0s autopkgtest [01:59:21]: starting date and time: 2026-02-10 01:59:21+0000
  0s autopkgtest [01:59:21]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op
  0s autopkgtest [01:59:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eugpld0_/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-cran-bio3d --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-20@sto01-15.secgroup --name adt-resolute-amd64-r-cran-bio3d-20260210-015920-juju-7f2275-prod-proposed-migration-environment-20-d9ffa9c9-12dd-4a4d-bc72-ac2b756c6b36 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/
  3s Creating nova instance adt-resolute-amd64-r-cran-bio3d-20260210-015920-juju-7f2275-prod-proposed-migration-environment-20-d9ffa9c9-12dd-4a4d-bc72-ac2b756c6b36 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
 75s autopkgtest [02:00:36]: testbed dpkg architecture: amd64
 75s autopkgtest [02:00:36]: testbed apt version: 3.1.14
 75s autopkgtest [02:00:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 75s autopkgtest [02:00:36]: testbed release detected to be: None
 76s autopkgtest [02:00:37]: 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/universe Sources [1637 kB]
 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB]
 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB]
 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB]
 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB]
 77s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B]
 77s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B]
 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB]
 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB]
 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB]
 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB]
 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B]
 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
 78s Fetched 4710 kB in 1s (4669 kB/s)
 78s Reading package lists...
 79s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
 79s Reading package lists...
 79s Reading package lists...
 80s Building dependency tree...
 80s Reading state information...
 80s Calculating upgrade...
 80s The following package was automatically installed and is no longer required:
 80s   libpython3.13
 80s Use 'sudo apt autoremove' to remove it.
 80s The following NEW packages will be installed:
 80s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
 80s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
 80s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
 80s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
 80s The following packages will be upgraded:
 80s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
 80s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
 80s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
 80s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
 80s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
 80s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
 80s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
 80s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
 80s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
 80s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
 80s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
 80s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
 80s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
 80s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
 80s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
 80s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
 80s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
 80s Need to get 237 MB of archives.
 80s After this operation, 339 MB of additional disk space will be used.
 80s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
 80s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
 80s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
 80s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
 80s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
 80s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
 80s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
 80s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
 80s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
 80s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
 80s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
 81s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
 81s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
 81s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
 81s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
 81s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
 81s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
 81s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
 81s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
 81s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
 81s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
 81s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
 81s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
 81s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
 81s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
 81s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
 81s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
 81s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
 81s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
 81s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
 81s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
 81s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
 81s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
 81s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
 81s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
 81s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
 81s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
 81s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
 81s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
 81s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
 81s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
 81s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
 81s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
 81s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
 81s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
 81s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
 81s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
 81s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
 81s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
 81s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
 81s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
 81s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
 81s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
 81s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
 81s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
 81s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
 81s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
 81s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
 81s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
 81s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
 81s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
 81s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
 81s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
 81s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
 81s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
 81s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
 90s 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]
 91s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
 91s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
 91s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
 91s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
 91s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
 91s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
 91s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
 92s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
 93s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
 93s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
 93s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
 93s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
 93s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
 93s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
 93s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
 93s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
 93s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
 93s dpkg-preconfigure: unable to re-open stdin: No such file or directory
 93s Fetched 237 MB in 13s (18.2 MB/s)
 93s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 93s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
 93s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
 93s Setting up debianutils (5.23.2build1) ...
 94s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 94s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
 94s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
 94s Setting up dash (0.5.12-12ubuntu3) ...
 94s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 94s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
 94s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
 94s Setting up findutils (4.10.0-3build2) ...
 94s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 94s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
 94s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
 94s Setting up sed (4.9-2build3) ...
 94s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
 94s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
 94s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
 94s Setting up tar (1.35+dfsg-3.1build2) ...
 94s (Reading database ... 
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104s Setting up libjansson4:amd64 (2.14-2build4) ...
104s Setting up libglib2.0-data (2.87.2-2) ...
104s Setting up pollinate (4.33-4ubuntu5) ...
114s Setting up busybox-static (1:1.37.0-7ubuntu1) ...
114s Setting up libwrap0:amd64 (7.6.q-36build2) ...
114s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
115s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
115s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
115s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
115s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ...
115s Setting up patch (2.8-2build1) ...
115s Setting up libsensors5:amd64 (1:3.6.2-2build1) ...
115s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
115s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
115s Setting up lsof (4.99.4+dfsg-2build2) ...
115s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
115s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
115s Setting up dracut-install (109-11ubuntu1) ...
115s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
115s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
115s Setting up pnp.ids (0.394-1build1) ...
115s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
115s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
116s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
116s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
116s Setting up mawk (1.3.4.20260129-1) ...
116s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
116s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
116s Setting up linux-image-virtual (6.19.0-3.3) ...
116s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
116s Setting up libbsd0:amd64 (0.12.2-2build2) ...
116s Setting up libdrm-common (2.4.131-1) ...
116s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
116s Setting up dbus-bin (1.16.2-2ubuntu3) ...
116s Setting up libonig5:amd64 (6.9.10-1build1) ...
116s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
116s Setting up ethtool (1:6.15-3build1) ...
116s Setting up python3-referencing (0.36.2-1ubuntu2) ...
116s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
116s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
116s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
116s Setting up tcpdump (4.99.5-2ubuntu3) ...
116s Setting up linux-image-generic (6.19.0-3.3) ...
116s Setting up wget (1.25.0-2ubuntu4) ...
116s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
116s Setting up iptables (1.8.11-2ubuntu3) ...
116s Setting up iproute2 (6.18.0-1ubuntu1) ...
116s Setting up linux-headers-generic (6.19.0-3.3) ...
116s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
116s Setting up hwdata (0.394-1build1) ...
116s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
116s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
116s No schema files found: doing nothing.
116s Setting up dbus (1.16.2-2ubuntu3) ...
116s A reboot is required to replace the running dbus-daemon.
116s Please reboot the system when convenient.
116s Setting up shared-mime-info (2.4-5build3) ...
117s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
117s Setting up pciutils (1:3.14.0-1build2) ...
117s Setting up python3-markdown-it (3.0.0-3build1) ...
117s Setting up libdrm2:amd64 (2.4.131-1) ...
117s Setting up libpython3.14:amd64 (3.14.2-1) ...
117s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
117s Setting up linux-tools-common (6.19.0-3.3) ...
117s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
117s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
117s Setting up apt (3.1.15) ...
118s Setting up linux-headers-virtual (6.19.0-3.3) ...
118s Setting up linux-generic (6.19.0-3.3) ...
118s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
118s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
118s Setting up ubuntu-standard (1.564) ...
118s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
118s Setting up linux-virtual (6.19.0-3.3) ...
118s Setting up linux-perf (6.19.0-3.3) ...
118s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
118s Processing triggers for debianutils (5.23.2build1) ...
118s Processing triggers for install-info (7.2-5) ...
118s Processing triggers for initramfs-tools (0.150ubuntu7) ...
118s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
122s Processing triggers for libc-bin (2.42-2ubuntu4) ...
122s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
122s /etc/kernel/postinst.d/initramfs-tools:
122s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
127s /etc/kernel/postinst.d/zz-update-grub:
127s Sourcing file `/etc/default/grub'
127s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
127s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
127s Generating grub configuration file ...
127s Found linux image: /boot/vmlinuz-6.19.0-3-generic
127s Found initrd image: /boot/initrd.img-6.19.0-3-generic
127s Found linux image: /boot/vmlinuz-6.18.0-9-generic
127s Found initrd image: /boot/initrd.img-6.18.0-9-generic
127s Warning: os-prober will not be executed to detect other bootable partitions.
127s Systems on them will not be added to the GRUB boot configuration.
127s Check GRUB_DISABLE_OS_PROBER documentation entry.
127s Adding boot menu entry for UEFI Firmware Settings ...
127s done
127s autopkgtest [02:01:28]: upgrading testbed (apt dist-upgrade and autopurge)
128s Reading package lists...
128s Building dependency tree...
128s Reading state information...
128s Calculating upgrade...
128s The following package was automatically installed and is no longer required:
128s   libpython3.13
128s Use 'sudo apt autoremove' to remove it.
128s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s Solving dependencies...
129s The following packages will be REMOVED:
129s   libpython3.13*
129s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
129s After this operation, 7599 kB disk space will be freed.
129s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
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(Reading database ... 60%
(Reading database ... 65%
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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.)
129s Removing libpython3.13:amd64 (3.13.11-1) ...
129s Processing triggers for libc-bin (2.42-2ubuntu4) ...
129s autopkgtest [02:01:30]: rebooting testbed after setup commands that affected boot
158s autopkgtest [02:01:59]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026
163s autopkgtest [02:02:04]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-bio3d
164s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-bio3d 2.4-5-1 (dsc) [2285 B]
164s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-bio3d 2.4-5-1 (tar) [1544 kB]
164s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-bio3d 2.4-5-1 (diff) [5468 B]
164s gpgv: Signature made Wed Jan 29 00:14:06 2025 UTC
164s gpgv:                using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502
164s gpgv:                issuer "plessy@debian.org"
164s gpgv: Can't check signature: No public key
164s dpkg-source: warning: cannot verify inline signature for ./r-cran-bio3d_2.4-5-1.dsc: no acceptable signature found
164s autopkgtest [02:02:05]: testing package r-cran-bio3d version 2.4-5-1
166s autopkgtest [02:02:07]: build not needed
169s autopkgtest [02:02:10]: test run-unit-test: preparing testbed
169s Reading package lists...
169s Building dependency tree...
169s Reading state information...
169s Solving dependencies...
169s The following NEW packages will be installed:
169s   fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
169s   fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax
169s   javascript-common libamd3 libasan8 libblas3 libboost-dev libboost1.90-dev
169s   libc-dev-bin libc6-dev libcairo2 libcolamd3 libcrypt-dev libdatrie1
169s   libdeflate0 libfontconfig1 libgcc-15-dev libgfortran5 libglpk40 libgomp1
169s   libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhwasan0 libice6
169s   libitm1 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap libjs-bootstrap4
169s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
169s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
169s   libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js
169s   libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker liblapack3
169s   liblerc4 liblsan0 libltdl7 liblua5.4-0 libnetcdf22 libpango-1.0-0
169s   libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0
169s   libquadmath0 libsharpyuv0 libsm6 libstdc++-15-dev libsuitesparseconfig7
169s   libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtsan2 libubsan1
169s   libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxss1 libxt6t64
169s   linux-libc-dev node-bootstrap-sass node-html5shiv node-normalize.css pandoc
169s   pandoc-data r-base-core r-bioc-biocgenerics r-bioc-biostrings
169s   r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-s4vectors
169s   r-bioc-ucsc.utils r-bioc-xvector r-bioc-zlibbioc r-cran-askpass
169s   r-cran-base64enc r-cran-bh r-cran-bigmemory r-cran-bigmemory.sri
169s   r-cran-bio3d r-cran-bitops r-cran-brio r-cran-bslib r-cran-cachem
169s   r-cran-callr r-cran-cli r-cran-commonmark r-cran-cpp11 r-cran-crayon
169s   r-cran-curl r-cran-desc r-cran-diffobj r-cran-digest r-cran-evaluate
169s   r-cran-fastmap r-cran-fontawesome r-cran-fs r-cran-glue r-cran-highr
169s   r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-igraph r-cran-jquerylib
169s   r-cran-jsonlite r-cran-knitr r-cran-later r-cran-lattice r-cran-lifecycle
169s   r-cran-littler r-cran-magrittr r-cran-matrix r-cran-memoise r-cran-mime
169s   r-cran-ncdf4 r-cran-openssl r-cran-pkgbuild r-cran-pkgconfig
169s   r-cran-pkgkitten r-cran-pkgload r-cran-praise r-cran-processx
169s   r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs r-cran-rcpp r-cran-rcurl
169s   r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-sass r-cran-shiny
169s   r-cran-sourcetools r-cran-sys r-cran-testthat r-cran-tinytex r-cran-uuid
169s   r-cran-vctrs r-cran-waldo r-cran-withr r-cran-xfun r-cran-xml r-cran-xtable
169s   r-cran-yaml rpcsvc-proto unzip x11-common xdg-utils zip zlib1g-dev
169s 0 upgraded, 177 newly installed, 0 to remove and 0 not upgraded.
169s Need to get 198 MB of archives.
169s After this operation, 752 MB of additional disk space will be used.
169s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
169s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
170s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
170s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
170s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
170s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB]
170s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
170s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
170s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B]
170s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
170s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [22.0 kB]
170s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.12.1+dfsg-1 [35.8 kB]
170s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
170s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
170s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
170s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
170s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
170s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
170s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
170s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
170s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
170s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
170s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
170s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
170s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
170s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
170s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
171s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB]
171s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B]
171s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
171s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
171s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
171s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
171s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
171s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [27.4 kB]
171s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
171s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
171s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
171s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB]
171s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB]
171s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
171s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
171s Get:43 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.5-1 [17.9 kB]
171s Get:44 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.6+repack-2 [1433 kB]
171s Get:45 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.6+repack-2 [59.9 kB]
171s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
171s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
171s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
171s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
171s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
171s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB]
172s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
172s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB]
172s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
172s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
172s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
172s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
172s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
172s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B]
172s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
172s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB]
172s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB]
172s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB]
172s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
172s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
172s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
172s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnetcdf22 amd64 1:4.9.3-1build1 [561 kB]
172s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
172s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
172s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
172s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
172s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
172s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
172s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
172s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
172s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
172s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
172s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
172s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
172s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
172s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
172s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
172s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
172s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
172s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
172s Get:86 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
172s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
172s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
172s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
172s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
172s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
172s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
172s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
173s Get:94 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
173s Get:95 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
173s Get:96 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
174s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
174s Get:98 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
174s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
174s Get:100 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
174s Get:101 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
174s Get:102 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
174s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
174s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
174s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
174s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
174s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
174s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
174s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
174s Get:110 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
174s Get:111 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
174s Get:112 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
174s Get:113 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
174s Get:114 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
174s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bigmemory.sri all 0.1.8-1 [13.4 kB]
174s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB]
174s Get:117 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
175s Get:118 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
175s Get:119 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB]
175s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bigmemory amd64 4.6.4-2 [488 kB]
175s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bio3d amd64 2.4-5-1 [3028 kB]
175s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
175s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB]
175s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
175s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
175s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
175s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
175s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
175s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB]
175s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
175s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
175s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
175s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
175s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB]
175s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
175s Get:136 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
175s Get:137 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
175s Get:138 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
175s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
175s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
175s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
175s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
175s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diffobj amd64 0.3.5-1build1 [1156 kB]
175s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
175s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
175s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
175s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
175s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
175s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
175s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
175s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
175s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
175s Get:153 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB]
175s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
176s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
176s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
176s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-igraph amd64 2.1.4-1build1 [5218 kB]
176s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
176s Get:159 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
176s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
176s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ncdf4 amd64 1.23-1build1 [279 kB]
176s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgbuild all 1.4.8-1 [219 kB]
176s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rprojroot all 2.1.1-1 [131 kB]
176s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgload all 1.4.1-1 [252 kB]
176s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-praise all 1.0.0-4build2 [20.9 kB]
176s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
176s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB]
176s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB]
176s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
176s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
176s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
176s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
176s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
176s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB]
176s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-waldo all 0.6.2-1 [153 kB]
176s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB]
176s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
177s Preconfiguring packages ...
177s Fetched 198 MB in 7s (28.0 MB/s)
177s Selecting previously unselected package fonts-dejavu-mono.
177s (Reading database ... 
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(Reading database ... 125269 files and directories currently installed.)
177s Preparing to unpack .../000-fonts-dejavu-mono_2.37-8build1_all.deb ...
177s Unpacking fonts-dejavu-mono (2.37-8build1) ...
177s Selecting previously unselected package fonts-dejavu-core.
177s Preparing to unpack .../001-fonts-dejavu-core_2.37-8build1_all.deb ...
177s Unpacking fonts-dejavu-core (2.37-8build1) ...
177s Selecting previously unselected package fontconfig-config.
177s Preparing to unpack .../002-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ...
177s Unpacking fontconfig-config (2.17.1-3ubuntu1) ...
177s Selecting previously unselected package libfontconfig1:amd64.
177s Preparing to unpack .../003-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ...
177s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
177s Selecting previously unselected package fontconfig.
177s Preparing to unpack .../004-fontconfig_2.17.1-3ubuntu1_amd64.deb ...
177s Unpacking fontconfig (2.17.1-3ubuntu1) ...
177s Selecting previously unselected package fonts-font-awesome.
177s Preparing to unpack .../005-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1build1_all.deb ...
177s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ...
177s Selecting previously unselected package fonts-glyphicons-halflings.
177s Preparing to unpack .../006-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ...
177s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
177s Selecting previously unselected package fonts-mathjax.
177s Preparing to unpack .../007-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ...
177s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ...
177s Selecting previously unselected package javascript-common.
177s Preparing to unpack .../008-javascript-common_12+nmu1build1_all.deb ...
177s Unpacking javascript-common (12+nmu1build1) ...
177s Selecting previously unselected package libgomp1:amd64.
177s Preparing to unpack .../009-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libsuitesparseconfig7:amd64.
177s Preparing to unpack .../010-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_amd64.deb ...
177s Unpacking libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ...
177s Selecting previously unselected package libamd3:amd64.
177s Preparing to unpack .../011-libamd3_1%3a7.12.1+dfsg-1_amd64.deb ...
177s Unpacking libamd3:amd64 (1:7.12.1+dfsg-1) ...
177s Selecting previously unselected package libasan8:amd64.
177s Preparing to unpack .../012-libasan8_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libblas3:amd64.
177s Preparing to unpack .../013-libblas3_3.12.1-7ubuntu1_amd64.deb ...
177s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ...
177s Selecting previously unselected package libitm1:amd64.
177s Preparing to unpack .../014-libitm1_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package liblsan0:amd64.
177s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libtsan2:amd64.
177s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libubsan1:amd64.
177s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libhwasan0:amd64.
177s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libquadmath0:amd64.
177s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ...
177s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ...
177s Selecting previously unselected package libgcc-15-dev:amd64.
177s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ...
177s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
178s Selecting previously unselected package libc-dev-bin.
178s Preparing to unpack .../021-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
178s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
178s Selecting previously unselected package linux-libc-dev:amd64.
178s Preparing to unpack .../022-linux-libc-dev_6.19.0-3.3_amd64.deb ...
178s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
178s Selecting previously unselected package libcrypt-dev:amd64.
178s Preparing to unpack .../023-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
178s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
178s Selecting previously unselected package rpcsvc-proto.
178s Preparing to unpack .../024-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
178s Unpacking rpcsvc-proto (1.4.3-1build1) ...
178s Selecting previously unselected package libc6-dev:amd64.
178s Preparing to unpack .../025-libc6-dev_2.42-2ubuntu4_amd64.deb ...
178s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
178s Selecting previously unselected package libstdc++-15-dev:amd64.
178s Preparing to unpack .../026-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ...
178s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
178s Selecting previously unselected package libboost1.90-dev:amd64.
178s Preparing to unpack .../027-libboost1.90-dev_1.90.0-2ubuntu1_amd64.deb ...
178s Unpacking libboost1.90-dev:amd64 (1.90.0-2ubuntu1) ...
179s Selecting previously unselected package libboost-dev:amd64.
179s Preparing to unpack .../028-libboost-dev_1.90.0.0ubuntu3_amd64.deb ...
179s Unpacking libboost-dev:amd64 (1.90.0.0ubuntu3) ...
179s Selecting previously unselected package libpixman-1-0:amd64.
179s Preparing to unpack .../029-libpixman-1-0_0.46.4-1_amd64.deb ...
179s Unpacking libpixman-1-0:amd64 (0.46.4-1) ...
179s Selecting previously unselected package libxcb-render0:amd64.
179s Preparing to unpack .../030-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ...
179s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ...
179s Selecting previously unselected package libxcb-shm0:amd64.
179s Preparing to unpack .../031-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ...
179s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
179s Selecting previously unselected package libxrender1:amd64.
179s Preparing to unpack .../032-libxrender1_1%3a0.9.12-1_amd64.deb ...
179s Unpacking libxrender1:amd64 (1:0.9.12-1) ...
179s Selecting previously unselected package libcairo2:amd64.
179s Preparing to unpack .../033-libcairo2_1.18.4-3_amd64.deb ...
179s Unpacking libcairo2:amd64 (1.18.4-3) ...
179s Selecting previously unselected package libcolamd3:amd64.
179s Preparing to unpack .../034-libcolamd3_1%3a7.12.1+dfsg-1_amd64.deb ...
179s Unpacking libcolamd3:amd64 (1:7.12.1+dfsg-1) ...
179s Selecting previously unselected package libdatrie1:amd64.
179s Preparing to unpack .../035-libdatrie1_0.2.14-1_amd64.deb ...
179s Unpacking libdatrie1:amd64 (0.2.14-1) ...
179s Selecting previously unselected package libdeflate0:amd64.
179s Preparing to unpack .../036-libdeflate0_1.23-2build1_amd64.deb ...
179s Unpacking libdeflate0:amd64 (1.23-2build1) ...
179s Selecting previously unselected package libgfortran5:amd64.
179s Preparing to unpack .../037-libgfortran5_16-20260208-1ubuntu1_amd64.deb ...
179s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ...
179s Selecting previously unselected package libltdl7:amd64.
179s Preparing to unpack .../038-libltdl7_2.5.4-9_amd64.deb ...
179s Unpacking libltdl7:amd64 (2.5.4-9) ...
179s Selecting previously unselected package libglpk40:amd64.
179s Preparing to unpack .../039-libglpk40_5.0-2_amd64.deb ...
179s Unpacking libglpk40:amd64 (5.0-2) ...
179s Selecting previously unselected package libgraphite2-3:amd64.
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186s Setting up r-cran-testthat (3.2.3-1) ...
186s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
186s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
186s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
186s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
186s Setting up r-cran-rmarkdown (2.30+dfsg-1) ...
186s Processing triggers for libc-bin (2.42-2ubuntu4) ...
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187s Processing triggers for install-info (7.2-5) ...
187s autopkgtest [02:02:28]: test run-unit-test: [-----------------------
188s BEGIN TEST testthat.R
188s 
188s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
188s Copyright (C) 2025 The R Foundation for Statistical Computing
188s Platform: x86_64-pc-linux-gnu
188s 
188s R is free software and comes with ABSOLUTELY NO WARRANTY.
188s You are welcome to redistribute it under certain conditions.
188s Type 'license()' or 'licence()' for distribution details.
188s 
188s R is a collaborative project with many contributors.
188s Type 'contributors()' for more information and
188s 'citation()' on how to cite R or R packages in publications.
188s 
188s Type 'demo()' for some demos, 'help()' for on-line help, or
188s 'help.start()' for an HTML browser interface to help.
188s Type 'q()' to quit R.
188s 
188s > library(testthat)
188s > test_check("bio3d")
188s Loading required package: bio3d
191s [ FAIL 0 | WARN 0 | SKIP 29 | PASS 174 ]
191s 
191s == Skipped tests (29) ==========================================================
192s * On CRAN (29): 'test-aanma.R:5:3', 'test-aanma.pdbs.R:10:3',
192s   'test-clean.pdb.R:24:3', 'test-cmap.R:20:3', 'test-cna.R:5:3',
192s   'test-core.find.R:5:3', 'test-dccm.R:27:3', 'test-dccm.R:47:3',
192s   'test-dssp.R:4:3', 'test-fitting.R:64:3', 'test-fitting.R:91:4',
192s   'test-fitting.R:116:4', 'test-get.pdb.R:4:3', 'test-get.pdb.R:24:3',
192s   'test-get.seq.R:4:3', 'test-mol2.R:34:3', 'test-mol2.R:49:3',
192s   'test-mol2.R:82:3', 'test-nma.pdbs.R:5:3', 'test-pdb.annotate.R:5:3',
192s   'test-pdbsplit.R:5:3', 'test-read.all.R:6:3', 'test-read.cif.R:5:3',
192s   'test-read.cif.R:49:3', 'test-read.ncdf.R:4:4', 'test-read.pdb.R:43:3',
192s   'test-read.pdb.R:121:3', 'test-read.pdb.R:141:3', 'test-seqaln.R:5:3'
192s 
192s [ FAIL 0 | WARN 0 | SKIP 29 | PASS 174 ]
192s > 
192s autopkgtest [02:02:33]: test run-unit-test: -----------------------]
192s run-unit-test        PASS
192s autopkgtest [02:02:33]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
193s autopkgtest [02:02:34]: test pkg-r-autopkgtest: preparing testbed
212s Creating nova instance adt-resolute-amd64-r-cran-bio3d-20260210-015920-juju-7f2275-prod-proposed-migration-environment-20-d9ffa9c9-12dd-4a4d-bc72-ac2b756c6b36 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)...
281s autopkgtest [02:04:02]: testbed dpkg architecture: amd64
281s autopkgtest [02:04:02]: testbed apt version: 3.1.14
281s autopkgtest [02:04:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup
281s autopkgtest [02:04:02]: testbed release detected to be: resolute
282s autopkgtest [02:04:03]: updating testbed package index (apt update)
282s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB]
282s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
282s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
282s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
282s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB]
282s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB]
282s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB]
282s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB]
282s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB]
283s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B]
283s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B]
283s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB]
283s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB]
283s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB]
283s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB]
283s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B]
283s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B]
283s Fetched 4710 kB in 1s (4921 kB/s)
284s Reading package lists...
284s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease
285s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease
285s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease
285s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease
285s Reading package lists...
285s Reading package lists...
285s Building dependency tree...
285s Reading state information...
285s Calculating upgrade...
285s The following package was automatically installed and is no longer required:
285s   libpython3.13
285s Use 'sudo apt autoremove' to remove it.
286s The following NEW packages will be installed:
286s   gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib
286s   linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic
286s   linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic
286s   linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic
286s The following packages will be upgraded:
286s   3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static
286s   cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common
286s   dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install
286s   ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2
286s   iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0
286s   libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common
286s   libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64
286s   libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0
286s   libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0
286s   libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64
286s   libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0
286s   libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic
286s   linux-headers-virtual linux-image-generic linux-image-virtual linux-perf
286s   linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids
286s   pollinate python3-linkify-it python3-markdown-it python3-referencing sed
286s   shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget
286s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
286s Need to get 237 MB of archives.
286s After this operation, 339 MB of additional disk space will be used.
286s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB]
286s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB]
286s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB]
286s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB]
286s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB]
286s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB]
286s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB]
286s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB]
286s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB]
286s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB]
286s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB]
286s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB]
286s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB]
286s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB]
286s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB]
286s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B]
286s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB]
286s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB]
286s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB]
286s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB]
286s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB]
286s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB]
286s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB]
286s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB]
286s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB]
286s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB]
286s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB]
286s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB]
286s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB]
286s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB]
286s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB]
286s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB]
286s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB]
286s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB]
286s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB]
286s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB]
286s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB]
286s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB]
286s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB]
286s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB]
286s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB]
286s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB]
286s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB]
286s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB]
286s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B]
286s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB]
286s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB]
286s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB]
286s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB]
286s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB]
286s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB]
286s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB]
286s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB]
286s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB]
286s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB]
286s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B]
286s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB]
286s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB]
286s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B]
286s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB]
286s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB]
286s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB]
286s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB]
286s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB]
286s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB]
286s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB]
286s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB]
286s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB]
286s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB]
286s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B]
286s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB]
286s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB]
286s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB]
286s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B]
286s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB]
286s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B]
286s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB]
286s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB]
286s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB]
287s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB]
287s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB]
287s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB]
289s 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]
290s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB]
290s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B]
290s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB]
290s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B]
290s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB]
290s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B]
290s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB]
290s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB]
290s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB]
290s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB]
290s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB]
290s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB]
290s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B]
290s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB]
290s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB]
290s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB]
290s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB]
290s dpkg-preconfigure: unable to re-open stdin: No such file or directory
290s Fetched 237 MB in 5s (52.1 MB/s)
290s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
290s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ...
290s Unpacking debianutils (5.23.2build1) over (5.23.2) ...
290s Setting up debianutils (5.23.2build1) ...
291s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
291s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ...
291s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ...
291s Setting up dash (0.5.12-12ubuntu3) ...
291s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
291s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ...
291s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ...
291s Setting up findutils (4.10.0-3build2) ...
291s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
291s Preparing to unpack .../sed_4.9-2build3_amd64.deb ...
291s Unpacking sed (4.9-2build3) over (4.9-2build2) ...
291s Setting up sed (4.9-2build3) ...
291s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
291s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ...
291s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ...
291s Setting up tar (1.35+dfsg-3.1build2) ...
291s (Reading database ... 
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(Reading database ... 83957 files and directories currently installed.)
291s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ...
291s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ...
291s Setting up libattr1:amd64 (1:2.5.2-3build2) ...
291s Selecting previously unselected package gcc-16-base:amd64.
291s (Reading database ... 
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298s Setting up liblsof0 (4.99.4+dfsg-2build2) ...
298s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ...
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298s Setting up libidn2-0:amd64 (2.3.8-4build1) ...
298s Setting up amd64-microcode (3.20251202.1ubuntu1) ...
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300s Setting up pollinate (4.33-4ubuntu5) ...
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310s Setting up libwrap0:amd64 (7.6.q-36build2) ...
310s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
311s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic
311s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic
311s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ...
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311s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ...
311s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ...
311s Setting up lsof (4.99.4+dfsg-2build2) ...
311s Setting up libpci3:amd64 (1:3.14.0-1build2) ...
311s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ...
311s Setting up dracut-install (109-11ubuntu1) ...
311s Setting up dmsetup (2:1.02.205-2ubuntu3) ...
311s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ...
311s Setting up pnp.ids (0.394-1build1) ...
311s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ...
311s Setting up python3-linkify-it (2.0.3-1ubuntu3) ...
312s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ...
312s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ...
312s Setting up mawk (1.3.4.20260129-1) ...
312s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ...
312s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ...
312s Setting up linux-image-virtual (6.19.0-3.3) ...
312s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ...
312s Setting up libbsd0:amd64 (0.12.2-2build2) ...
312s Setting up libdrm-common (2.4.131-1) ...
312s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ...
312s Setting up dbus-bin (1.16.2-2ubuntu3) ...
312s Setting up libonig5:amd64 (6.9.10-1build1) ...
312s Setting up libbpf1:amd64 (1:1.6.2-1build1) ...
312s Setting up ethtool (1:6.15-3build1) ...
312s Setting up python3-referencing (0.36.2-1ubuntu2) ...
312s Setting up libxkbcommon0:amd64 (1.13.1-1) ...
312s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ...
312s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ...
312s Setting up tcpdump (4.99.5-2ubuntu3) ...
312s Setting up linux-image-generic (6.19.0-3.3) ...
312s Setting up wget (1.25.0-2ubuntu4) ...
312s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ...
312s Setting up iptables (1.8.11-2ubuntu3) ...
312s Setting up iproute2 (6.18.0-1ubuntu1) ...
312s Setting up linux-headers-generic (6.19.0-3.3) ...
312s Setting up dbus-daemon (1.16.2-2ubuntu3) ...
312s Setting up hwdata (0.394-1build1) ...
312s Setting up dbus-user-session (1.16.2-2ubuntu3) ...
312s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ...
312s No schema files found: doing nothing.
312s Setting up dbus (1.16.2-2ubuntu3) ...
312s A reboot is required to replace the running dbus-daemon.
312s Please reboot the system when convenient.
312s Setting up shared-mime-info (2.4-5build3) ...
313s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ...
313s Setting up pciutils (1:3.14.0-1build2) ...
313s Setting up python3-markdown-it (3.0.0-3build1) ...
313s Setting up libdrm2:amd64 (2.4.131-1) ...
313s Setting up libpython3.14:amd64 (3.14.2-1) ...
313s Setting up libapt-pkg7.0:amd64 (3.1.15) ...
313s Setting up linux-tools-common (6.19.0-3.3) ...
313s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ...
313s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ...
313s Setting up apt (3.1.15) ...
313s Setting up linux-headers-virtual (6.19.0-3.3) ...
313s Setting up linux-generic (6.19.0-3.3) ...
313s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ...
313s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ...
313s Setting up ubuntu-standard (1.564) ...
313s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ...
313s Setting up linux-virtual (6.19.0-3.3) ...
313s Setting up linux-perf (6.19.0-3.3) ...
313s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ...
313s Processing triggers for debianutils (5.23.2build1) ...
313s Processing triggers for install-info (7.2-5) ...
313s Processing triggers for initramfs-tools (0.150ubuntu7) ...
313s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic
318s Processing triggers for libc-bin (2.42-2ubuntu4) ...
318s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ...
318s /etc/kernel/postinst.d/initramfs-tools:
318s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic
322s /etc/kernel/postinst.d/zz-update-grub:
322s Sourcing file `/etc/default/grub'
322s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg'
322s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg'
322s Generating grub configuration file ...
322s Found linux image: /boot/vmlinuz-6.19.0-3-generic
322s Found initrd image: /boot/initrd.img-6.19.0-3-generic
322s Found linux image: /boot/vmlinuz-6.18.0-9-generic
322s Found initrd image: /boot/initrd.img-6.18.0-9-generic
322s Warning: os-prober will not be executed to detect other bootable partitions.
322s Systems on them will not be added to the GRUB boot configuration.
322s Check GRUB_DISABLE_OS_PROBER documentation entry.
322s Adding boot menu entry for UEFI Firmware Settings ...
322s done
322s autopkgtest [02:04:43]: upgrading testbed (apt dist-upgrade and autopurge)
323s Reading package lists...
323s Building dependency tree...
323s Reading state information...
323s Calculating upgrade...
323s The following package was automatically installed and is no longer required:
323s   libpython3.13
323s Use 'sudo apt autoremove' to remove it.
323s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
323s Reading package lists...
323s Building dependency tree...
323s Reading state information...
323s Solving dependencies...
323s The following packages will be REMOVED:
323s   libpython3.13*
324s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
324s After this operation, 7599 kB disk space will be freed.
324s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125273 files and directories currently installed.)
324s Removing libpython3.13:amd64 (3.13.11-1) ...
324s Processing triggers for libc-bin (2.42-2ubuntu4) ...
324s autopkgtest [02:04:45]: rebooting testbed after setup commands that affected boot
354s Reading package lists...
354s Building dependency tree...
354s Reading state information...
354s Solving dependencies...
354s The following NEW packages will be installed:
354s   build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu
354s   dctrl-tools fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono
354s   fonts-font-awesome fonts-glyphicons-halflings fonts-mathjax g++ g++-15
354s   g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15
354s   gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15
354s   gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools
354s   javascript-common libamd3 libasan8 libblas-dev libblas3 libboost-dev
354s   libboost1.90-dev libbz2-dev libc-dev-bin libc6-dev libcairo2 libcc1-0
354s   libcolamd3 libcrypt-dev libdatrie1 libdeflate-dev libdeflate0 libfontconfig1
354s   libgcc-15-dev libgfortran-15-dev libgfortran5 libglpk40 libgomp1
354s   libgraphite2-3 libharfbuzz0b libhdf5-310 libhdf5-hl-310 libhwasan0 libice6
354s   libicu-dev libisl23 libitm1 libjbig0 libjpeg-dev libjpeg-turbo8
354s   libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjs-bootstrap libjs-bootstrap4
354s   libjs-d3 libjs-es5-shim libjs-highlight.js libjs-jquery
354s   libjs-jquery-datatables libjs-jquery-selectize.js libjs-jquery-ui libjs-json
354s   libjs-mathjax libjs-microplugin.js libjs-modernizr libjs-popper.js
354s   libjs-prettify libjs-sifter.js libjs-twitter-bootstrap-datepicker
354s   liblapack-dev liblapack3 liblerc4 liblsan0 libltdl7 liblua5.4-0 liblzma-dev
354s   libmpc3 libncurses-dev libnetcdf22 libpango-1.0-0 libpangocairo-1.0-0
354s   libpangoft2-1.0-0 libpaper-utils libpaper2 libpcre2-16-0 libpcre2-32-0
354s   libpcre2-dev libpcre2-posix3 libpixman-1-0 libpkgconf3 libpng-dev
354s   libquadmath0 libreadline-dev libsharpyuv0 libsm6 libstdc++-15-dev
354s   libsuitesparseconfig7 libsz2 libtcl8.6 libthai-data libthai0 libtiff6
354s   libtirpc-dev libtk8.6 libtsan2 libubsan1 libwebp7 libxcb-render0 libxcb-shm0
354s   libxft2 libxrender1 libxss1 libxt6t64 libzstd-dev linux-libc-dev
354s   node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data
354s   pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev
354s   r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomeinfodb
354s   r-bioc-genomeinfodbdata r-bioc-iranges r-bioc-s4vectors r-bioc-ucsc.utils
354s   r-bioc-xvector r-bioc-zlibbioc r-cran-askpass r-cran-base64enc r-cran-bh
354s   r-cran-bigmemory r-cran-bigmemory.sri r-cran-bio3d r-cran-bitops r-cran-brio
354s   r-cran-bslib r-cran-cachem r-cran-callr r-cran-cli r-cran-commonmark
354s   r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-desc r-cran-diffobj
354s   r-cran-digest r-cran-evaluate r-cran-fastmap r-cran-fontawesome r-cran-fs
354s   r-cran-glue r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr
354s   r-cran-igraph r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-later
354s   r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix
354s   r-cran-memoise r-cran-mime r-cran-ncdf4 r-cran-openssl r-cran-pkgbuild
354s   r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-praise
354s   r-cran-processx r-cran-promises r-cran-ps r-cran-r6 r-cran-rappdirs
354s   r-cran-rcpp r-cran-rcurl r-cran-rlang r-cran-rmarkdown r-cran-rprojroot
354s   r-cran-sass r-cran-shiny r-cran-sourcetools r-cran-sys r-cran-testthat
354s   r-cran-tinytex r-cran-uuid r-cran-vctrs r-cran-waldo r-cran-withr
354s   r-cran-xfun r-cran-xml r-cran-xtable r-cran-yaml rpcsvc-proto unzip
354s   x11-common xdg-utils zip zlib1g-dev
354s 0 upgraded, 223 newly installed, 0 to remove and 0 not upgraded.
354s Need to get 289 MB of archives.
354s After this operation, 1054 MB of additional disk space will be used.
354s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB]
354s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB]
355s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB]
355s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB]
355s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB]
355s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB]
355s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB]
355s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB]
355s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B]
355s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B]
355s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB]
355s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB]
355s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB]
355s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB]
355s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB]
355s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB]
355s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB]
355s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB]
355s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB]
355s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB]
355s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB]
356s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB]
356s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB]
356s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B]
356s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B]
356s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB]
356s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB]
357s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB]
357s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B]
357s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B]
357s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B]
357s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB]
357s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB]
357s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB]
357s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB]
357s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB]
357s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB]
357s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB]
357s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB]
357s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB]
357s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB]
357s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB]
357s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB]
358s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB]
358s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B]
358s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B]
358s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB]
358s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B]
358s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [22.0 kB]
358s Get:50 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.12.1+dfsg-1 [35.8 kB]
358s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB]
358s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB]
358s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB]
358s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B]
358s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB]
358s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB]
358s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB]
358s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B]
358s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB]
358s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB]
358s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [27.4 kB]
358s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB]
358s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB]
358s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB]
358s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB]
358s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB]
358s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB]
358s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB]
358s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.5-1 [17.9 kB]
358s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.6+repack-2 [1433 kB]
358s Get:71 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.6+repack-2 [59.9 kB]
358s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB]
358s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB]
358s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB]
358s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB]
358s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB]
358s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B]
358s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B]
358s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B]
358s Get:80 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB]
358s Get:81 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB]
359s Get:82 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB]
359s Get:83 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB]
359s Get:84 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB]
359s Get:85 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB]
359s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB]
359s Get:87 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB]
359s Get:88 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB]
359s Get:89 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B]
359s Get:90 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB]
359s Get:91 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB]
359s Get:92 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB]
359s Get:93 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB]
359s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB]
359s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB]
359s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB]
359s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB]
359s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB]
359s Get:99 http://ftpmaster.internal/ubuntu resolute/universe amd64 libnetcdf22 amd64 1:4.9.3-1build1 [561 kB]
359s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB]
359s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB]
359s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB]
359s Get:103 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB]
359s Get:104 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB]
359s Get:105 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB]
359s Get:106 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB]
359s Get:107 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB]
359s Get:108 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB]
359s Get:109 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B]
359s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB]
359s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB]
359s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB]
359s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB]
359s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB]
359s Get:115 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB]
359s Get:116 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB]
359s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB]
359s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB]
359s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB]
359s Get:120 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB]
359s Get:121 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB]
359s Get:122 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B]
359s Get:123 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB]
359s Get:124 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB]
359s Get:125 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB]
359s Get:126 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB]
359s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB]
359s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB]
359s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB]
359s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB]
360s Get:131 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB]
360s Get:132 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB]
360s Get:133 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB]
360s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB]
361s Get:135 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB]
361s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB]
361s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB]
361s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB]
361s Get:139 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B]
361s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B]
361s Get:141 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB]
361s Get:142 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB]
361s Get:143 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB]
361s Get:144 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB]
361s Get:145 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB]
361s Get:146 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB]
361s Get:147 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB]
361s Get:148 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB]
361s Get:149 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB]
361s Get:150 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB]
361s Get:151 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB]
361s Get:152 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB]
361s Get:153 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB]
361s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB]
361s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB]
362s Get:156 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB]
362s Get:157 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB]
362s Get:158 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB]
362s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB]
362s Get:160 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B]
362s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bigmemory.sri all 0.1.8-1 [13.4 kB]
362s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB]
362s Get:163 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB]
362s Get:164 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB]
362s Get:165 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-uuid amd64 1.2-1-1 [48.5 kB]
362s Get:166 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bigmemory amd64 4.6.4-2 [488 kB]
362s Get:167 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bio3d amd64 2.4-5-1 [3028 kB]
362s Get:168 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB]
362s Get:169 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB]
362s Get:170 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB]
362s Get:171 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB]
362s Get:172 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB]
362s Get:173 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB]
362s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB]
362s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB]
362s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB]
362s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB]
362s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB]
362s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB]
362s Get:180 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB]
363s Get:181 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB]
363s Get:182 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB]
363s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB]
363s Get:184 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB]
363s Get:185 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB]
363s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB]
363s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB]
363s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-desc all 1.4.3-1 [359 kB]
363s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diffobj amd64 0.3.5-1build1 [1156 kB]
363s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB]
363s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB]
363s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB]
363s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB]
363s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB]
363s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB]
363s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB]
363s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB]
363s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB]
363s Get:199 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB]
363s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB]
363s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB]
363s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB]
363s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-igraph amd64 2.1.4-1build1 [5218 kB]
363s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB]
363s Get:205 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB]
363s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB]
363s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ncdf4 amd64 1.23-1build1 [279 kB]
364s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgbuild all 1.4.8-1 [219 kB]
364s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rprojroot all 2.1.1-1 [131 kB]
364s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgload all 1.4.1-1 [252 kB]
364s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-praise all 1.0.0-4build2 [20.9 kB]
364s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB]
364s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB]
364s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB]
364s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB]
364s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB]
364s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB]
364s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB]
364s Get:219 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB]
364s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB]
364s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-waldo all 0.6.2-1 [153 kB]
364s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB]
364s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB]
364s Preconfiguring packages ...
364s Fetched 289 MB in 10s (29.6 MB/s)
364s Selecting previously unselected package libc-dev-bin.
365s (Reading database ... 
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 125269 files and directories currently installed.)
365s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ...
365s Unpacking libc-dev-bin (2.42-2ubuntu4) ...
365s Selecting previously unselected package linux-libc-dev:amd64.
365s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ...
365s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ...
365s Selecting previously unselected package libcrypt-dev:amd64.
365s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ...
365s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ...
365s Selecting previously unselected package rpcsvc-proto.
365s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ...
365s Unpacking rpcsvc-proto (1.4.3-1build1) ...
365s Selecting previously unselected package libc6-dev:amd64.
365s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ...
365s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ...
365s Selecting previously unselected package libisl23:amd64.
365s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ...
365s Unpacking libisl23:amd64 (0.27-1build1) ...
365s Selecting previously unselected package libmpc3:amd64.
365s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ...
365s Unpacking libmpc3:amd64 (1.3.1-2) ...
365s Selecting previously unselected package cpp-15-x86-64-linux-gnu.
365s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ...
365s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
365s Selecting previously unselected package cpp-15.
365s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ...
365s Unpacking cpp-15 (15.2.0-12ubuntu1) ...
365s Selecting previously unselected package cpp-x86-64-linux-gnu.
365s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ...
365s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
365s Selecting previously unselected package cpp.
365s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ...
365s Unpacking cpp (4:15.2.0-4ubuntu1) ...
365s Selecting previously unselected package libcc1-0:amd64.
365s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libgomp1:amd64.
365s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libitm1:amd64.
365s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libasan8:amd64.
365s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package liblsan0:amd64.
365s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libtsan2:amd64.
365s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libubsan1:amd64.
365s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ...
365s Selecting previously unselected package libhwasan0:amd64.
365s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ...
365s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ...
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370s Selecting previously unselected package r-bioc-biocgenerics.
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370s Selecting previously unselected package r-cran-curl.
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370s Selecting previously unselected package r-cran-askpass.
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370s Selecting previously unselected package r-cran-openssl.
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370s Selecting previously unselected package r-cran-r6.
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370s Selecting previously unselected package r-bioc-ucsc.utils.
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370s Selecting previously unselected package r-bioc-genomeinfodbdata.
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370s Selecting previously unselected package r-cran-crayon.
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370s Selecting previously unselected package r-bioc-biostrings.
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370s Selecting previously unselected package r-cran-base64enc.
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370s Selecting previously unselected package r-cran-bh.
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370s Selecting previously unselected package r-cran-bigmemory.sri.
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370s Selecting previously unselected package r-cran-littler.
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370s Selecting previously unselected package r-cran-pkgkitten.
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370s Selecting previously unselected package r-cran-rcpp.
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370s Selecting previously unselected package r-cran-uuid.
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370s Selecting previously unselected package r-cran-bigmemory.
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370s Selecting previously unselected package r-cran-bio3d.
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370s Selecting previously unselected package r-cran-bitops.
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370s Selecting previously unselected package r-cran-brio.
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370s Selecting previously unselected package r-cran-rlang.
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370s Selecting previously unselected package r-cran-fastmap.
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370s Selecting previously unselected package r-cran-cachem.
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370s Selecting previously unselected package r-cran-digest.
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370s Selecting previously unselected package r-cran-htmltools.
370s Preparing to unpack .../173-r-cran-htmltools_0.5.8.1-1_amd64.deb ...
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370s Selecting previously unselected package r-cran-jquerylib.
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370s Selecting previously unselected package r-cran-cli.
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370s Selecting previously unselected package r-cran-lifecycle.
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370s Selecting previously unselected package r-cran-memoise.
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370s Selecting previously unselected package r-cran-fs.
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370s Selecting previously unselected package r-cran-rappdirs.
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371s Selecting previously unselected package r-cran-cpp11.
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371s Selecting previously unselected package r-cran-glue.
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371s Selecting previously unselected package r-cran-knitr.
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371s Selecting previously unselected package r-cran-ncdf4.
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371s Selecting previously unselected package r-cran-pkgbuild.
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371s Selecting previously unselected package r-cran-rprojroot.
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371s Selecting previously unselected package r-cran-pkgload.
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371s Selecting previously unselected package r-cran-praise.
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371s Selecting previously unselected package r-cran-rcurl.
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371s Selecting previously unselected package r-cran-tinytex.
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371s Selecting previously unselected package libjs-modernizr.
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372s Selecting previously unselected package r-cran-xtable.
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372s Selecting previously unselected package r-cran-sourcetools.
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372s Unpacking r-cran-sourcetools (0.1.7-1-1) ...
372s Selecting previously unselected package r-cran-withr.
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372s Unpacking r-cran-withr (3.0.2+dfsg-1) ...
372s Selecting previously unselected package libjs-twitter-bootstrap-datepicker.
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372s Selecting previously unselected package r-cran-shiny.
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372s Selecting previously unselected package r-cran-rmarkdown.
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372s Selecting previously unselected package r-cran-waldo.
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372s Selecting previously unselected package r-cran-testthat.
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372s Selecting previously unselected package r-cran-xml.
372s Preparing to unpack .../222-r-cran-xml_3.99-0.20-1_amd64.deb ...
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372s Setting up libjs-json (0~20221030+~1.0.8-1build1) ...
372s Setting up javascript-common (12+nmu1build1) ...
372s Setting up libgraphite2-3:amd64 (1.3.14-11ubuntu1) ...
372s Setting up libpixman-1-0:amd64 (0.46.4-1) ...
372s Setting up libsharpyuv0:amd64 (1.5.0-0.1build1) ...
372s Setting up fonts-mathjax (2.7.9+dfsg-1build1) ...
372s Setting up liblerc4:amd64 (4.0.0+ds-5ubuntu2) ...
372s Setting up libzstd-dev:amd64 (1.5.7+dfsg-3) ...
372s Setting up libjs-mathjax (2.7.9+dfsg-1build1) ...
372s Setting up libxrender1:amd64 (1:0.9.12-1) ...
372s Setting up libdatrie1:amd64 (0.2.14-1) ...
372s Setting up libjs-popper.js (1.16.1+ds-6build1) ...
372s Setting up libxcb-render0:amd64 (1.17.0-2ubuntu1) ...
372s Setting up libjs-sifter.js (0.6.0+dfsg-3) ...
372s Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ...
372s Setting up unzip (6.0-29ubuntu1) ...
372s Setting up x11-common (1:7.7+24ubuntu1) ...
372s Setting up node-html5shiv (3.7.3+dfsg-5) ...
372s Setting up libdeflate0:amd64 (1.23-2build1) ...
372s Setting up linux-libc-dev:amd64 (6.19.0-3.3) ...
372s Setting up libjs-microplugin.js (0.0.3+dfsg-2) ...
372s Setting up libxcb-shm0:amd64 (1.17.0-2ubuntu1) ...
372s Setting up libgomp1:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libjs-modernizr (3.13.0-0.1build1) ...
372s Setting up libjbig0:amd64 (2.1-6.1ubuntu3) ...
372s Setting up libpcre2-16-0:amd64 (10.46-1) ...
372s Setting up libjs-es5-shim (4.6.7-2) ...
372s Setting up zip (3.0-15ubuntu3) ...
372s Setting up libpcre2-32-0:amd64 (10.46-1) ...
372s Setting up libblas3:amd64 (3.12.1-7ubuntu1) ...
372s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
372s Setting up libtirpc-dev:amd64 (1.3.6+ds-1) ...
372s Setting up libpkgconf3:amd64 (1.8.1-4build1) ...
372s Setting up rpcsvc-proto (1.4.3-1build1) ...
372s Setting up libquadmath0:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libjs-d3 (3.5.17-4build1) ...
372s Setting up fonts-dejavu-mono (2.37-8build1) ...
372s Setting up libmpc3:amd64 (1.3.1-2) ...
372s Setting up libtcl8.6:amd64 (8.6.17+dfsg-1build1) ...
372s Setting up icu-devtools (78.2-1ubuntu1) ...
372s Setting up fonts-dejavu-core (2.37-8build1) ...
372s Setting up pkgconf-bin (1.8.1-4build1) ...
372s Setting up libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ...
372s Setting up libltdl7:amd64 (2.5.4-9) ...
372s Setting up libgfortran5:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libwebp7:amd64 (1.5.0-0.1build1) ...
372s Setting up liblzma-dev:amd64 (5.8.2-2) ...
372s Setting up libubsan1:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libpcre2-posix3:amd64 (10.46-1) ...
372s Setting up libjs-highlight.js (10.7.3+dfsg-2) ...
372s Setting up libhwasan0:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libcrypt-dev:amd64 (1:4.5.1-1) ...
372s Setting up libasan8:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ...
372s Setting up liblua5.4-0:amd64 (5.4.8-1) ...
372s Setting up libharfbuzz0b:amd64 (12.3.2-1) ...
372s Setting up libthai-data (0.1.30-1) ...
372s Setting up node-bootstrap-sass (3.4.3-2) ...
372s Setting up libjs-prettify (2015.12.04+dfsg-3) ...
372s Setting up libxss1:amd64 (1:1.2.3-1build4) ...
372s Setting up libjs-bootstrap4 (4.6.2+dfsg-1) ...
372s Setting up libpaper2:amd64 (2.2.5-0.3build1) ...
372s Setting up pandoc-data (3.1.11.1-3build1) ...
372s Setting up libtsan2:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ...
372s Setting up libisl23:amd64 (0.27-1build1) ...
372s Setting up libc-dev-bin (2.42-2ubuntu4) ...
372s Setting up libdeflate-dev:amd64 (1.23-2build1) ...
372s Setting up node-normalize.css (8.0.1-5.1) ...
372s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1build1) ...
372s Setting up xdg-utils (1.2.1-2ubuntu2) ...
372s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
372s Setting up libcc1-0:amd64 (16-20260208-1ubuntu1) ...
372s Setting up liblsan0:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libblas-dev:amd64 (3.12.1-7ubuntu1) ...
372s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
372s Setting up libsz2:amd64 (1.1.5-1) ...
372s Setting up dctrl-tools (2.24-3build4) ...
372s Setting up libjs-bootstrap (3.4.1+dfsg-6) ...
372s Setting up libitm1:amd64 (16-20260208-1ubuntu1) ...
372s Setting up libjs-jquery-selectize.js (0.12.6+dfsg-1.1) ...
372s Setting up libjpeg8:amd64 (8c-2ubuntu12) ...
372s Setting up libice6:amd64 (2:1.1.1-1build1) ...
372s Setting up liblapack3:amd64 (3.12.1-7ubuntu1) ...
372s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
372s Setting up libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ...
372s Setting up libamd3:amd64 (1:7.12.1+dfsg-1) ...
372s Setting up libcolamd3:amd64 (1:7.12.1+dfsg-1) ...
372s Setting up fontconfig-config (2.17.1-3ubuntu1) ...
372s Setting up libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ...
372s Setting up libpaper-utils (2.2.5-0.3build1) ...
372s Setting up cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
372s Setting up libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ...
372s Setting up libjs-jquery-datatables (1.11.5+dfsg-2build1) ...
372s Setting up pkgconf:amd64 (1.8.1-4build1) ...
372s Setting up gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
372s Setting up libthai0:amd64 (0.1.30-1) ...
372s Setting up libjs-jquery-ui (1.13.2+dfsg-1build1) ...
372s Setting up pandoc (3.1.11.1+ds-4) ...
372s Setting up libglpk40:amd64 (5.0-2) ...
372s Setting up liblapack-dev:amd64 (3.12.1-7ubuntu1) ...
372s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
372s Setting up libhdf5-310:amd64 (1.14.6+repack-2) ...
372s Setting up cpp-15 (15.2.0-12ubuntu1) ...
372s Setting up libtiff6:amd64 (4.7.0-3ubuntu3) ...
372s Setting up libc6-dev:amd64 (2.42-2ubuntu4) ...
372s Setting up libfontconfig1:amd64 (2.17.1-3ubuntu1) ...
372s Setting up libsm6:amd64 (2:1.2.6-1build1) ...
372s Setting up libicu-dev:amd64 (78.2-1ubuntu1) ...
372s Setting up libbz2-dev:amd64 (1.0.8-6build2) ...
372s Setting up cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
372s Setting up gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
372s Setting up libhdf5-hl-310:amd64 (1.14.6+repack-2) ...
372s Setting up fontconfig (2.17.1-3ubuntu1) ...
374s Regenerating fonts cache... done.
374s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ...
374s Setting up libxft2:amd64 (2.3.6-1build2) ...
374s Setting up libncurses-dev:amd64 (6.6+20251231-1) ...
374s Setting up libpcre2-dev:amd64 (10.46-1) ...
374s Setting up gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
374s Setting up libtk8.6:amd64 (8.6.17-1) ...
374s Setting up libpango-1.0-0:amd64 (1.57.0-1) ...
374s Setting up libnetcdf22:amd64 (1:4.9.3-1build1) ...
374s Setting up libreadline-dev:amd64 (8.3-3) ...
374s Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
374s Setting up libcairo2:amd64 (1.18.4-3) ...
374s Setting up gcc-15 (15.2.0-12ubuntu1) ...
374s Setting up libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ...
374s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ...
374s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ...
374s Setting up cpp (4:15.2.0-4ubuntu1) ...
374s Setting up libboost1.90-dev:amd64 (1.90.0-2ubuntu1) ...
374s Setting up libboost-dev:amd64 (1.90.0.0ubuntu3) ...
374s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ...
374s Setting up libjpeg8-dev:amd64 (8c-2ubuntu12) ...
374s Setting up gfortran-15 (15.2.0-12ubuntu1) ...
374s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ...
374s Setting up g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ...
374s Setting up libpng-dev:amd64 (1.6.54-1) ...
374s Setting up libjpeg-dev:amd64 (8c-2ubuntu12) ...
374s Setting up gcc (4:15.2.0-4ubuntu1) ...
374s Setting up r-base-core (4.5.2-1ubuntu2) ...
374s Creating config file /etc/R/Renviron with new version
374s Setting up r-cran-crayon (1.5.3-1) ...
374s Setting up r-cran-sourcetools (0.1.7-1-1) ...
374s Setting up r-cran-lattice (0.22-9-1) ...
374s Setting up r-cran-ps (1.9.0-1) ...
374s Setting up r-cran-xml (3.99-0.20-1) ...
374s Setting up g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ...
374s Setting up r-cran-commonmark (1.9.5-1) ...
375s Setting up r-cran-r6 (2.6.1-1) ...
375s Setting up r-cran-pkgkitten (0.2.4-1) ...
375s Setting up g++-15 (15.2.0-12ubuntu1) ...
375s Setting up r-cran-magrittr (2.0.3-1) ...
375s Setting up r-cran-rappdirs (0.3.3-1build1) ...
375s Setting up r-bioc-genomeinfodbdata (1.2.13-2) ...
375s Setting up r-cran-littler (0.3.22-1) ...
375s Setting up r-cran-bh (1.84.0-1) ...
375s Setting up r-cran-ncdf4 (1.23-1build1) ...
375s Setting up r-cran-fs (1.6.5+dfsg-1) ...
375s Setting up r-cran-rcpp (1.1.0-1) ...
375s Setting up r-cran-curl (7.0.0+dfsg-1) ...
375s Setting up r-cran-brio (1.1.5-1) ...
375s Setting up r-cran-diffobj (0.3.5-1build1) ...
375s Setting up r-cran-bigmemory.sri (0.1.8-1) ...
375s Setting up r-bioc-biocgenerics (0.52.0-2) ...
375s Setting up r-cran-rlang (1.1.5-3) ...
375s Setting up r-cran-bio3d (2.4-5-1) ...
375s Setting up r-cran-uuid (1.2-1-1) ...
375s Setting up r-cran-xfun (0.55+dfsg-1) ...
375s Setting up r-cran-sys (3.4.3-1) ...
375s Setting up r-cran-withr (3.0.2+dfsg-1) ...
375s Setting up r-cran-processx (3.8.6-1) ...
375s Setting up r-cran-mime (0.12-2) ...
375s Setting up r-cran-praise (1.0.0-4build2) ...
375s Setting up r-cran-base64enc (0.1-3-3build1) ...
375s Setting up r-cran-digest (0.6.39-1) ...
375s Setting up r-cran-yaml (2.3.10-1) ...
375s Setting up r-cran-evaluate (1.0.5-1) ...
375s Setting up r-cran-bigmemory (4.6.4-2) ...
375s Setting up r-cran-highr (0.11+dfsg-1) ...
375s Setting up r-cran-glue (1.8.0-1) ...
375s Setting up r-cran-xtable (1:1.8-4-2build1) ...
375s Setting up r-cran-cli (3.6.4-1) ...
375s Setting up gfortran (4:15.2.0-4ubuntu1) ...
375s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
375s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist
375s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
375s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist
375s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ...
375s Setting up r-cran-bitops (1.0-9-1) ...
375s Setting up r-cran-rprojroot (2.1.1-1) ...
375s Setting up r-bioc-zlibbioc (1.52.0+dfsg-2) ...
375s Setting up r-cran-askpass (1.2.1-1) ...
375s Setting up r-cran-fastmap (1.2.0-1) ...
375s Setting up r-cran-jsonlite (1.9.1+dfsg-1) ...
375s Setting up r-cran-pkgconfig (2.0.3-2build2) ...
375s Setting up r-cran-cpp11 (0.5.3-1) ...
375s Setting up r-bioc-s4vectors (0.44.0+dfsg-2) ...
375s Setting up r-cran-waldo (0.6.2-1) ...
375s Setting up r-cran-later (1.4.1+dfsg-1) ...
375s Setting up r-cran-matrix (1.7-4-1) ...
375s Setting up r-cran-htmltools (0.5.8.1-1) ...
375s Setting up r-cran-tinytex (0.58-1) ...
375s Setting up r-cran-knitr (1.51+dfsg-1) ...
375s Setting up g++ (4:15.2.0-4ubuntu1) ...
375s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
375s Setting up r-cran-cachem (1.1.0-1) ...
375s Setting up r-cran-sass (0.4.9+dfsg-1) ...
375s Setting up build-essential (12.12ubuntu2) ...
375s Setting up r-bioc-iranges (2.40.1-3) ...
375s Setting up r-cran-rcurl (1.98-1.16+dfsg-1) ...
375s Setting up r-cran-vctrs (0.6.5-1) ...
375s Setting up r-cran-openssl (2.3.2+dfsg-1) ...
375s Setting up r-base-dev (4.5.2-1ubuntu2) ...
375s Setting up r-cran-callr (3.7.6-1) ...
375s Setting up r-cran-desc (1.4.3-1) ...
375s Setting up r-cran-fontawesome (0.5.3-1) ...
375s Setting up r-cran-igraph (2.1.4-1build1) ...
375s Setting up r-cran-jquerylib (0.1.4+dfsg-5) ...
375s Setting up r-cran-httr (1.4.7+dfsg-1) ...
375s Setting up r-cran-memoise (2.0.1-1build1) ...
375s Setting up r-cran-promises (1.3.2+dfsg-1) ...
375s Setting up pkg-r-autopkgtest (20250812) ...
375s Setting up r-bioc-xvector (0.46.0-2) ...
375s Setting up r-cran-pkgbuild (1.4.8-1) ...
375s Setting up r-cran-pkgload (1.4.1-1) ...
375s Setting up r-bioc-ucsc.utils (1.2.0+ds-2) ...
375s Setting up r-cran-httpuv (1.6.15+dfsg-1) ...
375s Setting up r-cran-testthat (3.2.3-1) ...
375s Setting up r-bioc-genomeinfodb (1.42.3+dfsg-1) ...
375s Setting up r-cran-bslib (0.9.0+dfsg-3build1) ...
375s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ...
375s Setting up r-cran-shiny (1.10.0+dfsg-2) ...
375s Setting up r-cran-rmarkdown (2.30+dfsg-1) ...
375s Processing triggers for libc-bin (2.42-2ubuntu4) ...
375s Processing triggers for man-db (2.13.1-1build1) ...
375s Processing triggers for install-info (7.2-5) ...
379s autopkgtest [02:05:40]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest
379s autopkgtest [02:05:40]: test pkg-r-autopkgtest: [-----------------------
379s Test: Try to load the R library bio3d
379s 
379s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
379s Copyright (C) 2025 The R Foundation for Statistical Computing
379s Platform: x86_64-pc-linux-gnu
379s 
379s R is free software and comes with ABSOLUTELY NO WARRANTY.
379s You are welcome to redistribute it under certain conditions.
379s Type 'license()' or 'licence()' for distribution details.
379s 
379s R is a collaborative project with many contributors.
379s Type 'contributors()' for more information and
379s 'citation()' on how to cite R or R packages in publications.
379s 
379s Type 'demo()' for some demos, 'help()' for on-line help, or
379s 'help.start()' for an HTML browser interface to help.
379s Type 'q()' to quit R.
379s 
379s > library('bio3d')
379s > 
379s autopkgtest [02:05:40]: test pkg-r-autopkgtest: -----------------------]
380s pkg-r-autopkgtest    PASS
380s autopkgtest [02:05:41]: test pkg-r-autopkgtest:  - - - - - - - - - - results - - - - - - - - - -
380s autopkgtest [02:05:41]: @@@@@@@@@@@@@@@@@@@@ summary
380s run-unit-test        PASS
380s pkg-r-autopkgtest    PASS