-dev libio-string-perl libisl23 libitm1 libjbig0 libjpeg-dev
155s   libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap
155s   libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
155s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
155s   libjs-lunr libjs-mathjax libjs-microplugin.js libjs-modernizr
155s   libjs-popper.js libjs-prettify libjs-sifter.js
155s   libjs-twitter-bootstrap-datepicker libkpathsea6 liblapack-dev liblapack3
155s   liblatex-tounicode-perl liblerc4 liblsan0 libltdl7 liblua5.4-0 liblzma-dev
155s   libmpc3 libmpfi0 libncurses-dev libpango-1.0-0 libpangocairo-1.0-0
155s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0
155s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev
155s   libpotrace0 libptexenc1 libquadmath0 libreadline-dev libsharpyuv0 libsm6
155s   libstdc++-15-dev libsuitesparseconfig7 libsynctex2 libtcl8.6 libteckit0
155s   libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev libtk8.6 libtsan2
155s   libubsan1 libwebp7 libxaw7 libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6
155s   libxpm4 libxrender1 libxss1 libxt6t64 libzstd-dev libzzip-0-13t64
155s   linux-libc-dev node-bootstrap-sass node-html5shiv node-normalize.css pandoc
155s   pandoc-data pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
155s   r-bioc-annotate r-bioc-annotationdbi r-bioc-biobase r-bioc-biocgenerics
155s   r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion r-bioc-biomformat
155s   r-bioc-biostrings r-bioc-delayedarray r-bioc-deseq2 r-bioc-genefilter
155s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicranges
155s   r-bioc-iranges r-bioc-keggrest r-bioc-limma r-bioc-matrixgenerics
155s   r-bioc-metagenomeseq r-bioc-multtest r-bioc-phyloseq r-bioc-s4arrays
155s   r-bioc-s4vectors r-bioc-sparsearray r-bioc-summarizedexperiment
155s   r-bioc-ucsc.utils r-bioc-wrench r-bioc-xvector r-bioc-zlibbioc r-cran-abind
155s   r-cran-ade4 r-cran-ape r-cran-askpass r-cran-base64enc r-cran-bh
155s   r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob
155s   r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem r-cran-callr
155s   r-cran-catools r-cran-cli r-cran-cluster r-cran-codetools r-cran-commonmark
155s   r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi
155s   r-cran-desc r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-farver
155s   r-cran-fastmap r-cran-fontawesome r-cran-foreach r-cran-formatr r-cran-fs
155s   r-cran-futile.logger r-cran-futile.options r-cran-gdata r-cran-ggplot2
155s   r-cran-glmnet r-cran-glue r-cran-gplots r-cran-gtable r-cran-gtools
155s   r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-igraph
155s   r-cran-isoband r-cran-iterators r-cran-jquerylib r-cran-jsonlite
155s   r-cran-kernsmooth r-cran-knitr r-cran-labeling r-cran-lambda.r r-cran-later
155s   r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-locfit r-cran-magrittr
155s   r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mgcv
155s   r-cran-mime r-cran-nlme r-cran-openssl r-cran-permute r-cran-pixmap
155s   r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload
155s   r-cran-plogr r-cran-plyr r-cran-png r-cran-praise r-cran-processx
155s   r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer
155s   r-cran-rcpp r-cran-rcpparmadillo r-cran-rcppeigen r-cran-reshape2
155s   r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite r-cran-s7
155s   r-cran-sass r-cran-scales r-cran-shape r-cran-shiny r-cran-snow
155s   r-cran-sourcetools r-cran-sp r-cran-statmod r-cran-stringi r-cran-stringr
155s   r-cran-survival r-cran-sys r-cran-testthat r-cran-tinytex r-cran-vctrs
155s   r-cran-vegan r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xfun
155s   r-cran-xml r-cran-xtable r-cran-yaml rpcsvc-proto t1utils tex-common
155s   texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base unzip
155s   x11-common xdg-utils zip zlib1g-dev
155s 0 upgraded, 312 newly installed, 0 to remove and 0 not upgraded.
155s Need to get 492 MB of archives.
155s After this operation, 1472 MB of additional disk space will be used.
155s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
155s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
155s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
155s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
155s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
155s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
155s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
155s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
155s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
155s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
155s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
155s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
155s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
155s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
156s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
156s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
156s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
156s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
156s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
156s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
156s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
156s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
156s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
156s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
156s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
156s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
156s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
157s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
157s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
157s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
157s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
157s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
157s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
157s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
157s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
157s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
157s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
157s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB]
157s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
157s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lmodern all 2.005-1build1 [4788 kB]
157s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
157s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
157s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
157s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
157s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
157s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
157s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
157s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
157s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B]
157s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [22.0 kB]
157s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.12.1+dfsg-1 [35.8 kB]
157s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-string-perl all 1.08-4 [11.1 kB]
157s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblatex-tounicode-perl all 1.93-1 [29.2 kB]
157s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB]
157s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
157s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
157s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB]
157s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B]
157s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
157s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
157s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
157s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
157s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
157s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
158s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [27.4 kB]
158s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
158s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
158s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
158s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB]
158s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB]
158s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
158s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
158s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
158s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
158s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
158s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
158s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
158s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
158s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
158s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
158s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
158s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB]
158s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
158s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB]
158s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
158s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
158s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
158s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
158s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
158s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B]
158s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
158s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB]
158s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB]
158s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
158s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB]
158s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5build1 [66.0 kB]
158s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
158s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
158s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
158s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
158s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpfi0 amd64 1.5.4+ds-4build1 [36.6 kB]
158s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
158s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
158s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
158s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
158s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
158s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
158s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
158s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
158s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
158s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
158s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
158s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
158s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
158s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
158s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
158s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpotrace0 amd64 1.16-2build2 [17.9 kB]
158s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 libptexenc1 amd64 2025.20250727.75242+ds-5build1 [46.4 kB]
158s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
158s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
158s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
158s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsynctex2 amd64 2025.20250727.75242+ds-5build1 [62.1 kB]
158s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
158s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 libteckit0 amd64 2.5.13+ds-1 [431 kB]
158s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5build1 [125 kB]
158s Get:126 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
158s Get:127 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
159s Get:128 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
159s Get:129 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
159s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
159s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
159s Get:132 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
159s Get:133 http://ftpmaster.internal/ubuntu resolute/main amd64 libxmu6 amd64 2:1.1.3-4 [48.9 kB]
159s Get:134 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB]
159s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 libxaw7 amd64 2:1.0.16-1build1 [190 kB]
159s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB]
159s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
159s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [30.1 kB]
159s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
159s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
159s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
159s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
159s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
159s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
159s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
159s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
159s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
160s Get:148 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
160s Get:149 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
160s Get:150 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
160s Get:151 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
160s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
160s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
160s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
160s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
160s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
160s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
160s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB]
160s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
160s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB]
160s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
160s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
160s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
160s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
160s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
160s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB]
160s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
160s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
160s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
160s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
160s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB]
160s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
160s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
160s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
160s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
160s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
160s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
160s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
160s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
160s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
160s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
160s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
160s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
160s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
160s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
161s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
161s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
161s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
161s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
161s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB]
161s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
161s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
161s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
161s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotate all 1.84.0+dfsg-2 [1870 kB]
161s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
161s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lambda.r all 1.2.4-2build2 [118 kB]
161s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.options all 1.0.1-3build2 [20.5 kB]
161s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.logger all 1.4.3-4build2 [98.4 kB]
161s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-snow all 1:0.4.4-2build1 [98.7 kB]
161s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB]
161s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
161s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
162s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
162s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
162s Get:205 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
162s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
162s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
162s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
162s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
162s Get:210 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
162s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
162s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB]
162s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
162s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB]
162s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
162s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
162s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
162s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB]
162s Get:219 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB]
162s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB]
162s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
162s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
162s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
162s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
162s Get:225 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
162s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
162s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
162s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
162s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
162s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
162s Get:231 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
162s Get:232 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB]
163s Get:233 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bookdown all 0.42+dfsg-1 [1409 kB]
163s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB]
163s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 tex-common all 6.20 [30.0 kB]
163s Get:236 http://ftpmaster.internal/ubuntu resolute/main amd64 t1utils amd64 1.41-4build4 [62.7 kB]
163s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-binaries amd64 2025.20250727.75242+ds-5build1 [8747 kB]
163s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-base all 2025.20260124-1 [22.8 MB]
163s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-base all 2025.20260124-1 [1321 kB]
164s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-bibtex-extra all 2025.20260124-1 [80.6 MB]
166s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocversion all 3.20.0-2 [11.1 kB]
166s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB]
166s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plyr amd64 1.8.9-1 [832 kB]
166s Get:244 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB]
166s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
166s Get:246 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biomformat all 1.34.0+dfsg-2 [229 kB]
166s Get:247 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
167s Get:248 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
167s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB]
167s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
167s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1391 kB]
167s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
167s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
167s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
167s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-locfit amd64 1.5-9.12-1 [552 kB]
167s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB]
167s Get:257 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB]
167s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB]
167s Get:259 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB]
167s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB]
167s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
167s Get:262 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB]
167s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB]
167s Get:264 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB]
167s Get:265 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpparmadillo amd64 15.2.3-1-1 [919 kB]
167s Get:266 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-deseq2 amd64 1.46.0+dfsg-2 [1250 kB]
168s Get:267 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-survival amd64 3.8-6-1 [8274 kB]
168s Get:268 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genefilter amd64 1.88.0-2 [1243 kB]
168s Get:269 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-statmod amd64 1.5.0-1 [295 kB]
168s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-limma amd64 3.62.2+dfsg-1 [1969 kB]
168s Get:271 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-iterators all 1.0.14-1build1 [336 kB]
168s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-foreach all 1.5.2-1build1 [124 kB]
168s Get:273 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shape all 1.4.6.1-1 [749 kB]
168s Get:274 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB]
168s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glmnet amd64 4.1-8-1 [1926 kB]
169s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtools amd64 3.9.5-1build1 [345 kB]
169s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
169s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-catools amd64 1.18.3-1 [209 kB]
169s Get:279 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
169s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-kernsmooth amd64 2.23-26-1build1 [93.6 kB]
169s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gdata all 3.0.1-1build1 [491 kB]
169s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gplots all 3.3.0-1 [3825 kB]
170s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-wrench all 1.24.0+dfsg-2 [59.4 kB]
170s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-metagenomeseq all 1.48.1-1 [2142 kB]
170s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-multtest amd64 2.62.0-2 [844 kB]
170s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pixmap all 0.4-14-1 [217 kB]
170s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sp amd64 1:2.2-0+dfsg-1 [1444 kB]
170s Get:288 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ade4 amd64 1.7-23-1 [5414 kB]
171s Get:289 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB]
171s Get:290 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ape amd64 5.8-1-1 [2918 kB]
171s Get:291 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cluster amd64 2.1.8.2-1 [570 kB]
171s Get:292 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB]
171s Get:293 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-igraph amd64 2.1.4-1build1 [5218 kB]
171s Get:294 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB]
171s Get:295 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
171s Get:296 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-reshape2 amd64 1.4.4-2build2 [123 kB]
171s Get:297 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-permute all 0.9-8-1 [237 kB]
171s Get:298 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-4-1 [3556 kB]
172s Get:299 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vegan amd64 2.6-10+dfsg-3 [3137 kB]
172s Get:300 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-phyloseq all 1.50.0+dfsg-2 [2205 kB]
172s Get:301 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB]
172s Get:302 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
172s Get:303 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
172s Get:304 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
172s Get:305 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
172s Get:306 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diffobj amd64 0.3.5-1build1 [1156 kB]
172s Get:307 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgbuild all 1.4.8-1 [219 kB]
172s Get:308 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rprojroot all 2.1.1-1 [131 kB]
172s Get:309 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgload all 1.4.1-1 [252 kB]
172s Get:310 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-praise all 1.0.0-4build2 [20.9 kB]
172s Get:311 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-waldo all 0.6.2-1 [153 kB]
172s Get:312 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB]
172s Preconfiguring packages ...
172s Fetched 492 MB in 17s (29.1 MB/s)
172s Selecting previously unselected package libc-dev-bin.
173s (Reading database ... 
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(Reading database ... 125269 files and directories currently installed.)
173s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
173s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
173s Selecting previously unselected package linux-libc-dev:amd64.
173s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
173s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
173s Selecting previously unselected package libcrypt-dev:amd64.
173s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
173s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
173s Selecting previously unselected package rpcsvc-proto.
173s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
173s Unpacking rpcsvc-proto (1.4.3-1build1) ...
173s Selecting previously unselected package libc6-dev:amd64.
173s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
173s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
173s Selecting previously unselected package libisl23:amd64.
173s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
173s Unpacking libisl23:amd64 (0.27-1build1) ...
173s Selecting previously unselected package libmpc3:amd64.
173s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
173s Unpacking libmpc3:amd64 (1.3.1-2) ...
173s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
173s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package cpp-15.
173s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package cpp-x86-64-linux-gnu.
173s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package cpp.
173s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
173s Unpacking cpp (4:15.2.0-4ubuntu1) ...
173s Selecting previously unselected package libcc1-0:amd64.
173s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libgomp1:amd64.
173s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libitm1:amd64.
173s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libasan8:amd64.
173s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package liblsan0:amd64.
173s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libtsan2:amd64.
173s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libubsan1:amd64.
173s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libhwasan0:amd64.
173s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libquadmath0:amd64.
173s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ...
173s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ...
173s Selecting previously unselected package libgcc-15-dev:amd64.
173s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ...
173s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
173s Selecting previously unselected package gcc-15-x86-64-linux-gnu.
173s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
173s 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) ...
174s Selecting previously unselected package g++-15-x86-64-linux-gnu.
174s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
174s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
174s Selecting previously unselected package g++-15.
174s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ...
174s Unpacking g++-15 (15.2.0-12ubuntu1) ...
174s Selecting previously unselected package g++-x86-64-linux-gnu.
174s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
174s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
174s Selecting previously unselected package g++.
174s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ...
174s Unpacking g++ (4:15.2.0-4ubuntu1) ...
174s Selecting previously unselected package build-essential.
174s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ...
174s Unpacking build-essential (12.12ubuntu2) ...
174s Selecting previously unselected package dctrl-tools.
174s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ...
174s Unpacking dctrl-tools (2.24-3build4) ...
174s Selecting previously unselected package fonts-dejavu-mono.
174s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ...
174s Unpacking fonts-dejavu-mono (2.37-8build1) ...
174s Selecting previously unselected package fonts-dejavu-core.
174s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ...
174s Unpacking fonts-dejavu-core (2.37-8build1) ...
174s Selecting previously unselected package fontconfig-config.
174s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ...
174s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
174s Selecting previously unselected package libfontconfig1:amd64.
174s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ...
174s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
174s Selecting previously unselected package fontconfig.
174s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ...
174s Unpacking fontconfig (2.17.1-3ubuntu1) ...
174s Selecting previously unselected package fonts-font-awesome.
174s Preparing to unpack .../037-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ...
174s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ...
174s Selecting previously unselected package fonts-glyphicons-halflings.
174s Preparing to unpack .../038-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ...
174s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
174s Selecting previously unselected package fonts-lmodern.
174s Preparing to unpack .../039-fonts-lmodern_2.005-1build1_all.deb ...
174s Unpacking fonts-lmodern (2.005-1build1) ...
174s Selecting previously unselected package fonts-mathjax.
174s Preparing to unpack .../040-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
174s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ...
174s Selecting previously unselected package libgfortran5:amd64.
174s Preparing to unpack .../041-libgfortran5_16-20260208-1ubuntu1_amd64.deb ...
174s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ...
174s Selecting previously unselected package libgfortran-15-dev:amd64.
174s Preparing to unpack .../042-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ...
174s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ...
174s Selecting previously unselected package gfortran-15-x86-64-linux-gnu.
174s Preparing to unpack .../043-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
174s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
174s Selecting previously unselected package gfortran-15.
174s Preparing to unpack .../044-gfortran-15_15.2.0-12ubuntu1_amd64.deb ...
174s Unpacking gfortran-15 (15.2.0-12ubuntu1) ...
174s Selecting previously unselected package gfortran-x86-64-linux-gnu.
174s Preparing to unpack .../045-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
174s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
174s Selecting previously unselected package gfortran.
174s Preparing to unpack .../046-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ...
174s Unpacking gfortran (4:15.2.0-4ubuntu1) ...
174s Selecting previously unselected package icu-devtools.
174s Preparing to unpack .../047-icu-devtools_78.2-1ubuntu1_amd64.deb ...
174s Unpacking icu-devtools (78.2-1ubuntu1) ...
174s Selecting previously unselected package javascript-common.
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174s Selecting previously unselected package libblas3:amd64.
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175s Selecting previously unselected package libboost1.90-dev:amd64.
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176s Selecting previously unselected package libjs-jquery.
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176s Selecting previously unselected package libjs-jquery-datatables.
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176s Selecting previously unselected package libjs-sifter.js.
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176s Selecting previously unselected package libjs-microplugin.js.
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176s Selecting previously unselected package libjs-jquery-selectize.js.
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176s Selecting previously unselected package libjs-prettify.
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176s Selecting previously unselected package libkpathsea6:amd64.
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176s Selecting previously unselected package liblapack3:amd64.
176s Preparing to unpack .../096-liblapack3_3.12.1-7ubuntu1_amd64.deb ...
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176s Selecting previously unselected package liblapack-dev:amd64.
176s Preparing to unpack .../097-liblapack-dev_3.12.1-7ubuntu1_amd64.deb ...
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176s Selecting previously unselected package liblerc4:amd64.
176s Preparing to unpack .../098-liblerc4_4.0.0+ds-5ubuntu2_amd64.deb ...
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176s Selecting previously unselected package liblua5.4-0:amd64.
176s Preparing to unpack .../099-liblua5.4-0_5.4.8-1_amd64.deb ...
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176s Selecting previously unselected package libmpfi0:amd64.
176s Preparing to unpack .../100-libmpfi0_1.5.4+ds-4build1_amd64.deb ...
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176s Selecting previously unselected package libncurses-dev:amd64.
176s Preparing to unpack .../101-libncurses-dev_6.6+20251231-1_amd64.deb ...
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176s Selecting previously unselected package libthai-data.
177s Preparing to unpack .../102-libthai-data_0.1.30-1_all.deb ...
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177s Selecting previously unselected package libthai0:amd64.
177s Preparing to unpack .../103-libthai0_0.1.30-1_amd64.deb ...
177s Unpacking libthai0:amd64 (0.1.30-1) ...
177s Selecting previously unselected package libpango-1.0-0:amd64.
177s Preparing to unpack .../104-libpango-1.0-0_1.57.0-1_amd64.deb ...
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177s Selecting previously unselected package libpangoft2-1.0-0:amd64.
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177s Selecting previously unselected package libpangocairo-1.0-0:amd64.
177s Preparing to unpack .../106-libpangocairo-1.0-0_1.57.0-1_amd64.deb ...
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177s Selecting previously unselected package libpaper2:amd64.
177s Preparing to unpack .../107-libpaper2_2.2.5-0.3build1_amd64.deb ...
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177s Selecting previously unselected package libpaper-utils.
177s Preparing to unpack .../108-libpaper-utils_2.2.5-0.3build1_amd64.deb ...
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177s Selecting previously unselected package libpcre2-16-0:amd64.
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177s Selecting previously unselected package libpcre2-dev:amd64.
177s Preparing to unpack .../112-libpcre2-dev_10.46-1_amd64.deb ...
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177s Selecting previously unselected package libpkgconf3:amd64.
177s Preparing to unpack .../113-libpkgconf3_1.8.1-4build1_amd64.deb ...
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177s Selecting previously unselected package zlib1g-dev:amd64.
177s Preparing to unpack .../114-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_amd64.deb ...
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177s Selecting previously unselected package libpng-dev:amd64.
177s Preparing to unpack .../115-libpng-dev_1.6.54-1_amd64.deb ...
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177s Selecting previously unselected package libpotrace0:amd64.
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177s Selecting previously unselected package libptexenc1:amd64.
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177s Selecting previously unselected package libreadline-dev:amd64.
177s Preparing to unpack .../118-libreadline-dev_8.3-3_amd64.deb ...
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177s Selecting previously unselected package libsharpyuv0:amd64.
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177s Selecting previously unselected package libsm6:amd64.
177s Preparing to unpack .../120-libsm6_2%3a1.2.6-1build1_amd64.deb ...
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177s Selecting previously unselected package libsynctex2:amd64.
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177s Selecting previously unselected package libtcl8.6:amd64.
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177s Selecting previously unselected package libteckit0:amd64.
177s Preparing to unpack .../123-libteckit0_2.5.13+ds-1_amd64.deb ...
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177s Selecting previously unselected package libtexlua53-5:amd64.
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177s Selecting previously unselected package libjbig0:amd64.
177s Preparing to unpack .../125-libjbig0_2.1-6.1ubuntu3_amd64.deb ...
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177s Selecting previously unselected package libwebp7:amd64.
177s Preparing to unpack .../126-libwebp7_1.5.0-0.1build1_amd64.deb ...
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177s Selecting previously unselected package libtiff6:amd64.
177s Preparing to unpack .../127-libtiff6_4.7.0-3ubuntu3_amd64.deb ...
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177s Selecting previously unselected package libxft2:amd64.
177s Preparing to unpack .../128-libxft2_2.3.6-1build2_amd64.deb ...
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177s Selecting previously unselected package libxss1:amd64.
177s Preparing to unpack .../129-libxss1_1%3a1.2.3-1build4_amd64.deb ...
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177s Selecting previously unselected package libtk8.6:amd64.
177s Preparing to unpack .../130-libtk8.6_8.6.17-1_amd64.deb ...
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177s Selecting previously unselected package libxt6t64:amd64.
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177s Selecting previously unselected package libxmu6:amd64.
177s Preparing to unpack .../132-libxmu6_2%3a1.1.3-4_amd64.deb ...
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177s Selecting previously unselected package libxpm4:amd64.
177s Preparing to unpack .../133-libxpm4_1%3a3.5.17-1build3_amd64.deb ...
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177s Selecting previously unselected package libxaw7:amd64.
177s Preparing to unpack .../134-libxaw7_2%3a1.0.16-1build1_amd64.deb ...
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177s Selecting previously unselected package libxi6:amd64.
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177s Selecting previously unselected package libzstd-dev:amd64.
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177s Selecting previously unselected package libzzip-0-13t64:amd64.
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177s Unpacking libzzip-0-13t64:amd64 (0.13.78+dfsg.1-0.2) ...
177s Selecting previously unselected package node-bootstrap-sass.
177s Preparing to unpack .../138-node-bootstrap-sass_3.4.3-2_all.deb ...
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177s Selecting previously unselected package node-html5shiv.
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177s Selecting previously unselected package node-normalize.css.
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177s Selecting previously unselected package pandoc-data.
177s Preparing to unpack .../141-pandoc-data_3.1.11.1-3build1_all.deb ...
177s Unpacking pandoc-data (3.1.11.1-3build1) ...
177s Selecting previously unselected package pandoc.
177s Preparing to unpack .../142-pandoc_3.1.11.1+ds-4_amd64.deb ...
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178s Preparing to unpack .../144-unzip_6.0-29ubuntu1_amd64.deb ...
178s Unpacking unzip (6.0-29ubuntu1) ...
178s Selecting previously unselected package xdg-utils.
178s Preparing to unpack .../145-xdg-utils_1.2.1-2ubuntu2_all.deb ...
178s Unpacking xdg-utils (1.2.1-2ubuntu2) ...
178s Selecting previously unselected package r-base-core.
178s Preparing to unpack .../146-r-base-core_4.5.2-1ubuntu2_amd64.deb ...
178s Unpacking r-base-core (4.5.2-1ubuntu2) ...
178s Selecting previously unselected package liblzma-dev:amd64.
178s Preparing to unpack .../147-liblzma-dev_5.8.2-2_amd64.deb ...
178s Unpacking liblzma-dev:amd64 (5.8.2-2) ...
178s Selecting previously unselected package pkgconf-bin.
178s Preparing to unpack .../148-pkgconf-bin_1.8.1-4build1_amd64.deb ...
178s Unpacking pkgconf-bin (1.8.1-4build1) ...
178s Selecting previously unselected package pkgconf:amd64.
178s Preparing to unpack .../149-pkgconf_1.8.1-4build1_amd64.deb ...
178s Unpacking pkgconf:amd64 (1.8.1-4build1) ...
178s Selecting previously unselected package libtirpc-dev:amd64.
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178s Unpacking libtirpc-dev:amd64 (1.3.6+ds-1) ...
178s Selecting previously unselected package r-base-dev.
178s Preparing to unpack .../151-r-base-dev_4.5.2-1ubuntu2_all.deb ...
178s Unpacking r-base-dev (4.5.2-1ubuntu2) ...
178s Selecting previously unselected package pkg-r-autopkgtest.
178s Preparing to unpack .../152-pkg-r-autopkgtest_20250812_all.deb ...
178s Unpacking pkg-r-autopkgtest (20250812) ...
178s Selecting previously unselected package r-bioc-biocgenerics.
178s Preparing to unpack .../153-r-bioc-biocgenerics_0.52.0-2_all.deb ...
178s Unpacking r-bioc-biocgenerics (0.52.0-2) ...
178s Selecting previously unselected package r-bioc-biobase.
178s Preparing to unpack .../154-r-bioc-biobase_2.66.0-2_amd64.deb ...
178s Unpacking r-bioc-biobase (2.66.0-2) ...
178s Selecting previously unselected package r-bioc-s4vectors.
178s Preparing to unpack .../155-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ...
178s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ...
178s Selecting previously unselected package r-bioc-iranges.
178s Preparing to unpack .../156-r-bioc-iranges_2.40.1-3_amd64.deb ...
178s Unpacking r-bioc-iranges (2.40.1-3) ...
178s Selecting previously unselected package r-cran-dbi.
178s Preparing to unpack .../157-r-cran-dbi_1.2.3-1build1_all.deb ...
178s Unpacking r-cran-dbi (1.2.3-1build1) ...
178s Selecting previously unselected package r-cran-bit.
178s Preparing to unpack .../158-r-cran-bit_4.6.0+dfsg-1_amd64.deb ...
178s Unpacking r-cran-bit (4.6.0+dfsg-1) ...
178s Selecting previously unselected package r-cran-bit64.
178s Preparing to unpack .../159-r-cran-bit64_4.6.0-1-4_amd64.deb ...
178s Unpacking r-cran-bit64 (4.6.0-1-4) ...
178s Selecting previously unselected package r-cran-rlang.
178s Preparing to unpack .../160-r-cran-rlang_1.1.5-3_amd64.deb ...
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178s Selecting previously unselected package r-cran-cli.
178s Preparing to unpack .../161-r-cran-cli_3.6.4-1_amd64.deb ...
178s Unpacking r-cran-cli (3.6.4-1) ...
178s Selecting previously unselected package r-cran-glue.
178s Preparing to unpack .../162-r-cran-glue_1.8.0-1_amd64.deb ...
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178s Selecting previously unselected package r-cran-lifecycle.
178s Preparing to unpack .../163-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ...
178s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ...
178s Selecting previously unselected package r-cran-vctrs.
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178s Selecting previously unselected package r-cran-blob.
178s Preparing to unpack .../165-r-cran-blob_1.3.0-1_all.deb ...
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178s Selecting previously unselected package r-cran-fastmap.
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178s Selecting previously unselected package r-cran-cachem.
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178s Selecting previously unselected package r-cran-memoise.
178s Preparing to unpack .../168-r-cran-memoise_2.0.1-1build1_all.deb ...
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178s Selecting previously unselected package r-cran-pkgconfig.
178s Preparing to unpack .../169-r-cran-pkgconfig_2.0.3-2build2_all.deb ...
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179s Selecting previously unselected package r-cran-plogr.
179s Preparing to unpack .../170-r-cran-plogr_0.2.0-3build2_all.deb ...
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179s Selecting previously unselected package r-cran-cpp11.
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179s Selecting previously unselected package r-cran-rsqlite.
179s Preparing to unpack .../172-r-cran-rsqlite_2.3.9-1_amd64.deb ...
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179s Selecting previously unselected package r-cran-curl.
179s Preparing to unpack .../173-r-cran-curl_7.0.0+dfsg-1_amd64.deb ...
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179s Selecting previously unselected package r-cran-jsonlite.
179s Preparing to unpack .../174-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ...
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179s Selecting previously unselected package r-cran-mime.
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179s Selecting previously unselected package r-cran-sys.
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179s Selecting previously unselected package r-cran-askpass.
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179s Selecting previously unselected package r-cran-openssl.
179s Preparing to unpack .../178-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ...
179s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
179s Selecting previously unselected package r-cran-r6.
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179s Selecting previously unselected package r-cran-httr.
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179s Selecting previously unselected package r-cran-png.
179s Preparing to unpack .../181-r-cran-png_0.1-8-1build2_amd64.deb ...
179s Unpacking r-cran-png (0.1-8-1build2) ...
179s Selecting previously unselected package r-bioc-zlibbioc.
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179s Selecting previously unselected package r-bioc-xvector.
179s Preparing to unpack .../183-r-bioc-xvector_0.46.0-2_amd64.deb ...
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179s Selecting previously unselected package r-bioc-ucsc.utils.
179s Preparing to unpack .../184-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ...
179s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ...
179s Selecting previously unselected package r-bioc-genomeinfodbdata.
179s Preparing to unpack .../185-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ...
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179s Selecting previously unselected package r-bioc-genomeinfodb.
179s Preparing to unpack .../186-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ...
179s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
179s Selecting previously unselected package r-cran-crayon.
179s Preparing to unpack .../187-r-cran-crayon_1.5.3-1_all.deb ...
179s Unpacking r-cran-crayon (1.5.3-1) ...
179s Selecting previously unselected package r-bioc-biostrings.
179s Preparing to unpack .../188-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ...
179s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ...
179s Selecting previously unselected package r-bioc-keggrest.
179s Preparing to unpack .../189-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ...
179s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ...
179s Selecting previously unselected package r-bioc-annotationdbi.
179s Preparing to unpack .../190-r-bioc-annotationdbi_1.68.0-2_all.deb ...
179s Unpacking r-bioc-annotationdbi (1.68.0-2) ...
179s Selecting previously unselected package r-cran-xml.
179s Preparing to unpack .../191-r-cran-xml_3.99-0.20-1_amd64.deb ...
179s Unpacking r-cran-xml (3.99-0.20-1) ...
179s Selecting previously unselected package r-cran-xtable.
179s Preparing to unpack .../192-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-bioc-annotate.
179s Preparing to unpack .../193-r-bioc-annotate_1.84.0+dfsg-2_all.deb ...
179s Unpacking r-bioc-annotate (1.84.0+dfsg-2) ...
179s Selecting previously unselected package r-cran-formatr.
179s Preparing to unpack .../194-r-cran-formatr_1.14-2_all.deb ...
179s Unpacking r-cran-formatr (1.14-2) ...
179s Selecting previously unselected package r-cran-lambda.r.
179s Preparing to unpack .../195-r-cran-lambda.r_1.2.4-2build2_all.deb ...
179s Unpacking r-cran-lambda.r (1.2.4-2build2) ...
179s Selecting previously unselected package r-cran-futile.options.
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179s Unpacking r-cran-futile.options (1.0.1-3build2) ...
179s Selecting previously unselected package r-cran-futile.logger.
179s Preparing to unpack .../197-r-cran-futile.logger_1.4.3-4build2_all.deb ...
179s Unpacking r-cran-futile.logger (1.4.3-4build2) ...
179s Selecting previously unselected package r-cran-snow.
179s Preparing to unpack .../198-r-cran-snow_1%3a0.4.4-2build1_all.deb ...
179s Unpacking r-cran-snow (1:0.4.4-2build1) ...
179s Selecting previously unselected package r-cran-codetools.
179s Preparing to unpack .../199-r-cran-codetools_0.2-20-1build1_all.deb ...
179s Unpacking r-cran-codetools (0.2-20-1build1) ...
179s Selecting previously unselected package r-cran-bh.
179s Preparing to unpack .../200-r-cran-bh_1.84.0-1_all.deb ...
179s Unpacking r-cran-bh (1.84.0-1) ...
179s Selecting previously unselected package r-bioc-biocparallel.
179s Preparing to unpack .../201-r-bioc-biocparallel_1.40.0-2_amd64.deb ...
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179s Selecting previously unselected package r-cran-base64enc.
179s Preparing to unpack .../202-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 .../203-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 .../204-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.
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179s Unpacking r-cran-evaluate (1.0.5-1) ...
179s Selecting previously unselected package r-cran-xfun.
179s Preparing to unpack .../206-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 .../207-r-cran-highr_0.11+dfsg-1_all.deb ...
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179s Selecting previously unselected package r-cran-yaml.
179s Preparing to unpack .../208-r-cran-yaml_2.3.10-1_amd64.deb ...
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179s Selecting previously unselected package libjs-mathjax.
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180s Selecting previously unselected package r-cran-knitr.
180s Preparing to unpack .../210-r-cran-knitr_1.51+dfsg-1_all.deb ...
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180s Selecting previously unselected package r-cran-jquerylib.
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180s Selecting previously unselected package r-cran-fs.
180s Preparing to unpack .../212-r-cran-fs_1.6.5+dfsg-1_amd64.deb ...
180s Unpacking r-cran-fs (1.6.5+dfsg-1) ...
180s Selecting previously unselected package r-cran-rappdirs.
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180s Unpacking r-cran-rappdirs (0.3.3-1build1) ...
180s Selecting previously unselected package r-cran-sass.
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180s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
180s Selecting previously unselected package r-cran-bslib.
180s Preparing to unpack .../215-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ...
180s Unpacking r-cran-bslib (0.9.0+dfsg-3build1) ...
180s Selecting previously unselected package r-cran-fontawesome.
180s Preparing to unpack .../216-r-cran-fontawesome_0.5.3-1_all.deb ...
180s Unpacking r-cran-fontawesome (0.5.3-1) ...
180s Selecting previously unselected package r-cran-tinytex.
180s Preparing to unpack .../217-r-cran-tinytex_0.58-1_all.deb ...
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180s Selecting previously unselected package libjs-modernizr.
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180s Selecting previously unselected package r-cran-littler.
180s Preparing to unpack .../219-r-cran-littler_0.3.22-1_amd64.deb ...
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180s Selecting previously unselected package r-cran-pkgkitten.
180s Preparing to unpack .../220-r-cran-pkgkitten_0.2.4-1_all.deb ...
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180s Selecting previously unselected package r-cran-rcpp.
180s Preparing to unpack .../221-r-cran-rcpp_1.1.0-1_amd64.deb ...
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180s Selecting previously unselected package r-cran-later.
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180s Selecting previously unselected package r-cran-magrittr.
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180s Selecting previously unselected package r-cran-promises.
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180s Selecting previously unselected package r-cran-httpuv.
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180s Selecting previously unselected package r-cran-sourcetools.
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180s Selecting previously unselected package r-cran-withr.
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180s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
180s Selecting previously unselected package r-cran-commonmark.
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180s Unpacking r-cran-commonmark (1.9.5-1) ...
180s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
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180s Selecting previously unselected package r-cran-shiny.
180s Preparing to unpack .../230-r-cran-shiny_1.10.0+dfsg-2_all.deb ...
180s Unpacking r-cran-shiny (1.10.0+dfsg-2) ...
180s Selecting previously unselected package r-cran-rmarkdown.
180s Preparing to unpack .../231-r-cran-rmarkdown_2.30+dfsg-1_all.deb ...
180s Unpacking r-cran-rmarkdown (2.30+dfsg-1) ...
180s Selecting previously unselected package r-cran-bookdown.
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180s Unpacking r-cran-bookdown (0.42+dfsg-1) ...
180s Selecting previously unselected package r-cran-biocmanager.
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180s Selecting previously unselected package tex-common.
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180s Selecting previously unselected package t1utils.
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180s Unpacking t1utils (1.41-4build4) ...
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182s Selecting previously unselected package r-bioc-biocversion.
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182s Selecting previously unselected package r-bioc-biocstyle.
182s Preparing to unpack .../241-r-bioc-biocstyle_2.34.0+dfsg-1_all.deb ...
182s Unpacking r-bioc-biocstyle (2.34.0+dfsg-1) ...
182s Selecting previously unselected package r-cran-plyr.
182s Preparing to unpack .../242-r-cran-plyr_1.8.9-1_amd64.deb ...
182s Unpacking r-cran-plyr (1.8.9-1) ...
182s Selecting previously unselected package r-cran-lattice.
182s Preparing to unpack .../243-r-cran-lattice_0.22-7-1_amd64.deb ...
182s Unpacking r-cran-lattice (0.22-7-1) ...
182s Selecting previously unselected package r-cran-matrix.
182s Preparing to unpack .../244-r-cran-matrix_1.7-4-1_amd64.deb ...
182s Unpacking r-cran-matrix (1.7-4-1) ...
182s Selecting previously unselected package r-bioc-biomformat.
182s Preparing to unpack .../245-r-bioc-biomformat_1.34.0+dfsg-2_all.deb ...
182s Unpacking r-bioc-biomformat (1.34.0+dfsg-2) ...
182s Selecting previously unselected package r-cran-matrixstats.
182s Preparing to unpack .../246-r-cran-matrixstats_1.5.0-1_amd64.deb ...
182s Unpacking r-cran-matrixstats (1.5.0-1) ...
182s Selecting previously unselected package r-bioc-matrixgenerics.
182s Preparing to unpack .../247-r-bioc-matrixgenerics_1.18.1-1_all.deb ...
182s Unpacking r-bioc-matrixgenerics (1.18.1-1) ...
182s Selecting previously unselected package r-cran-abind.
182s Preparing to unpack .../248-r-cran-abind_1.4-8-1build1_all.deb ...
182s Unpacking r-cran-abind (1.4-8-1build1) ...
182s Selecting previously unselected package r-bioc-s4arrays.
182s Preparing to unpack .../249-r-bioc-s4arrays_1.6.0+dfsg-2_amd64.deb ...
182s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ...
182s Selecting previously unselected package r-bioc-sparsearray.
182s Preparing to unpack .../250-r-bioc-sparsearray_1.6.2+dfsg-2_amd64.deb ...
182s Unpacking r-bioc-sparsearray (1.6.2+dfsg-2) ...
182s Selecting previously unselected package r-bioc-delayedarray.
182s Preparing to unpack .../251-r-bioc-delayedarray_0.32.0+dfsg-2_amd64.deb ...
182s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ...
182s Selecting previously unselected package r-bioc-genomicranges.
182s Preparing to unpack .../252-r-bioc-genomicranges_1.58.0+dfsg-2_amd64.deb ...
182s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ...
182s Selecting previously unselected package r-bioc-summarizedexperiment.
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182s Selecting previously unselected package r-cran-locfit.
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187s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
187s Setting up libcairo2:amd64 (1.18.4-3) ...
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187s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
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187s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ...
187s Setting up cpp (4:15.2.0-4ubuntu1) ...
187s Setting up libboost1.90-dev:amd64 (1.90.0-2ubuntu1) ...
187s Setting up libboost-dev:amd64 (1.90.0.0ubuntu3) ...
187s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ...
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187s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ...
187s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
187s Setting up libxmu6:amd64 (2:1.1.3-4) ...
187s Setting up libpng-dev:amd64 (1.6.54-1) ...
187s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ...
187s Setting up libxaw7:amd64 (2:1.0.16-1build1) ...
187s Setting up gcc (4:15.2.0-4ubuntu1) ...
187s Setting up r-base-core (4.5.2-1ubuntu2) ...
187s Creating config file /etc/R/Renviron with new version
187s Setting up r-cran-crayon (1.5.3-1) ...
187s Setting up r-cran-labeling (0.4.3-1) ...
187s Setting up r-cran-sourcetools (0.1.7-1-1) ...
187s Setting up r-cran-futile.options (1.0.1-3build2) ...
187s Setting up r-cran-lattice (0.22-7-1) ...
187s Setting up r-cran-ps (1.9.0-1) ...
187s Setting up r-cran-nlme (3.1.168-1) ...
187s Setting up r-cran-farver (2.1.2-1) ...
187s Setting up r-cran-formatr (1.14-2) ...
187s Setting up r-cran-xml (3.99-0.20-1) ...
187s Setting up r-cran-viridislite (0.4.3-1) ...
187s Setting up r-cran-locfit (1.5-9.12-1) ...
187s Setting up texlive-binaries (2025.20250727.75242+ds-5build1) ...
187s update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
187s update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
187s Setting up r-cran-pixmap (0.4-14-1) ...
187s Setting up r-cran-cluster (2.1.8.2-1) ...
187s Setting up r-cran-statmod (1.5.0-1) ...
187s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
187s Setting up r-cran-commonmark (1.9.5-1) ...
187s Setting up r-cran-r6 (2.6.1-1) ...
187s Setting up r-cran-pkgkitten (0.2.4-1) ...
187s 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
187s tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
188s tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
188s tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
188s Setting up g++-15 (15.2.0-12ubuntu1) ...
188s Setting up r-cran-magrittr (2.0.3-1) ...
188s Setting up r-cran-rappdirs (0.3.3-1build1) ...
188s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
188s Setting up r-cran-littler (0.3.22-1) ...
188s Setting up r-cran-permute (0.9-8-1) ...
188s Setting up r-cran-bh (1.84.0-1) ...
188s Setting up r-cran-fs (1.6.5+dfsg-1) ...
188s Setting up r-cran-rcpp (1.1.0-1) ...
188s Setting up r-cran-curl (7.0.0+dfsg-1) ...
188s Setting up r-cran-codetools (0.2-20-1build1) ...
188s Setting up r-cran-brio (1.1.5-1) ...
188s Setting up r-cran-diffobj (0.3.5-1build1) ...
188s Setting up r-bioc-biocgenerics (0.52.0-2) ...
188s Setting up r-cran-rlang (1.1.5-3) ...
188s Setting up r-cran-matrixstats (1.5.0-1) ...
188s Setting up r-bioc-matrixgenerics (1.18.1-1) ...
188s Setting up r-cran-xfun (0.55+dfsg-1) ...
188s Setting up r-cran-sys (3.4.3-1) ...
188s Setting up r-cran-plogr (0.2.0-3build2) ...
188s Setting up r-cran-withr (3.0.2+dfsg-1) ...
188s Setting up r-cran-processx (3.8.6-1) ...
188s Setting up r-cran-mime (0.12-2) ...
188s Setting up r-cran-praise (1.0.0-4build2) ...
188s Setting up r-cran-base64enc (0.1-3-3build1) ...
188s Setting up r-cran-iterators (1.0.14-1build1) ...
188s Setting up r-cran-abind (1.4-8-1build1) ...
188s Setting up r-cran-digest (0.6.39-1) ...
188s Setting up r-cran-ape (5.8-1-1) ...
188s Setting up r-cran-yaml (2.3.10-1) ...
188s Setting up r-cran-lambda.r (1.2.4-2build2) ...
188s Setting up r-cran-evaluate (1.0.5-1) ...
188s Setting up r-cran-dbi (1.2.3-1build1) ...
188s Setting up r-cran-highr (0.11+dfsg-1) ...
188s Setting up r-cran-foreach (1.5.2-1build1) ...
188s Setting up r-cran-mass (7.3-65-1) ...
188s Setting up r-cran-snow (1:0.4.4-2build1) ...
188s Setting up r-cran-gtools (3.9.5-1build1) ...
188s Setting up r-cran-data.table (1.17.0+dfsg-1) ...
188s Setting up r-cran-glue (1.8.0-1) ...
188s Setting up r-cran-bit (4.6.0+dfsg-1) ...
188s Setting up r-cran-xtable (1:1.8-4-2build1) ...
188s Setting up r-cran-cli (3.6.4-1) ...
188s Setting up gfortran (4:15.2.0-4ubuntu1) ...
188s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
188s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
188s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
188s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
188s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
188s Setting up r-cran-bitops (1.0-9-1) ...
188s Setting up r-bioc-biocversion (3.20.0-2) ...
188s Setting up r-cran-rprojroot (2.1.1-1) ...
188s Setting up r-cran-bit64 (4.6.0-1-4) ...
188s Setting up r-cran-biocmanager (1.30.25+dfsg-1) ...
188s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
188s Setting up r-cran-shape (1.4.6.1-1) ...
188s Setting up r-cran-askpass (1.2.1-1) ...
188s Setting up r-cran-fastmap (1.2.0-1) ...
188s Setting up r-cran-png (0.1-8-1build2) ...
188s Setting up r-bioc-biobase (2.66.0-2) ...
188s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
188s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
188s Setting up r-cran-sp (1:2.2-0+dfsg-1) ...
188s Setting up r-cran-stringi (1.8.4-1build2) ...
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188s Setting up r-cran-s7 (0.2.0-1) ...
188s Setting up r-cran-cpp11 (0.5.3-1) ...
188s Setting up r-cran-plyr (1.8.9-1) ...
188s Setting up r-cran-rcolorbrewer (1.1-3-1build2) ...
188s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
188s Setting up r-cran-isoband (0.2.7-1) ...
188s Setting up r-cran-futile.logger (1.4.3-4build2) ...
188s Setting up r-cran-waldo (0.6.2-1) ...
188s Setting up r-cran-scales (1.4.0-1) ...
188s Setting up r-bioc-limma (3.62.2+dfsg-1) ...
188s Setting up r-cran-gtable (0.3.6+dfsg-1) ...
188s Setting up r-cran-later (1.4.1+dfsg-1) ...
188s Setting up r-cran-matrix (1.7-4-1) ...
188s Setting up r-cran-htmltools (0.5.8.1-1) ...
188s Setting up r-cran-tinytex (0.58-1) ...
188s Setting up r-cran-kernsmooth (2.23-26-1build1) ...
188s Setting up r-cran-knitr (1.51+dfsg-1) ...
188s Setting up r-cran-mgcv (1.9-4-1) ...
188s Setting up g++ (4:15.2.0-4ubuntu1) ...
188s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
188s Setting up r-cran-cachem (1.1.0-1) ...
188s Setting up r-bioc-wrench (1.24.0+dfsg-2) ...
188s Setting up r-cran-sass (0.4.9+dfsg-1) ...
188s Setting up build-essential (12.12ubuntu2) ...
188s Setting up r-cran-catools (1.18.3-1) ...
188s Setting up r-cran-rcpparmadillo (15.2.3-1-1) ...
188s Setting up r-bioc-iranges (2.40.1-3) ...
188s Setting up r-cran-gdata (3.0.1-1build1) ...
188s Setting up r-cran-vctrs (0.6.5-1) ...
188s Setting up r-cran-rcppeigen (0.3.4.0.2-1) ...
188s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
188s Setting up r-base-dev (4.5.2-1ubuntu2) ...
188s Setting up r-bioc-s4arrays (1.6.0+dfsg-2) ...
188s Setting up r-cran-stringr (1.5.1-1) ...
188s Setting up r-bioc-biocparallel (1.40.0-2) ...
188s Setting up r-cran-callr (3.7.6-1) ...
188s Setting up r-cran-ggplot2 (4.0.2+dfsg-1) ...
188s Setting up r-bioc-biomformat (1.34.0+dfsg-2) ...
188s Setting up r-cran-desc (1.4.3-1) ...
188s Setting up r-cran-fontawesome (0.5.3-1) ...
188s Setting up r-cran-survival (3.8-6-1) ...
188s Setting up r-cran-igraph (2.1.4-1build1) ...
188s Setting up r-cran-ade4 (1.7-23-1) ...
188s Setting up r-cran-jquerylib (0.1.4+dfsg-5) ...
188s Setting up texlive-bibtex-extra (2025.20260124-1) ...
188s Setting up r-cran-reshape2 (1.4.4-2build2) ...
188s Setting up r-cran-httr (1.4.7+dfsg-1) ...
188s Setting up r-cran-memoise (2.0.1-1build1) ...
188s Setting up r-cran-promises (1.3.2+dfsg-1) ...
188s Setting up r-cran-vegan (2.6-10+dfsg-3) ...
188s Setting up r-cran-blob (1.3.0-1) ...
188s Setting up pkg-r-autopkgtest (20250812) ...
188s Setting up r-bioc-xvector (0.46.0-2) ...
188s Setting up r-cran-pkgbuild (1.4.8-1) ...
188s Setting up r-cran-gplots (3.3.0-1) ...
188s Setting up r-cran-rsqlite (2.3.9-1) ...
188s Setting up r-cran-glmnet (4.1-8-1) ...
188s Setting up r-bioc-multtest (2.62.0-2) ...
188s Setting up r-cran-pkgload (1.4.1-1) ...
188s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
188s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ...
188s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
188s Setting up r-bioc-metagenomeseq (1.48.1-1) ...
188s Setting up r-cran-testthat (3.2.3-1) ...
188s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
188s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
188s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
188s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
188s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
188s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
188s Setting up r-cran-rmarkdown (2.30+dfsg-1) ...
188s Setting up r-cran-bookdown (0.42+dfsg-1) ...
188s Setting up r-bioc-phyloseq (1.50.0+dfsg-2) ...
188s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
188s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ...
188s Setting up r-bioc-deseq2 (1.46.0+dfsg-2) ...
188s Setting up r-bioc-annotationdbi (1.68.0-2) ...
188s Setting up r-bioc-annotate (1.84.0+dfsg-2) ...
188s Setting up r-bioc-genefilter (1.88.0-2) ...
188s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ...
188s Processing triggers for libc-bin (2.42-2ubuntu4) ...
188s 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) ...
190s Running updmap-sys. This may take some time... done.
190s Running mktexlsr /var/lib/texmf ... done.
190s Building format(s) --all.
205s 	This may take some time... done.
205s autopkgtest [04:19:36]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
205s autopkgtest [04:19:36]: test pkg-r-autopkgtest: [-----------------------
206s Test: Try to load the R library phyloseq
206s 
206s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
206s Copyright (C) 2025 The R Foundation for Statistical Computing
206s Platform: x86_64-pc-linux-gnu
206s 
206s R is free software and comes with ABSOLUTELY NO WARRANTY.
206s You are welcome to redistribute it under certain conditions.
206s Type 'license()' or 'licence()' for distribution details.
206s 
206s R is a collaborative project with many contributors.
206s Type 'contributors()' for more information and
206s 'citation()' on how to cite R or R packages in publications.
206s 
206s Type 'demo()' for some demos, 'help()' for on-line help, or
206s 'help.start()' for an HTML browser interface to help.
206s Type 'q()' to quit R.
206s 
206s > library('phyloseq')
209s > 
209s Test: Run tests for phyloseq
209s Start: testthat-phyloseq.R
209s 
209s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
209s Copyright (C) 2025 The R Foundation for Statistical Computing
209s Platform: x86_64-pc-linux-gnu
209s 
209s R is free software and comes with ABSOLUTELY NO WARRANTY.
209s You are welcome to redistribute it under certain conditions.
209s Type 'license()' or 'licence()' for distribution details.
209s 
209s R is a collaborative project with many contributors.
209s Type 'contributors()' for more information and
209s 'citation()' on how to cite R or R packages in publications.
209s 
209s Type 'demo()' for some demos, 'help()' for on-line help, or
209s 'help.start()' for an HTML browser interface to help.
209s Type 'q()' to quit R.
209s 
209s > library("testthat")
209s > packageVersion("phyloseq")
209s [1] ‘1.50.0’
209s > # As suggested for opt-out option on testing by users, recommended by CRAN
209s > # http://adv-r.had.co.nz/Testing.html
209s > # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
209s > # library(testthat)
209s > # library(yourpackage)
209s > # test_package("yourpackage")
209s > # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
209s > # library(testthat)
209s > # test_check("yourpackage")
209s > # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
209s > test_check("phyloseq")
209s Loading required package: phyloseq
213s Processing otu/tax file...
213s Reading file into memory prior to parsing...
213s Detecting first header line...
213s Header is on line 2  
213s Converting input file to a table...
213s Defining OTU table... 
213s Parsing taxonomy table...
213s Processing phylogenetic tree...
213s  /usr/lib/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
216s Found biom-format file, now parsing it... 
216s Done parsing biom... 
216s Importing Sample Metdadata from mapping file...
216s Merging the imported objects... 
216s Successfully merged, phyloseq-class created. 
216s  Returning... 
216s Found biom-format file, now parsing it... 
216s Done parsing biom... 
216s Importing Sample Metdadata from mapping file...
216s Merging the imported objects... 
216s Successfully merged, phyloseq-class created. 
216s  Returning... 
216s Reading `ucfile` into memory and parsing into table 
216s Initially read 100 entries. 
216s ... Now removing unassigned OTUs (* or NA)... 
216s Removed 7 entries that had no OTU assignment. 
216s A total of 93 will be assigned to the OTU table.
220s Processing map file...
220s Processing otu/tax file...
220s Reading file into memory prior to parsing...
220s Detecting first header line...
220s Header is on line 2  
220s Converting input file to a table...
220s Defining OTU table... 
220s Parsing taxonomy table...
221s Processing phylogenetic tree...
221s  /usr/lib/R/site-library/phyloseq/extdata/GP_tree_rand_short.newick.gz ...
221s Processing Reference Sequences...
240s [ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]
240s 
240s [ FAIL 0 | WARN 51 | SKIP 0 | PASS 604 ]
240s > 
241s autopkgtest [04:20:12]: test pkg-r-autopkgtest: -----------------------]
241s pkg-r-autopkgtest    PASS
241s autopkgtest [04:20:12]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
241s autopkgtest [04:20:12]: @@@@@@@@@@@@@@@@@@@@ summary
241s pkg-r-autopkgtest    PASS