0s autopkgtest [01:44:31]: starting date and time: 2026-02-10 01:44:31+0000
  0s autopkgtest [01:44:31]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [01:44:31]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yisnfrd7/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-bioc-shortread --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-27.secgroup --name adt-resolute-amd64-r-bioc-shortread-20260210-014431-juju-7f2275-prod-proposed-migration-environment-15-be53f584-08e3-48db-915b-e0cef5d98e70 --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/
  4s Creating nova instance adt-resolute-amd64-r-bioc-shortread-20260210-014431-juju-7f2275-prod-proposed-migration-environment-15-be53f584-08e3-48db-915b-e0cef5d98e70 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 75s autopkgtest [01:45:46]: testbed dpkg architecture: amd64
 75s autopkgtest [01:45:46]: testbed apt version: 3.1.14
 75s autopkgtest [01:45:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 75s autopkgtest [01:45:46]: testbed release detected to be: None
 76s autopkgtest [01:45:47]: updating testbed package index (apt update)
 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB]
 77s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB]
 77s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB]
 79s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB]
 79s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB]
 79s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B]
 80s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B]
 80s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB]
 82s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB]
 82s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB]
 82s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B]
 82s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB]
 83s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 83s Fetched 4710 kB in 7s (715 kB/s)
 84s Reading package lists...
 84s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 84s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 84s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 84s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 85s Reading package lists...
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 85s Calculating upgrade...
 86s The following package was automatically installed and is no longer required:
 86s   libpython3.13
 86s Use 'sudo apt autoremove' to remove it.
 86s The following NEW packages will be installed:
 86s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 86s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 86s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 86s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 86s The following packages will be upgraded:
 86s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 86s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 86s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 86s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 86s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
 86s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 86s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 86s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 86s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 86s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 86s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 86s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 86s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 86s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 86s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 86s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 86s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 86s Need to get 237 MB of archives.
 86s After this operation, 339 MB of additional disk space will be used.
 86s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 86s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 86s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 86s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 86s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 87s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 87s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 87s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 87s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 87s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 87s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 88s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 89s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 91s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 91s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 91s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 91s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 91s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 91s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 91s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 91s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 91s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 91s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 92s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 92s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 92s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 92s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 92s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 94s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 94s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 94s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 94s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 94s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 94s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 95s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 96s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 96s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 96s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 96s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 97s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 97s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 97s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 97s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 97s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 98s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 98s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 98s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 98s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 98s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 98s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 99s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 99s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 99s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 99s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 99s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 99s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 99s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 99s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 99s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 99s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 99s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
101s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
101s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
102s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
102s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
102s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
103s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
103s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
104s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
104s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
104s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
104s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
104s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
104s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
104s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
104s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
104s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
104s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
105s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
108s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
110s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
110s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
183s 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]
190s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
190s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
190s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
190s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
190s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
190s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
190s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
195s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
196s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
196s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
198s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
198s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
198s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
198s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
198s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
198s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
198s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
199s dpkg-preconfigure: unable to re-open stdin: No such file or directory
199s Fetched 237 MB in 1min 53s (2099 kB/s)
199s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
199s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
199s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
199s Setting up debianutils (5.23.2build1) ...
199s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
199s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
199s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
199s Setting up dash (0.5.12-12ubuntu3) ...
199s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
199s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
199s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
199s Setting up findutils (4.10.0-3build2) ...
199s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
199s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
199s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
199s Setting up sed (4.9-2build3) ...
199s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
199s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
199s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
199s Setting up tar (1.35+dfsg-3.1build2) ...
199s (Reading database ... 
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209s Setting up libjansson4:amd64 (2.14-2build4) ...
209s Setting up libglib2.0-data (2.87.2-2) ...
209s Setting up pollinate (4.33-4ubuntu5) ...
220s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
220s Setting up libwrap0:amd64 (7.6.q-36build2) ...
220s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
221s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
221s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
221s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
221s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
221s Setting up patch (2.8-2build1) ...
221s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
221s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
221s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
221s Setting up lsof (4.99.4+dfsg-2build2) ...
221s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
221s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
221s Setting up dracut-install (109-11ubuntu1) ...
221s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
221s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
221s Setting up pnp.ids (0.394-1build1) ...
221s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
221s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
221s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
221s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
221s Setting up mawk (1.3.4.20260129-1) ...
221s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
221s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
221s Setting up linux-image-virtual (6.19.0-3.3) ...
221s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
221s Setting up libbsd0:amd64 (0.12.2-2build2) ...
221s Setting up libdrm-common (2.4.131-1) ...
221s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
221s Setting up dbus-bin (1.16.2-2ubuntu3) ...
221s Setting up libonig5:amd64 (6.9.10-1build1) ...
221s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
221s Setting up ethtool (1:6.15-3build1) ...
221s Setting up python3-referencing (0.36.2-1ubuntu2) ...
221s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
221s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
221s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
221s Setting up tcpdump (4.99.5-2ubuntu3) ...
221s Setting up linux-image-generic (6.19.0-3.3) ...
221s Setting up wget (1.25.0-2ubuntu4) ...
221s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
221s Setting up iptables (1.8.11-2ubuntu3) ...
221s Setting up iproute2 (6.18.0-1ubuntu1) ...
221s Setting up linux-headers-generic (6.19.0-3.3) ...
221s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
221s Setting up hwdata (0.394-1build1) ...
221s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
221s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
221s No schema files found: doing nothing.
221s Setting up dbus (1.16.2-2ubuntu3) ...
221s A reboot is required to replace the running dbus-daemon.
221s Please reboot the system when convenient.
222s Setting up shared-mime-info (2.4-5build3) ...
222s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
222s Setting up pciutils (1:3.14.0-1build2) ...
222s Setting up python3-markdown-it (3.0.0-3build1) ...
223s Setting up libdrm2:amd64 (2.4.131-1) ...
223s Setting up libpython3.14:amd64 (3.14.2-1) ...
223s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
223s Setting up linux-tools-common (6.19.0-3.3) ...
223s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
223s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
223s Setting up apt (3.1.15) ...
223s Setting up linux-headers-virtual (6.19.0-3.3) ...
223s Setting up linux-generic (6.19.0-3.3) ...
223s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
223s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
223s Setting up ubuntu-standard (1.564) ...
223s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
223s Setting up linux-virtual (6.19.0-3.3) ...
223s Setting up linux-perf (6.19.0-3.3) ...
223s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
223s Processing triggers for debianutils (5.23.2build1) ...
223s Processing triggers for install-info (7.2-5) ...
223s Processing triggers for initramfs-tools (0.150ubuntu7) ...
223s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
228s Processing triggers for libc-bin (2.42-2ubuntu4) ...
228s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
228s /etc/kernel/postinst.d/initramfs-tools:
228s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
232s /etc/kernel/postinst.d/zz-update-grub:
232s Sourcing file `/etc/default/grub'
232s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
232s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
232s Generating grub configuration file ...
232s Found linux image: /boot/vmlinuz-6.19.0-3-generic
232s Found initrd image: /boot/initrd.img-6.19.0-3-generic
232s Found linux image: /boot/vmlinuz-6.18.0-9-generic
232s Found initrd image: /boot/initrd.img-6.18.0-9-generic
232s Warning: os-prober will not be executed to detect other bootable partitions.
232s Systems on them will not be added to the GRUB boot configuration.
232s Check GRUB_DISABLE_OS_PROBER documentation entry.
232s Adding boot menu entry for UEFI Firmware Settings ...
232s done
232s autopkgtest [01:48:23]: upgrading testbed (apt dist-upgrade and autopurge)
233s Reading package lists...
233s Building dependency tree...
233s Reading state information...
233s Calculating upgrade...
233s The following package was automatically installed and is no longer required:
233s   libpython3.13
233s Use 'sudo apt autoremove' to remove it.
233s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
233s Reading package lists...
233s Building dependency tree...
233s Reading state information...
234s Solving dependencies...
234s The following packages will be REMOVED:
234s   libpython3.13*
234s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
234s After this operation, 7599 kB disk space will be freed.
234s (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%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
234s Removing libpython3.13:amd64 (3.13.11-1) ...
234s Processing triggers for libc-bin (2.42-2ubuntu4) ...
234s autopkgtest [01:48:25]: rebooting testbed after setup commands that affected boot
263s autopkgtest [01:48:54]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
266s autopkgtest [01:48:57]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-shortread
268s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-shortread 1.64.0-3 (dsc) [2409 B]
268s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-shortread 1.64.0-3 (tar) [5321 kB]
268s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-shortread 1.64.0-3 (diff) [6160 B]
268s gpgv: Signature made Mon Jan 27 12:34:30 2025 UTC
268s gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
268s gpgv:                issuer "crusoe@debian.org"
268s gpgv: Can't check signature: No public key
268s dpkg-source: warning: cannot verify inline signature for ./r-bioc-shortread_1.64.0-3.dsc: no acceptable signature found
268s autopkgtest [01:48:59]: testing package r-bioc-shortread version 1.64.0-3
269s autopkgtest [01:49:00]: build not needed
274s autopkgtest [01:49:05]: test pkg-r-autopkgtest: preparing testbed
274s Reading package lists...
274s Building dependency tree...
274s Reading state information...
274s Solving dependencies...
274s The following NEW packages will be installed:
274s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
274s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
274s   fonts-font-awesome fonts-glyphicons-halflings fonts-lmodern fonts-mathjax
274s   g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15
274s   gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15
274s   gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools
274s   javascript-common libasan8 libbibtex-parser-perl libblas-dev libblas3
274s   libboost-dev libboost1.90-dev libbz2-dev libc-dev-bin libc6-dev libcairo2
274s   libcc1-0 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1
274s   libgcc-15-dev libgfortran-15-dev libgfortran5 libgomp1 libgraphite2-3
274s   libharfbuzz0b libhwasan0 libice6 libicu-dev libio-string-perl libisl23
274s   libitm1 libjbig0 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8
274s   libjpeg8-dev libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim
274s   libjs-highlight.js libjs-jquery libjs-jquery-datatables
275s   libjs-jquery-selectize.js libjs-jquery-ui libjs-json libjs-lunr
275s   libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js
275s   libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker
275s   libkpathsea6 liblapack-dev liblapack3 liblatex-tounicode-perl liblerc4
275s   liblsan0 liblua5.4-0 liblzma-dev libmpc3 libmpfi0 libncurses-dev
275s   libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
275s   libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3
275s   libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libptexenc1 libquadmath0
275s   libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev libsynctex2 libtcl8.6
275s   libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev
275s   libtk8.6 libtsan2 libubsan1 libwebp7 libxaw7 libxcb-render0 libxcb-shm0
275s   libxft2 libxi6 libxmu6 libxpm4 libxrender1 libxss1 libxt6t64 libzstd-dev
275s   libzzip-0-13t64 linux-libc-dev node-bootstrap-sass node-html5shiv
275s   node-normalize.css pandoc pandoc-data pkg-r-autopkgtest pkgconf pkgconf-bin
275s   r-base-core r-base-dev r-bioc-annotationdbi r-bioc-biobase
275s   r-bioc-biocfilecache r-bioc-biocgenerics r-bioc-biocio r-bioc-biocparallel
275s   r-bioc-biocstyle r-bioc-biocversion r-bioc-biomart r-bioc-biostrings
275s   r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
275s   r-bioc-genomicalignments r-bioc-genomicfeatures r-bioc-genomicranges
275s   r-bioc-iranges r-bioc-keggrest r-bioc-matrixgenerics r-bioc-pwalign
275s   r-bioc-rhtslib r-bioc-rsamtools r-bioc-rtracklayer r-bioc-s4arrays
275s   r-bioc-s4vectors r-bioc-shortread r-bioc-sparsearray
275s   r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc
275s   r-cran-abind r-cran-askpass r-cran-base64enc r-cran-bh r-cran-biocmanager
275s   r-cran-bit r-cran-bit64 r-cran-bitops r-cran-blob r-cran-bookdown
275s   r-cran-bslib r-cran-cachem r-cran-cli r-cran-codetools r-cran-commonmark
275s   r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-dbi r-cran-dbplyr
275s   r-cran-deldir r-cran-digest r-cran-dplyr r-cran-evaluate r-cran-fansi
275s   r-cran-fastmap r-cran-filelock r-cran-fontawesome r-cran-formatr r-cran-fs
275s   r-cran-futile.logger r-cran-futile.options r-cran-generics r-cran-glue
275s   r-cran-highr r-cran-hms r-cran-htmltools r-cran-httpuv r-cran-httr
275s   r-cran-httr2 r-cran-hwriter r-cran-interp r-cran-jpeg r-cran-jquerylib
275s   r-cran-jsonlite r-cran-knitr r-cran-lambda.r r-cran-later r-cran-lattice
275s   r-cran-latticeextra r-cran-lifecycle r-cran-littler r-cran-magrittr
275s   r-cran-mass r-cran-matrix r-cran-matrixstats r-cran-memoise r-cran-mime
275s   r-cran-openssl r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plogr
275s   r-cran-png r-cran-prettyunits r-cran-progress r-cran-promises r-cran-purrr
275s   r-cran-r6 r-cran-rappdirs r-cran-rcolorbrewer r-cran-rcpp r-cran-rcppeigen
275s   r-cran-rcurl r-cran-restfulr r-cran-rjson r-cran-rlang r-cran-rmarkdown
275s   r-cran-rsqlite r-cran-runit r-cran-sass r-cran-shiny r-cran-snow
275s   r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys r-cran-tibble
275s   r-cran-tidyr r-cran-tidyselect r-cran-tinytex r-cran-utf8 r-cran-vctrs
275s   r-cran-withr r-cran-xfun r-cran-xml r-cran-xml2 r-cran-xtable r-cran-yaml
275s   rpcsvc-proto t1utils tex-common texlive-base texlive-bibtex-extra
275s   texlive-binaries texlive-latex-base unzip x11-common xdg-utils zip
275s   zlib1g-dev
275s 0 upgraded, 287 newly installed, 0 to remove and 0 not upgraded.
275s Need to get 452 MB of archives.
275s After this operation, 1407 MB of additional disk space will be used.
275s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
275s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
275s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
275s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
275s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
275s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
275s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
275s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
276s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
276s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
276s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
276s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
276s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
276s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
276s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
276s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
276s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
276s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
276s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
276s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
277s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
277s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
277s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
277s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
277s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
277s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
277s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
277s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
277s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
277s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
277s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
277s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
277s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
278s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
278s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
278s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
278s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
278s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB]
278s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
278s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lmodern all 2.005-1build1 [4788 kB]
278s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
278s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
278s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
278s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
278s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
278s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
278s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
278s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
278s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B]
278s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-string-perl all 1.08-4 [11.1 kB]
278s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblatex-tounicode-perl all 1.93-1 [29.2 kB]
278s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB]
278s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
278s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
278s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB]
278s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B]
278s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
278s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
278s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
278s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
278s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
278s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
278s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
278s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
278s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
278s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
278s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
278s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
278s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
278s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
279s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
279s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
279s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
279s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
279s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
279s Get:76 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
279s Get:77 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB]
279s Get:78 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
279s Get:79 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB]
279s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
279s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
279s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
279s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
279s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
279s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B]
279s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
279s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB]
279s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB]
279s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB]
279s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB]
279s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5build1 [66.0 kB]
279s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
279s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
279s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
279s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
279s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpfi0 amd64 1.5.4+ds-4build1 [36.6 kB]
279s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
279s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
279s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
279s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
279s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
279s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
279s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
279s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
279s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
279s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
279s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
279s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
279s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
279s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
279s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
279s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpotrace0 amd64 1.16-2build2 [17.9 kB]
279s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 libptexenc1 amd64 2025.20250727.75242+ds-5build1 [46.4 kB]
279s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
279s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
279s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
279s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsynctex2 amd64 2025.20250727.75242+ds-5build1 [62.1 kB]
279s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
279s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 libteckit0 amd64 2.5.13+ds-1 [431 kB]
279s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5build1 [125 kB]
279s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
279s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
279s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
279s Get:124 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
279s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
279s Get:126 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
279s Get:127 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
279s Get:128 http://ftpmaster.internal/ubuntu resolute/main amd64 libxmu6 amd64 2:1.1.3-4 [48.9 kB]
279s Get:129 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB]
279s Get:130 http://ftpmaster.internal/ubuntu resolute/main amd64 libxaw7 amd64 2:1.0.16-1build1 [190 kB]
279s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB]
279s Get:132 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
279s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [30.1 kB]
279s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
279s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
279s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
279s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
279s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
280s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
280s Get:140 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
280s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
280s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
280s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
280s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
280s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
280s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
280s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
280s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
280s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
280s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB]
281s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
281s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
281s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB]
281s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB]
281s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB]
281s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
281s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
281s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
281s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
281s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
281s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB]
281s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
281s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
281s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
281s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
281s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB]
281s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
281s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB]
281s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
281s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
281s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
281s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
281s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
281s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
281s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
281s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
281s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB]
281s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
281s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
282s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
282s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
283s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
283s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
283s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
283s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB]
283s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB]
284s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB]
284s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
284s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB]
284s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pillar all 1.11.1+dfsg-1 [456 kB]
284s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fansi amd64 1.0.6-2 [626 kB]
284s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-3 [419 kB]
284s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
284s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyselect amd64 1.2.1+dfsg-1 [222 kB]
284s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dplyr amd64 1.1.4-4 [1536 kB]
284s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-purrr amd64 1.0.4-1 [552 kB]
284s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringi amd64 1.8.4-1build2 [908 kB]
284s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-stringr all 1.5.1-1 [290 kB]
284s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tidyr amd64 1.3.1-1 [1156 kB]
284s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbplyr all 2.5.1+dfsg-1 [1237 kB]
284s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-filelock amd64 1.0.3-1 [29.6 kB]
284s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocfilecache all 2.14.0+dfsg-2 [300 kB]
284s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB]
284s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formatr all 1.14-2 [152 kB]
284s Get:205 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lambda.r all 1.2.4-2build2 [118 kB]
284s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.options all 1.0.1-3build2 [20.5 kB]
284s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.logger all 1.4.3-4build2 [98.4 kB]
284s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-snow all 1:0.4.4-2build1 [98.7 kB]
284s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB]
284s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
284s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB]
284s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
284s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
284s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
284s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
284s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
284s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
284s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
284s Get:219 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
284s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
284s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB]
284s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
284s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB]
284s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
284s Get:225 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
285s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
285s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB]
285s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB]
285s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB]
285s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
285s Get:231 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
285s Get:232 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
285s Get:233 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
285s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
285s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
285s Get:236 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
285s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
285s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
285s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
285s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB]
285s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bookdown all 0.42+dfsg-1 [1409 kB]
285s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB]
285s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 tex-common all 6.20 [30.0 kB]
285s Get:244 http://ftpmaster.internal/ubuntu resolute/main amd64 t1utils amd64 1.41-4build4 [62.7 kB]
285s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-binaries amd64 2025.20250727.75242+ds-5build1 [8747 kB]
286s Get:246 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-base all 2025.20260124-1 [22.8 MB]
287s Get:247 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-base all 2025.20260124-1 [1321 kB]
287s Get:248 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-bibtex-extra all 2025.20260124-1 [80.6 MB]
295s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocversion all 3.20.0-2 [11.1 kB]
295s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB]
295s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hms all 1.1.4-1 [102 kB]
295s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-prettyunits all 1.2.0-1 [162 kB]
295s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-progress all 1.2.3-1 [91.9 kB]
295s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr2 all 1.1.1-2 [752 kB]
295s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml2 amd64 1.4.1-1 [329 kB]
295s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biomart all 2.62.1+dfsg-1 [444 kB]
296s Get:257 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB]
296s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
296s Get:259 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB]
296s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB]
296s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB]
296s Get:262 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB]
296s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1391 kB]
297s Get:264 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB]
297s Get:265 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB]
298s Get:266 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB]
298s Get:267 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
298s Get:268 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB]
298s Get:269 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB]
298s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB]
298s Get:271 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
298s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
298s Get:273 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB]
298s Get:274 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB]
298s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rtracklayer amd64 1.66.0-3 [5225 kB]
299s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB]
299s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-pwalign amd64 1.2.0-3 [757 kB]
299s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-hwriter all 1.3.2.1-1 [106 kB]
299s Get:279 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jpeg amd64 0.1-10-1 [31.4 kB]
299s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB]
299s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-deldir amd64 2.0-4-1build1 [270 kB]
299s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcppeigen amd64 0.3.4.0.2-1 [1428 kB]
299s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-interp amd64 1.1-6-1 [1454 kB]
299s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB]
299s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-latticeextra all 0.6-31-1 [2177 kB]
299s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-shortread amd64 1.64.0-3 [5247 kB]
299s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-runit all 0.4.33.1-1 [250 kB]
300s Preconfiguring packages ...
300s Fetched 452 MB in 25s (18.2 MB/s)
300s Selecting previously unselected package libc-dev-bin.
300s (Reading database ... 
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300s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
300s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
300s Selecting previously unselected package linux-libc-dev:amd64.
300s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
300s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
300s Selecting previously unselected package libcrypt-dev:amd64.
300s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
300s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
300s Selecting previously unselected package rpcsvc-proto.
300s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
300s Unpacking rpcsvc-proto (1.4.3-1build1) ...
300s Selecting previously unselected package libc6-dev:amd64.
300s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
300s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
300s Selecting previously unselected package libisl23:amd64.
300s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
300s Unpacking libisl23:amd64 (0.27-1build1) ...
300s Selecting previously unselected package libmpc3:amd64.
300s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
300s Unpacking libmpc3:amd64 (1.3.1-2) ...
300s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
300s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
300s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
300s Selecting previously unselected package cpp-15.
300s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
300s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
300s Selecting previously unselected package cpp-x86-64-linux-gnu.
300s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
300s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
300s Selecting previously unselected package cpp.
300s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
300s Unpacking cpp (4:15.2.0-4ubuntu1) ...
300s Selecting previously unselected package libcc1-0:amd64.
300s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libgomp1:amd64.
300s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libitm1:amd64.
300s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libasan8:amd64.
300s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package liblsan0:amd64.
300s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libtsan2:amd64.
300s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libubsan1:amd64.
300s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libhwasan0:amd64.
300s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libquadmath0:amd64.
300s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ...
300s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ...
300s Selecting previously unselected package libgcc-15-dev:amd64.
300s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ...
300s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package gcc-15-x86-64-linux-gnu.
301s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
301s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package gcc-15.
301s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ...
301s Unpacking gcc-15 (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package gcc-x86-64-linux-gnu.
301s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
301s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
301s Selecting previously unselected package gcc.
301s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ...
301s Unpacking gcc (4:15.2.0-4ubuntu1) ...
301s Selecting previously unselected package libstdc++-15-dev:amd64.
301s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ...
301s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package g++-15-x86-64-linux-gnu.
301s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
301s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package g++-15.
301s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ...
301s Unpacking g++-15 (15.2.0-12ubuntu1) ...
301s Selecting previously unselected package g++-x86-64-linux-gnu.
301s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
301s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
301s Selecting previously unselected package g++.
301s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ...
301s Unpacking g++ (4:15.2.0-4ubuntu1) ...
301s Selecting previously unselected package build-essential.
301s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ...
301s Unpacking build-essential (12.12ubuntu2) ...
301s Selecting previously unselected package dctrl-tools.
301s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ...
301s Unpacking dctrl-tools (2.24-3build4) ...
301s Selecting previously unselected package fonts-dejavu-mono.
301s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ...
301s Unpacking fonts-dejavu-mono (2.37-8build1) ...
301s Selecting previously unselected package fonts-dejavu-core.
301s Preparing to unpack .../033-fonts-dejavu-core_2.37-8build1_all.deb ...
301s Unpacking fonts-dejavu-core (2.37-8build1) ...
301s Selecting previously unselected package fontconfig-config.
301s Preparing to unpack .../034-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ...
301s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
301s Selecting previously unselected package libfontconfig1:amd64.
301s Preparing to unpack .../035-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ...
301s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
301s Selecting previously unselected package fontconfig.
301s Preparing to unpack .../036-fontconfig_2.17.1-3ubuntu1_amd64.deb ...
301s Unpacking fontconfig (2.17.1-3ubuntu1) ...
301s Selecting previously unselected package fonts-font-awesome.
301s Preparing to unpack .../037-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ...
301s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ...
301s Selecting previously unselected package fonts-glyphicons-halflings.
301s Preparing to unpack .../038-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ...
301s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
301s Selecting previously unselected package fonts-lmodern.
301s Preparing to unpack .../039-fonts-lmodern_2.005-1build1_all.deb ...
301s Unpacking fonts-lmodern (2.005-1build1) ...
301s Selecting previously unselected package fonts-mathjax.
301s Preparing to unpack .../040-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
301s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ...
301s Selecting previously unselected package libgfortran5:amd64.
301s Preparing to unpack .../041-libgfortran5_16-20260208-1ubuntu1_amd64.deb ...
301s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ...
302s Selecting previously unselected package libgfortran-15-dev:amd64.
302s Preparing to unpack .../042-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ...
302s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ...
302s Selecting previously unselected package gfortran-15-x86-64-linux-gnu.
302s Preparing to unpack .../043-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
302s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
302s Selecting previously unselected package gfortran-15.
302s Preparing to unpack .../044-gfortran-15_15.2.0-12ubuntu1_amd64.deb ...
302s Unpacking gfortran-15 (15.2.0-12ubuntu1) ...
302s Selecting previously unselected package gfortran-x86-64-linux-gnu.
302s Preparing to unpack .../045-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
302s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
302s Selecting previously unselected package gfortran.
302s Preparing to unpack .../046-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ...
302s Unpacking gfortran (4:15.2.0-4ubuntu1) ...
302s Selecting previously unselected package icu-devtools.
302s Preparing to unpack .../047-icu-devtools_78.2-1ubuntu1_amd64.deb ...
302s Unpacking icu-devtools (78.2-1ubuntu1) ...
302s Selecting previously unselected package javascript-common.
302s Preparing to unpack .../048-javascript-common_12+nmu1build1_all.deb ...
302s Unpacking javascript-common (12+nmu1build1) ...
302s Selecting previously unselected package libio-string-perl.
302s Preparing to unpack .../049-libio-string-perl_1.08-4_all.deb ...
302s Unpacking libio-string-perl (1.08-4) ...
302s Selecting previously unselected package liblatex-tounicode-perl.
302s Preparing to unpack .../050-liblatex-tounicode-perl_1.93-1_all.deb ...
302s Unpacking liblatex-tounicode-perl (1.93-1) ...
302s Selecting previously unselected package libbibtex-parser-perl.
302s Preparing to unpack .../051-libbibtex-parser-perl_1.93+dfsg-1_all.deb ...
302s Unpacking libbibtex-parser-perl (1.93+dfsg-1) ...
302s Selecting previously unselected package libblas3:amd64.
302s Preparing to unpack .../052-libblas3_3.12.1-7ubuntu1_amd64.deb ...
302s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ...
302s Selecting previously unselected package libblas-dev:amd64.
302s Preparing to unpack .../053-libblas-dev_3.12.1-7ubuntu1_amd64.deb ...
302s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ...
302s Selecting previously unselected package libboost1.90-dev:amd64.
302s Preparing to unpack .../054-libboost1.90-dev_1.90.0-2ubuntu1_amd64.deb ...
302s Unpacking libboost1.90-dev:amd64 (1.90.0-2ubuntu1) ...
303s Selecting previously unselected package libboost-dev:amd64.
303s Preparing to unpack .../055-libboost-dev_1.90.0.0ubuntu3_amd64.deb ...
303s Unpacking libboost-dev:amd64 (1.90.0.0ubuntu3) ...
303s Selecting previously unselected package libbz2-dev:amd64.
303s Preparing to unpack .../056-libbz2-dev_1.0.8-6build2_amd64.deb ...
303s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ...
303s Selecting previously unselected package libpixman-1-0:amd64.
303s Preparing to unpack .../057-libpixman-1-0_0.46.4-1_amd64.deb ...
303s Unpacking libpixman-1-0:amd64 (0.46.4-1) ...
303s Selecting previously unselected package libxcb-render0:amd64.
303s Preparing to unpack .../058-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ...
303s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ...
303s Selecting previously unselected package libxcb-shm0:amd64.
303s Preparing to unpack .../059-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ...
303s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
303s Selecting previously unselected package libxrender1:amd64.
303s Preparing to unpack .../060-libxrender1_1%3a0.9.12-1_amd64.deb ...
303s Unpacking libxrender1:amd64 (1:0.9.12-1) ...
303s Selecting previously unselected package libcairo2:amd64.
303s Preparing to unpack .../061-libcairo2_1.18.4-3_amd64.deb ...
303s Unpacking libcairo2:amd64 (1.18.4-3) ...
303s Selecting previously unselected package libdatrie1:amd64.
303s Preparing to unpack .../062-libdatrie1_0.2.14-1_amd64.deb ...
303s Unpacking libdatrie1:amd64 (0.2.14-1) ...
303s Selecting previously unselected package libdeflate0:amd64.
303s Preparing to unpack .../063-libdeflate0_1.23-2build1_amd64.deb ...
303s Unpacking libdeflate0:amd64 (1.23-2build1) ...
303s Selecting previously unselected package libdeflate-dev:amd64.
303s Preparing to unpack .../064-libdeflate-dev_1.23-2build1_amd64.deb ...
303s Unpacking libdeflate-dev:amd64 (1.23-2build1) ...
303s Selecting previously unselected package libgraphite2-3:amd64.
303s Preparing to unpack .../065-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ...
303s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ...
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306s Selecting previously unselected package r-cran-jsonlite.
306s Preparing to unpack .../169-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ...
306s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ...
306s Selecting previously unselected package r-cran-mime.
306s Preparing to unpack .../170-r-cran-mime_0.12-2_amd64.deb ...
306s Unpacking r-cran-mime (0.12-2) ...
306s Selecting previously unselected package r-cran-sys.
306s Preparing to unpack .../171-r-cran-sys_3.4.3-1_amd64.deb ...
306s Unpacking r-cran-sys (3.4.3-1) ...
306s Selecting previously unselected package r-cran-askpass.
306s Preparing to unpack .../172-r-cran-askpass_1.2.1-1_amd64.deb ...
306s Unpacking r-cran-askpass (1.2.1-1) ...
306s Selecting previously unselected package r-cran-openssl.
306s Preparing to unpack .../173-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ...
306s Unpacking r-cran-openssl (2.3.2+dfsg-1) ...
306s Selecting previously unselected package r-cran-r6.
306s Preparing to unpack .../174-r-cran-r6_2.6.1-1_all.deb ...
306s Unpacking r-cran-r6 (2.6.1-1) ...
306s Selecting previously unselected package r-cran-httr.
306s Preparing to unpack .../175-r-cran-httr_1.4.7+dfsg-1_all.deb ...
306s Unpacking r-cran-httr (1.4.7+dfsg-1) ...
306s Selecting previously unselected package r-cran-png.
306s Preparing to unpack .../176-r-cran-png_0.1-8-1build2_amd64.deb ...
306s Unpacking r-cran-png (0.1-8-1build2) ...
306s Selecting previously unselected package r-bioc-zlibbioc.
306s Preparing to unpack .../177-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ...
306s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ...
306s Selecting previously unselected package r-bioc-xvector.
306s Preparing to unpack .../178-r-bioc-xvector_0.46.0-2_amd64.deb ...
306s Unpacking r-bioc-xvector (0.46.0-2) ...
306s Selecting previously unselected package r-bioc-ucsc.utils.
306s Preparing to unpack .../179-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ...
306s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ...
306s Selecting previously unselected package r-bioc-genomeinfodbdata.
306s Preparing to unpack .../180-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ...
306s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ...
306s Selecting previously unselected package r-bioc-genomeinfodb.
306s Preparing to unpack .../181-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ...
306s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
306s Selecting previously unselected package r-cran-crayon.
306s Preparing to unpack .../182-r-cran-crayon_1.5.3-1_all.deb ...
306s Unpacking r-cran-crayon (1.5.3-1) ...
306s Selecting previously unselected package r-bioc-biostrings.
306s Preparing to unpack .../183-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ...
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306s Selecting previously unselected package r-bioc-keggrest.
306s Preparing to unpack .../184-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ...
306s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ...
306s Selecting previously unselected package r-bioc-annotationdbi.
306s Preparing to unpack .../185-r-bioc-annotationdbi_1.68.0-2_all.deb ...
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306s Selecting previously unselected package r-cran-generics.
306s Preparing to unpack .../186-r-cran-generics_0.1.4-1_all.deb ...
306s Unpacking r-cran-generics (0.1.4-1) ...
306s Selecting previously unselected package r-cran-magrittr.
306s Preparing to unpack .../187-r-cran-magrittr_2.0.3-1_amd64.deb ...
306s Unpacking r-cran-magrittr (2.0.3-1) ...
306s Selecting previously unselected package r-cran-utf8.
306s Preparing to unpack .../188-r-cran-utf8_1.2.4-1_amd64.deb ...
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306s Selecting previously unselected package r-cran-pillar.
306s Preparing to unpack .../189-r-cran-pillar_1.11.1+dfsg-1_all.deb ...
306s Unpacking r-cran-pillar (1.11.1+dfsg-1) ...
306s Selecting previously unselected package r-cran-fansi.
306s Preparing to unpack .../190-r-cran-fansi_1.0.6-2_amd64.deb ...
306s Unpacking r-cran-fansi (1.0.6-2) ...
306s Selecting previously unselected package r-cran-tibble.
306s Preparing to unpack .../191-r-cran-tibble_3.2.1+dfsg-3_amd64.deb ...
306s Unpacking r-cran-tibble (3.2.1+dfsg-3) ...
306s Selecting previously unselected package r-cran-withr.
306s Preparing to unpack .../192-r-cran-withr_3.0.2+dfsg-1_all.deb ...
306s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
306s Selecting previously unselected package r-cran-tidyselect.
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307s Unpacking r-cran-tidyselect (1.2.1+dfsg-1) ...
307s Selecting previously unselected package r-cran-dplyr.
307s Preparing to unpack .../194-r-cran-dplyr_1.1.4-4_amd64.deb ...
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307s Selecting previously unselected package r-cran-purrr.
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307s Selecting previously unselected package r-cran-stringi.
307s Preparing to unpack .../196-r-cran-stringi_1.8.4-1build2_amd64.deb ...
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307s Selecting previously unselected package r-cran-stringr.
307s Preparing to unpack .../197-r-cran-stringr_1.5.1-1_all.deb ...
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307s Selecting previously unselected package r-cran-tidyr.
307s Preparing to unpack .../198-r-cran-tidyr_1.3.1-1_amd64.deb ...
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307s Selecting previously unselected package r-cran-dbplyr.
307s Preparing to unpack .../199-r-cran-dbplyr_2.5.1+dfsg-1_all.deb ...
307s Unpacking r-cran-dbplyr (2.5.1+dfsg-1) ...
307s Selecting previously unselected package r-cran-filelock.
307s Preparing to unpack .../200-r-cran-filelock_1.0.3-1_amd64.deb ...
307s Unpacking r-cran-filelock (1.0.3-1) ...
307s Selecting previously unselected package r-bioc-biocfilecache.
307s Preparing to unpack .../201-r-bioc-biocfilecache_2.14.0+dfsg-2_all.deb ...
307s Unpacking r-bioc-biocfilecache (2.14.0+dfsg-2) ...
307s Selecting previously unselected package r-bioc-biocio.
307s Preparing to unpack .../202-r-bioc-biocio_1.16.0+dfsg-2_all.deb ...
307s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ...
307s Selecting previously unselected package r-cran-formatr.
307s Preparing to unpack .../203-r-cran-formatr_1.14-2_all.deb ...
307s Unpacking r-cran-formatr (1.14-2) ...
307s Selecting previously unselected package r-cran-lambda.r.
307s Preparing to unpack .../204-r-cran-lambda.r_1.2.4-2build2_all.deb ...
307s Unpacking r-cran-lambda.r (1.2.4-2build2) ...
307s Selecting previously unselected package r-cran-futile.options.
307s Preparing to unpack .../205-r-cran-futile.options_1.0.1-3build2_all.deb ...
307s Unpacking r-cran-futile.options (1.0.1-3build2) ...
307s Selecting previously unselected package r-cran-futile.logger.
307s Preparing to unpack .../206-r-cran-futile.logger_1.4.3-4build2_all.deb ...
307s Unpacking r-cran-futile.logger (1.4.3-4build2) ...
307s Selecting previously unselected package r-cran-snow.
307s Preparing to unpack .../207-r-cran-snow_1%3a0.4.4-2build1_all.deb ...
307s Unpacking r-cran-snow (1:0.4.4-2build1) ...
307s Selecting previously unselected package r-cran-codetools.
307s Preparing to unpack .../208-r-cran-codetools_0.2-20-1build1_all.deb ...
307s Unpacking r-cran-codetools (0.2-20-1build1) ...
307s Selecting previously unselected package r-cran-bh.
307s Preparing to unpack .../209-r-cran-bh_1.84.0-1_all.deb ...
307s Unpacking r-cran-bh (1.84.0-1) ...
307s Selecting previously unselected package r-bioc-biocparallel.
307s Preparing to unpack .../210-r-bioc-biocparallel_1.40.0-2_amd64.deb ...
307s Unpacking r-bioc-biocparallel (1.40.0-2) ...
307s Selecting previously unselected package r-cran-base64enc.
307s Preparing to unpack .../211-r-cran-base64enc_0.1-3-3build1_amd64.deb ...
307s Unpacking r-cran-base64enc (0.1-3-3build1) ...
307s Selecting previously unselected package r-cran-digest.
307s Preparing to unpack .../212-r-cran-digest_0.6.39-1_amd64.deb ...
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307s Selecting previously unselected package r-cran-htmltools.
307s Preparing to unpack .../213-r-cran-htmltools_0.5.8.1-1_amd64.deb ...
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307s Selecting previously unselected package r-cran-evaluate.
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307s Selecting previously unselected package r-cran-xfun.
307s Preparing to unpack .../215-r-cran-xfun_0.55+dfsg-1_amd64.deb ...
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307s Selecting previously unselected package r-cran-highr.
307s Preparing to unpack .../216-r-cran-highr_0.11+dfsg-1_all.deb ...
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307s Selecting previously unselected package r-cran-yaml.
307s Preparing to unpack .../217-r-cran-yaml_2.3.10-1_amd64.deb ...
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307s Selecting previously unselected package libjs-mathjax.
307s Preparing to unpack .../218-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ...
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307s Selecting previously unselected package r-cran-knitr.
307s Preparing to unpack .../219-r-cran-knitr_1.51+dfsg-1_all.deb ...
307s Unpacking r-cran-knitr (1.51+dfsg-1) ...
307s Selecting previously unselected package r-cran-jquerylib.
307s Preparing to unpack .../220-r-cran-jquerylib_0.1.4+dfsg-5_all.deb ...
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307s Selecting previously unselected package r-cran-fs.
307s Preparing to unpack .../221-r-cran-fs_1.6.5+dfsg-1_amd64.deb ...
307s Unpacking r-cran-fs (1.6.5+dfsg-1) ...
307s Selecting previously unselected package r-cran-rappdirs.
307s Preparing to unpack .../222-r-cran-rappdirs_0.3.3-1build1_amd64.deb ...
307s Unpacking r-cran-rappdirs (0.3.3-1build1) ...
307s Selecting previously unselected package r-cran-sass.
307s Preparing to unpack .../223-r-cran-sass_0.4.9+dfsg-1_amd64.deb ...
307s Unpacking r-cran-sass (0.4.9+dfsg-1) ...
307s Selecting previously unselected package r-cran-bslib.
307s Preparing to unpack .../224-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ...
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307s Selecting previously unselected package r-cran-fontawesome.
307s Preparing to unpack .../225-r-cran-fontawesome_0.5.3-1_all.deb ...
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307s Selecting previously unselected package r-cran-tinytex.
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307s Selecting previously unselected package libjs-modernizr.
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307s Selecting previously unselected package r-cran-littler.
307s Preparing to unpack .../228-r-cran-littler_0.3.22-1_amd64.deb ...
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307s Selecting previously unselected package r-cran-pkgkitten.
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307s Selecting previously unselected package r-cran-rcpp.
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308s Selecting previously unselected package r-cran-later.
308s Preparing to unpack .../231-r-cran-later_1.4.1+dfsg-1_amd64.deb ...
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308s Selecting previously unselected package r-cran-promises.
308s Preparing to unpack .../232-r-cran-promises_1.3.2+dfsg-1_amd64.deb ...
308s Unpacking r-cran-promises (1.3.2+dfsg-1) ...
308s Selecting previously unselected package r-cran-httpuv.
308s Preparing to unpack .../233-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ...
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308s Selecting previously unselected package r-cran-xtable.
308s Preparing to unpack .../234-r-cran-xtable_1%3a1.8-4-2build1_all.deb ...
308s Unpacking r-cran-xtable (1:1.8-4-2build1) ...
308s Selecting previously unselected package r-cran-sourcetools.
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308s Selecting previously unselected package r-cran-commonmark.
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308s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
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308s Selecting previously unselected package r-cran-shiny.
308s Preparing to unpack .../238-r-cran-shiny_1.10.0+dfsg-2_all.deb ...
308s Unpacking r-cran-shiny (1.10.0+dfsg-2) ...
308s Selecting previously unselected package r-cran-rmarkdown.
308s Preparing to unpack .../239-r-cran-rmarkdown_2.30+dfsg-1_all.deb ...
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308s Selecting previously unselected package r-cran-bookdown.
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308s Selecting previously unselected package r-cran-biocmanager.
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308s Selecting previously unselected package tex-common.
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308s Selecting previously unselected package t1utils.
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308s Selecting previously unselected package texlive-binaries.
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308s Selecting previously unselected package texlive-base.
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308s Selecting previously unselected package texlive-latex-base.
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309s Selecting previously unselected package texlive-bibtex-extra.
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310s Selecting previously unselected package r-bioc-biocversion.
310s Preparing to unpack .../248-r-bioc-biocversion_3.20.0-2_all.deb ...
310s Unpacking r-bioc-biocversion (3.20.0-2) ...
310s Selecting previously unselected package r-bioc-biocstyle.
310s Preparing to unpack .../249-r-bioc-biocstyle_2.34.0+dfsg-1_all.deb ...
310s Unpacking r-bioc-biocstyle (2.34.0+dfsg-1) ...
310s Selecting previously unselected package r-cran-hms.
310s Preparing to unpack .../250-r-cran-hms_1.1.4-1_all.deb ...
310s Unpacking r-cran-hms (1.1.4-1) ...
310s Selecting previously unselected package r-cran-prettyunits.
310s Preparing to unpack .../251-r-cran-prettyunits_1.2.0-1_all.deb ...
310s Unpacking r-cran-prettyunits (1.2.0-1) ...
310s Selecting previously unselected package r-cran-progress.
310s Preparing to unpack .../252-r-cran-progress_1.2.3-1_all.deb ...
310s Unpacking r-cran-progress (1.2.3-1) ...
310s Selecting previously unselected package r-cran-httr2.
310s Preparing to unpack .../253-r-cran-httr2_1.1.1-2_all.deb ...
310s Unpacking r-cran-httr2 (1.1.1-2) ...
310s Selecting previously unselected package r-cran-xml2.
310s Preparing to unpack .../254-r-cran-xml2_1.4.1-1_amd64.deb ...
310s Unpacking r-cran-xml2 (1.4.1-1) ...
310s Selecting previously unselected package r-bioc-biomart.
310s Preparing to unpack .../255-r-bioc-biomart_2.62.1+dfsg-1_all.deb ...
310s Unpacking r-bioc-biomart (2.62.1+dfsg-1) ...
310s Selecting previously unselected package r-cran-lattice.
310s Preparing to unpack .../256-r-cran-lattice_0.22-9-1_amd64.deb ...
310s Unpacking r-cran-lattice (0.22-9-1) ...
310s Selecting previously unselected package r-cran-matrix.
310s Preparing to unpack .../257-r-cran-matrix_1.7-4-1_amd64.deb ...
310s Unpacking r-cran-matrix (1.7-4-1) ...
310s Selecting previously unselected package r-cran-matrixstats.
310s Preparing to unpack .../258-r-cran-matrixstats_1.5.0-1_amd64.deb ...
310s Unpacking r-cran-matrixstats (1.5.0-1) ...
310s Selecting previously unselected package r-bioc-matrixgenerics.
310s Preparing to unpack .../259-r-bioc-matrixgenerics_1.18.1-1_all.deb ...
310s Unpacking r-bioc-matrixgenerics (1.18.1-1) ...
310s Selecting previously unselected package r-cran-abind.
310s Preparing to unpack .../260-r-cran-abind_1.4-8-1build1_all.deb ...
310s Unpacking r-cran-abind (1.4-8-1build1) ...
310s Selecting previously unselected package r-bioc-s4arrays.
310s Preparing to unpack .../261-r-bioc-s4arrays_1.6.0+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ...
310s Selecting previously unselected package r-bioc-sparsearray.
310s Preparing to unpack .../262-r-bioc-sparsearray_1.6.2+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-sparsearray (1.6.2+dfsg-2) ...
310s Selecting previously unselected package r-bioc-delayedarray.
310s Preparing to unpack .../263-r-bioc-delayedarray_0.32.0+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ...
310s Selecting previously unselected package r-bioc-genomicranges.
310s Preparing to unpack .../264-r-bioc-genomicranges_1.58.0+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ...
310s Selecting previously unselected package r-bioc-summarizedexperiment.
310s Preparing to unpack .../265-r-bioc-summarizedexperiment_1.36.0+dfsg-2_all.deb ...
310s Unpacking r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
310s Selecting previously unselected package r-cran-bitops.
310s Preparing to unpack .../266-r-cran-bitops_1.0-9-1_amd64.deb ...
310s Unpacking r-cran-bitops (1.0-9-1) ...
310s Selecting previously unselected package r-bioc-rhtslib.
310s Preparing to unpack .../267-r-bioc-rhtslib_3.2.0+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ...
310s Selecting previously unselected package r-bioc-rsamtools.
310s Preparing to unpack .../268-r-bioc-rsamtools_2.22.0+dfsg-2_amd64.deb ...
310s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ...
310s Selecting previously unselected package r-bioc-genomicalignments.
310s Preparing to unpack .../269-r-bioc-genomicalignments_1.42.0-2_amd64.deb ...
310s Unpacking r-bioc-genomicalignments (1.42.0-2) ...
310s Selecting previously unselected package r-cran-xml.
310s Preparing to unpack .../270-r-cran-xml_3.99-0.20-1_amd64.deb ...
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315s Setting up r-cran-stringr (1.5.1-1) ...
315s Setting up r-bioc-biocparallel (1.40.0-2) ...
315s Setting up r-bioc-rhtslib (3.2.0+dfsg-2) ...
315s Setting up r-cran-xml2 (1.4.1-1) ...
315s Setting up r-cran-tibble (3.2.1+dfsg-3) ...
315s Setting up r-cran-fontawesome (0.5.3-1) ...
315s Setting up r-bioc-biocio (1.16.0+dfsg-2) ...
315s Setting up r-cran-jquerylib (0.1.4+dfsg-5) ...
315s Setting up r-cran-tidyselect (1.2.1+dfsg-1) ...
315s Setting up texlive-bibtex-extra (2025.20260124-1) ...
315s Setting up r-cran-interp (1.1-6-1) ...
315s Setting up r-cran-httr2 (1.1.1-2) ...
315s Setting up r-cran-httr (1.4.7+dfsg-1) ...
315s Setting up r-cran-hms (1.1.4-1) ...
315s Setting up r-cran-memoise (2.0.1-1build1) ...
315s Setting up r-cran-promises (1.3.2+dfsg-1) ...
315s Setting up r-cran-purrr (1.0.4-1) ...
315s Setting up r-cran-blob (1.3.0-1) ...
315s Setting up pkg-r-autopkgtest (20250812) ...
315s Setting up r-bioc-xvector (0.46.0-2) ...
315s Setting up r-cran-dplyr (1.1.4-4) ...
315s Setting up r-cran-rsqlite (2.3.9-1) ...
315s Setting up r-cran-progress (1.2.3-1) ...
315s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
315s Setting up r-bioc-sparsearray (1.6.2+dfsg-2) ...
315s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
315s Setting up r-cran-latticeextra (0.6-31-1) ...
315s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
315s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
315s Setting up r-cran-tidyr (1.3.1-1) ...
315s Setting up r-cran-dbplyr (2.5.1+dfsg-1) ...
315s Setting up r-bioc-delayedarray (0.32.0+dfsg-2) ...
315s Setting up r-bioc-biocfilecache (2.14.0+dfsg-2) ...
315s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ...
315s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
315s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
315s Setting up r-cran-rmarkdown (2.30+dfsg-1) ...
315s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ...
315s Setting up r-cran-bookdown (0.42+dfsg-1) ...
315s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ...
315s Setting up r-bioc-pwalign (1.2.0-3) ...
315s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ...
315s Setting up r-bioc-annotationdbi (1.68.0-2) ...
315s Setting up r-bioc-biomart (2.62.1+dfsg-1) ...
315s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ...
315s Setting up r-bioc-genomicalignments (1.42.0-2) ...
315s Setting up r-bioc-rtracklayer (1.66.0-3) ...
315s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ...
315s Setting up r-bioc-shortread (1.64.0-3) ...
315s Processing triggers for libc-bin (2.42-2ubuntu4) ...
315s Processing triggers for man-db (2.13.1-1build1) ...
316s Processing triggers for install-info (7.2-5) ...
316s Processing triggers for tex-common (6.20) ...
316s Running updmap-sys. This may take some time... done.
316s Running mktexlsr /var/lib/texmf ... done.
316s Building format(s) --all.
330s 	This may take some time... done.
331s autopkgtest [01:50:02]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
331s autopkgtest [01:50:02]: test pkg-r-autopkgtest: [-----------------------
331s Test: Try to load the R library ShortRead
331s 
331s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
331s Copyright (C) 2025 The R Foundation for Statistical Computing
331s Platform: x86_64-pc-linux-gnu
331s 
331s R is free software and comes with ABSOLUTELY NO WARRANTY.
331s You are welcome to redistribute it under certain conditions.
331s Type 'license()' or 'licence()' for distribution details.
331s 
331s R is a collaborative project with many contributors.
331s Type 'contributors()' for more information and
331s 'citation()' on how to cite R or R packages in publications.
331s 
331s Type 'demo()' for some demos, 'help()' for on-line help, or
331s 'help.start()' for an HTML browser interface to help.
331s Type 'q()' to quit R.
331s 
331s > library('ShortRead')
331s Loading required package: BiocGenerics
331s 
331s Attaching package: ‘BiocGenerics’
331s 
331s The following objects are masked from ‘package:stats’:
331s 
331s     IQR, mad, sd, var, xtabs
331s 
331s The following objects are masked from ‘package:base’:
331s 
331s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
331s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
331s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
331s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
331s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
331s     table, tapply, union, unique, unsplit, which.max, which.min
331s 
331s Loading required package: BiocParallel
331s Loading required package: Biostrings
331s Loading required package: S4Vectors
331s Loading required package: stats4
332s 
332s Attaching package: ‘S4Vectors’
332s 
332s The following object is masked from ‘package:utils’:
332s 
332s     findMatches
332s 
332s The following objects are masked from ‘package:base’:
332s 
332s     expand.grid, I, unname
332s 
332s Loading required package: IRanges
332s Loading required package: XVector
332s Loading required package: GenomeInfoDb
332s 
332s Attaching package: ‘Biostrings’
332s 
332s The following object is masked from ‘package:base’:
332s 
332s     strsplit
332s 
332s Loading required package: Rsamtools
332s Loading required package: GenomicRanges
333s Loading required package: GenomicAlignments
333s Loading required package: SummarizedExperiment
333s Loading required package: MatrixGenerics
333s Loading required package: matrixStats
333s 
333s Attaching package: ‘MatrixGenerics’
333s 
333s The following objects are masked from ‘package:matrixStats’:
333s 
333s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
333s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
333s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
333s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
333s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
333s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
333s     colWeightedMeans, colWeightedMedians, colWeightedSds,
333s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
333s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
333s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
333s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
333s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
333s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
333s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
333s     rowWeightedSds, rowWeightedVars
333s 
333s Loading required package: Biobase
333s Welcome to Bioconductor
333s 
333s     Vignettes contain introductory material; view with
333s     'browseVignettes()'. To cite Bioconductor, see
333s     'citation("Biobase")', and for packages 'citation("pkgname")'.
333s 
333s 
333s Attaching package: ‘Biobase’
333s 
333s The following object is masked from ‘package:MatrixGenerics’:
333s 
333s     rowMedians
333s 
333s The following objects are masked from ‘package:matrixStats’:
333s 
333s     anyMissing, rowMedians
333s 
337s > 
337s Test: Run tests for ShortRead
337s Start: ShortRead_unit_tests.R
337s 
337s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
337s Copyright (C) 2025 The R Foundation for Statistical Computing
337s Platform: x86_64-pc-linux-gnu
337s 
337s R is free software and comes with ABSOLUTELY NO WARRANTY.
337s You are welcome to redistribute it under certain conditions.
337s Type 'license()' or 'licence()' for distribution details.
337s 
337s R is a collaborative project with many contributors.
337s Type 'contributors()' for more information and
337s 'citation()' on how to cite R or R packages in publications.
337s 
337s Type 'demo()' for some demos, 'help()' for on-line help, or
337s 'help.start()' for an HTML browser interface to help.
337s Type 'q()' to quit R.
337s 
337s > BiocGenerics:::testPackage("ShortRead")
337s 
337s Attaching package: ‘BiocGenerics’
337s 
337s The following objects are masked from ‘package:stats’:
337s 
337s     IQR, mad, sd, var, xtabs
337s 
337s The following objects are masked from ‘package:base’:
337s 
337s     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
337s     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
337s     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
337s     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
337s     Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
337s     table, tapply, union, unique, unsplit, which.max, which.min
337s 
337s 
337s Attaching package: ‘S4Vectors’
337s 
337s The following object is masked from ‘package:utils’:
337s 
337s     findMatches
337s 
337s The following objects are masked from ‘package:base’:
337s 
337s     expand.grid, I, unname
337s 
338s 
338s Attaching package: ‘Biostrings’
338s 
338s The following object is masked from ‘package:base’:
338s 
338s     strsplit
338s 
339s 
339s Attaching package: ‘MatrixGenerics’
339s 
339s The following objects are masked from ‘package:matrixStats’:
339s 
339s     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
339s     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
339s     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
339s     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
339s     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
339s     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
339s     colWeightedMeans, colWeightedMedians, colWeightedSds,
339s     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
339s     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
339s     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
339s     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
339s     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
339s     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
339s     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
339s     rowWeightedSds, rowWeightedVars
339s 
339s Welcome to Bioconductor
339s 
339s     Vignettes contain introductory material; view with
339s     'browseVignettes()'. To cite Bioconductor, see
339s     'citation("Biobase")', and for packages 'citation("pkgname")'.
339s 
339s 
339s Attaching package: ‘Biobase’
339s 
339s The following object is masked from ‘package:MatrixGenerics’:
339s 
339s     rowMedians
339s 
339s The following objects are masked from ‘package:matrixStats’:
339s 
339s     anyMissing, rowMedians
339s 
346s 
346s 
346s RUNIT TEST PROTOCOL -- Tue Feb 10 01:50:16 2026 
346s *********************************************** 
346s Number of test functions: 106 
346s Number of errors: 0 
346s Number of failures: 0 
346s 
346s  
346s 1 Test Suite : 
346s ShortRead RUnit Tests - 106 test functions, 0 errors, 0 failures
346s Number of test functions: 106 
346s Number of errors: 0 
346s Number of failures: 0 
346s > 
346s Warning message:
346s In for (i in seq_len(n)) { :
346s   closing unused connection 3 (/tmp/Rtmp6m6mKj/file15505d1cf5f6)
346s autopkgtest [01:50:17]: test pkg-r-autopkgtest: -----------------------]
347s pkg-r-autopkgtest    PASS
347s autopkgtest [01:50:18]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
347s autopkgtest [01:50:18]: @@@@@@@@@@@@@@@@@@@@ summary
347s pkg-r-autopkgtest    PASS