0s autopkgtest [04:16:28]: starting date and time: 2026-02-10 04:16:28+0000 0s autopkgtest [04:16:28]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [04:16:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zpudmmdv/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:r-cran-ggplot2 --apt-upgrade r-bioc-purecn --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-cran-ggplot2/4.0.2+dfsg-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-25.secgroup --name adt-resolute-amd64-r-bioc-purecn-20260210-041628-juju-7f2275-prod-proposed-migration-environment-2-afecb8e6-7b01-43fb-b00a-b7b222d2a5bc --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-amd64-r-bioc-purecn-20260210-041628-juju-7f2275-prod-proposed-migration-environment-2-afecb8e6-7b01-43fb-b00a-b7b222d2a5bc from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 74s autopkgtest [04:17:42]: testbed dpkg architecture: amd64 74s autopkgtest [04:17:42]: testbed apt version: 3.1.14 74s autopkgtest [04:17:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s autopkgtest [04:17:43]: testbed release detected to be: None 76s autopkgtest [04:17:44]: 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/multiverse Sources [31.1 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [181 kB] 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1735 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [220 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [268 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5980 B] 77s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [120 B] 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1791 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [768 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [32.6 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [5020 B] 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [26.4 kB] 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 78s Fetched 5189 kB in 2s (2847 kB/s) 79s 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 80s Reading package lists... 80s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Calculating upgrade... 81s The following package was automatically installed and is no longer required: 81s libpython3.13 81s Use 'sudo apt autoremove' to remove it. 81s The following NEW packages will be installed: 81s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 81s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 81s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 81s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 81s The following packages will be upgraded: 81s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 81s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 81s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 81s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 81s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 81s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 81s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 81s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 81s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 81s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 81s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 81s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 81s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 81s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 81s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 81s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 81s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 81s Need to get 237 MB of archives. 81s After this operation, 339 MB of additional disk space will be used. 81s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 81s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 81s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 81s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 81s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 81s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 81s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 81s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 81s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 81s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 81s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 81s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 81s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 81s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 81s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 81s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 81s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 81s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 81s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 81s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 81s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 81s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 81s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 81s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 81s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 81s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 81s 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] 82s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 82s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 82s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 82s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 86s 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] 86s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 86s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 86s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 86s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 86s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 86s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 86s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 87s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 87s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 87s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 87s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 87s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 87s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 87s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 87s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 87s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 87s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 87s dpkg-preconfigure: unable to re-open stdin: No such file or directory 87s Fetched 237 MB in 6s (38.0 MB/s) 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 87s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 87s Setting up debianutils (5.23.2build1) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 87s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 87s Setting up dash (0.5.12-12ubuntu3) ... 87s (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 ... 83957 files and directories currently installed.) 87s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 88s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 88s Setting up findutils (4.10.0-3build2) ... 88s (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 ... 83957 files and directories currently installed.) 88s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 88s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 88s Setting up sed (4.9-2build3) ... 88s (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 ... 83957 files and directories currently installed.) 88s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 88s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 88s Setting up tar (1.35+dfsg-3.1build2) ... 88s (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 ... 83957 files and directories currently installed.) 88s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 88s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 88s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 88s Selecting previously unselected package gcc-16-base:amd64. 88s (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 ... 83957 files and directories currently installed.) 88s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 88s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 88s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 88s (Reading database ... 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(7.7.0+6.19.0-3.3) ... 95s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 95s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 95s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 95s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 95s Setting up libsensors-config (1:3.6.2-2build1) ... 95s Setting up less (668-1build1) ... 95s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 95s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 95s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 95s amd64-microcode: microcode will be updated at next boot 95s Setting up man-db (2.13.1-1build1) ... 96s Updating database of manual pages ... 97s man-db.service is a disabled or a static unit not running, not starting it. 97s Setting up libjansson4:amd64 (2.14-2build4) ... 97s Setting up libglib2.0-data (2.87.2-2) ... 97s Setting up pollinate (4.33-4ubuntu5) ... 107s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 107s Setting up libwrap0:amd64 (7.6.q-36build2) ... 107s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 109s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 109s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 109s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 109s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 109s Setting up patch (2.8-2build1) ... 109s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 109s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 109s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 109s Setting up lsof (4.99.4+dfsg-2build2) ... 109s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 109s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 109s Setting up dracut-install (109-11ubuntu1) ... 109s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 109s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 109s Setting up pnp.ids (0.394-1build1) ... 109s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 109s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 109s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 109s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 109s Setting up mawk (1.3.4.20260129-1) ... 109s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 109s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 109s Setting up linux-image-virtual (6.19.0-3.3) ... 109s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 109s Setting up libbsd0:amd64 (0.12.2-2build2) ... 109s Setting up libdrm-common (2.4.131-1) ... 109s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 109s Setting up dbus-bin (1.16.2-2ubuntu3) ... 109s Setting up libonig5:amd64 (6.9.10-1build1) ... 109s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 109s Setting up ethtool (1:6.15-3build1) ... 109s Setting up python3-referencing (0.36.2-1ubuntu2) ... 109s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 109s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 109s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 109s Setting up tcpdump (4.99.5-2ubuntu3) ... 109s Setting up linux-image-generic (6.19.0-3.3) ... 109s Setting up wget (1.25.0-2ubuntu4) ... 109s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 109s Setting up iptables (1.8.11-2ubuntu3) ... 109s Setting up iproute2 (6.18.0-1ubuntu1) ... 109s Setting up linux-headers-generic (6.19.0-3.3) ... 109s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 109s Setting up hwdata (0.394-1build1) ... 109s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 109s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 109s No schema files found: doing nothing. 109s Setting up dbus (1.16.2-2ubuntu3) ... 109s A reboot is required to replace the running dbus-daemon. 109s Please reboot the system when convenient. 109s Setting up shared-mime-info (2.4-5build3) ... 110s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 110s Setting up pciutils (1:3.14.0-1build2) ... 110s Setting up python3-markdown-it (3.0.0-3build1) ... 110s Setting up libdrm2:amd64 (2.4.131-1) ... 110s Setting up libpython3.14:amd64 (3.14.2-1) ... 110s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 110s Setting up linux-tools-common (6.19.0-3.3) ... 110s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 110s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 110s Setting up apt (3.1.15) ... 111s Setting up linux-headers-virtual (6.19.0-3.3) ... 111s Setting up linux-generic (6.19.0-3.3) ... 111s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 111s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 111s Setting up ubuntu-standard (1.564) ... 111s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 111s Setting up linux-virtual (6.19.0-3.3) ... 111s Setting up linux-perf (6.19.0-3.3) ... 111s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 111s Processing triggers for debianutils (5.23.2build1) ... 111s Processing triggers for install-info (7.2-5) ... 111s Processing triggers for initramfs-tools (0.150ubuntu7) ... 111s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 115s Processing triggers for libc-bin (2.42-2ubuntu4) ... 115s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 115s /etc/kernel/postinst.d/initramfs-tools: 115s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 119s /etc/kernel/postinst.d/zz-update-grub: 119s Sourcing file `/etc/default/grub' 119s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 119s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 119s Generating grub configuration file ... 120s Found linux image: /boot/vmlinuz-6.19.0-3-generic 120s Found initrd image: /boot/initrd.img-6.19.0-3-generic 120s Found linux image: /boot/vmlinuz-6.18.0-9-generic 120s Found initrd image: /boot/initrd.img-6.18.0-9-generic 120s Warning: os-prober will not be executed to detect other bootable partitions. 120s Systems on them will not be added to the GRUB boot configuration. 120s Check GRUB_DISABLE_OS_PROBER documentation entry. 120s Adding boot menu entry for UEFI Firmware Settings ... 120s done 120s autopkgtest [04:18:28]: upgrading testbed (apt dist-upgrade and autopurge) 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s The following package was automatically installed and is no longer required: 121s libpython3.13 121s Use 'sudo apt autoremove' to remove it. 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 121s The following packages will be REMOVED: 121s libpython3.13* 122s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 122s After this operation, 7599 kB disk space will be freed. 122s (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.) 122s Removing libpython3.13:amd64 (3.13.11-1) ... 122s Processing triggers for libc-bin (2.42-2ubuntu4) ... 122s autopkgtest [04:18:30]: rebooting testbed after setup commands that affected boot 150s autopkgtest [04:18:58]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 153s autopkgtest [04:19:01]: @@@@@@@@@@@@@@@@@@@@ apt-source r-bioc-purecn 155s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (dsc) [2504 B] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (tar) [5496 kB] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-bioc-purecn 2.12.0+dfsg-2 (diff) [6696 B] 155s gpgv: Signature made Tue Jan 14 08:02:30 2025 UTC 155s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 155s gpgv: issuer "crusoe@debian.org" 155s gpgv: Can't check signature: No public key 155s dpkg-source: warning: cannot verify inline signature for ./r-bioc-purecn_2.12.0+dfsg-2.dsc: no acceptable signature found 155s autopkgtest [04:19:03]: testing package r-bioc-purecn version 2.12.0+dfsg-2 156s autopkgtest [04:19:04]: build not needed 158s autopkgtest [04:19:06]: test pkg-r-autopkgtest: preparing testbed 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 159s Solving dependencies... 159s The following NEW packages will be installed: 159s build-essential comerr-dev cpp cpp-15 cpp-15-x86-64-linux-gnu 159s cpp-x86-64-linux-gnu dctrl-tools fontconfig fontconfig-config 159s fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome 159s fonts-glyphicons-halflings fonts-lmodern fonts-mathjax g++ g++-15 159s g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-15 159s gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 159s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu hdf5-helpers 159s icu-devtools javascript-common krb5-multidev libaec-dev libaec0 libasan8 159s libbibtex-parser-perl libblas-dev libblas3 libblosc1 libboost-dev 159s libboost1.90-dev libbrotli-dev libbz2-dev libc-dev-bin libc6-dev libcairo2 159s libcc1-0 libcrypt-dev libcurl4-openssl-dev libdatrie1 libdeflate-dev 159s libdeflate0 libevent-2.1-7t64 libfontconfig1 libgcc-15-dev 159s libgfortran-15-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 159s libgnutls-openssl27t64 libgnutls28-dev libgomp1 libgraphite2-3 libgssrpc4t64 159s libharfbuzz0b libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 159s libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libhwasan0 libice6 159s libicu-dev libidn2-dev libio-string-perl libisl23 libitm1 libjbig0 159s libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev 159s libjs-bootstrap libjs-bootstrap4 libjs-d3 libjs-es5-shim libjs-highlight.js 159s libjs-jquery libjs-jquery-datatables libjs-jquery-selectize.js 159s libjs-jquery-ui libjs-json libjs-lunr libjs-mathjax libjs-microplugin.js 159s libjs-modernizr libjs-popper.js libjs-prettify libjs-sifter.js 159s libjs-twitter-bootstrap-datepicker libkadm5clnt-mit12 libkadm5srv-mit12 159s libkdb5-10t64 libkpathsea6 libkrb5-dev liblapack-dev liblapack3 159s liblatex-tounicode-perl libldap-dev liblerc4 liblsan0 liblua5.4-0 159s liblzma-dev libmpc3 libmpfi0 libncurses-dev libnghttp2-dev libp11-kit-dev 159s libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils 159s libpaper2 libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 159s libpixman-1-0 libpkgconf3 libpng-dev libpotrace0 libpsl-dev libptexenc1 159s libquadmath0 libreadline-dev librtmp-dev libsharpyuv0 libsm6 libsnappy1v5 159s libssh2-1-dev libssl-dev libstdc++-15-dev libsynctex2 libsz2 libtasn1-6-dev 159s libtcl8.6 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 159s libtirpc-dev libtk8.6 libtsan2 libubsan1 libunbound8 libwebp7 libxaw7 159s libxcb-render0 libxcb-shm0 libxft2 libxi6 libxmu6 libxpm4 libxrender1 159s libxss1 libxt6t64 libzstd-dev libzzip-0-13t64 linux-libc-dev nettle-dev 159s node-bootstrap-sass node-html5shiv node-normalize.css pandoc pandoc-data 159s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-core r-base-dev 159s r-bioc-annotationdbi r-bioc-aroma.light r-bioc-biobase r-bioc-biocgenerics 159s r-bioc-biocio r-bioc-biocparallel r-bioc-biocstyle r-bioc-biocversion 159s r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray r-bioc-dnacopy 159s r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments 159s r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-keggrest 159s r-bioc-matrixgenerics r-bioc-org.hs.eg.db r-bioc-purecn r-bioc-rhdf5 159s r-bioc-rhdf5filters r-bioc-rhdf5lib r-bioc-rhtslib r-bioc-rsamtools 159s r-bioc-rtracklayer r-bioc-s4arrays r-bioc-s4vectors r-bioc-sparsearray 159s r-bioc-summarizedexperiment r-bioc-ucsc.utils r-bioc-variantannotation 159s r-bioc-xvector r-bioc-zlibbioc r-cran-abind r-cran-askpass r-cran-base64enc 159s r-cran-bh r-cran-biocmanager r-cran-bit r-cran-bit64 r-cran-bitops 159s r-cran-blob r-cran-bookdown r-cran-brio r-cran-bslib r-cran-cachem 159s r-cran-callr r-cran-cli r-cran-codetools r-cran-commonmark r-cran-covr 159s r-cran-cpp11 r-cran-crayon r-cran-curl r-cran-data.table r-cran-dbi 159s r-cran-desc r-cran-diffobj r-cran-digest r-cran-evaluate r-cran-farver 159s r-cran-fastmap r-cran-fontawesome r-cran-formatr r-cran-fs 159s r-cran-futile.logger r-cran-futile.options r-cran-future r-cran-getopt 159s r-cran-ggplot2 r-cran-globals r-cran-glue r-cran-gridextra r-cran-gtable 159s r-cran-highr r-cran-htmltools r-cran-httpuv r-cran-httr r-cran-isoband 159s r-cran-jquerylib r-cran-jsonlite r-cran-knitr r-cran-labeling 159s r-cran-lambda.r r-cran-later r-cran-lattice r-cran-lazyeval r-cran-lifecycle 159s r-cran-listenv r-cran-littler r-cran-magrittr r-cran-markdown r-cran-matrix 159s r-cran-matrixstats r-cran-mclust r-cran-memoise r-cran-mime r-cran-openssl 159s r-cran-optparse r-cran-parallelly r-cran-pkgbuild r-cran-pkgconfig 159s r-cran-pkgkitten r-cran-pkgload r-cran-plogr r-cran-png r-cran-praise 159s r-cran-processx r-cran-promises r-cran-ps r-cran-pscbs r-cran-r.cache 159s r-cran-r.methodss3 r-cran-r.oo r-cran-r.utils r-cran-r6 r-cran-rappdirs 159s r-cran-rcolorbrewer r-cran-rcpp r-cran-rcurl r-cran-restfulr r-cran-rex 159s r-cran-rjson r-cran-rlang r-cran-rmarkdown r-cran-rprojroot r-cran-rsqlite 159s r-cran-s7 r-cran-sass r-cran-scales r-cran-shiny r-cran-snow 159s r-cran-sourcetools r-cran-sys r-cran-testthat r-cran-tinytex r-cran-vctrs 159s r-cran-vgam r-cran-viridislite r-cran-waldo r-cran-withr r-cran-xfun 159s r-cran-xml r-cran-xtable r-cran-yaml rpcsvc-proto t1utils tex-common 159s texlive-base texlive-bibtex-extra texlive-binaries texlive-latex-base unzip 159s x11-common xdg-utils zip zlib1g-dev 159s 0 upgraded, 344 newly installed, 0 to remove and 0 not upgraded. 159s Need to get 564 MB of archives. 159s After this operation, 1893 MB of additional disk space will be used. 159s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 159s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 160s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 160s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 160s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 160s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 160s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 160s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 160s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 160s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 160s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 160s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 160s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 160s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 160s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 160s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 160s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 160s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 160s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 161s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 161s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 161s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 161s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 161s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 161s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 161s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 161s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 161s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 161s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 161s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 161s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 161s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 161s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 161s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 161s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 161s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 161s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 161s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1build1 [531 kB] 161s Get:39 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 161s Get:40 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-lmodern all 2.005-1build1 [4788 kB] 162s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 162s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 162s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 162s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 162s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 162s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 162s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 162s Get:48 http://ftpmaster.internal/ubuntu resolute/universe amd64 hdf5-helpers amd64 1.14.6+repack-2 [17.3 kB] 162s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 162s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 javascript-common all 12+nmu1build1 [4864 B] 162s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 comerr-dev amd64 2.1-1.47.2-3ubuntu2 [45.0 kB] 162s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libgssrpc4t64 amd64 1.22.1-2 [57.9 kB] 162s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libkadm5clnt-mit12 amd64 1.22.1-2 [40.2 kB] 162s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libkdb5-10t64 amd64 1.22.1-2 [41.6 kB] 162s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libkadm5srv-mit12 amd64 1.22.1-2 [55.0 kB] 162s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 krb5-multidev amd64 1.22.1-2 [126 kB] 162s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec0 amd64 1.1.5-1 [22.5 kB] 162s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 162s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 liblatex-tounicode-perl all 1.93-1 [29.2 kB] 162s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 libbibtex-parser-perl all 1.93+dfsg-1 [17.4 kB] 162s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 162s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 162s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 libsnappy1v5 amd64 1.2.2-2 [30.8 kB] 162s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 libblosc1 amd64 1.21.5+ds-2 [35.8 kB] 162s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost1.90-dev amd64 1.90.0-2ubuntu1 [11.5 MB] 162s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 libboost-dev amd64 1.90.0.0ubuntu3 [4764 B] 162s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 libbrotli-dev amd64 1.1.0-2build6 [355 kB] 162s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 162s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 162s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 162s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 162s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 162s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 162s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-dev amd64 2.3.8-4build1 [121 kB] 162s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libkrb5-dev amd64 1.22.1-2 [11.9 kB] 162s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libldap-dev amd64 2.6.10+dfsg-1ubuntu5 [315 kB] 162s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 162s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 162s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 162s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libnghttp2-dev amd64 1.64.0-1.1ubuntu1 [120 kB] 162s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libpsl-dev amd64 0.21.2-1.1build2 [78.7 kB] 162s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5ubuntu1 [9956 B] 162s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5ubuntu1 [342 kB] 162s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10build2 [145 kB] 162s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 libunbound8 amd64 1.24.2-1ubuntu1 [462 kB] 162s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 libgnutls-dane0t64 amd64 3.8.10-3ubuntu1 [24.5 kB] 162s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 libgnutls-openssl27t64 amd64 3.8.10-3ubuntu1 [24.8 kB] 162s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 libp11-kit-dev amd64 0.25.10-1 [29.3 kB] 162s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 libtasn1-6-dev amd64 4.21.0-2 [92.4 kB] 162s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 nettle-dev amd64 3.10.2-1 [1176 kB] 162s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 libgnutls28-dev amd64 3.8.10-3ubuntu1 [1096 kB] 162s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 162s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [69.2 kB] 162s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 libssl-dev amd64 3.5.3-1ubuntu2 [2936 kB] 163s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 libssh2-1-dev amd64 1.11.1-1build1 [288 kB] 163s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 163s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 libcurl4-openssl-dev amd64 8.18.0-1ubuntu1 [543 kB] 163s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 163s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 163s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 163s Get:101 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 163s Get:102 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 163s Get:103 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsz2 amd64 1.1.5-1 [17.9 kB] 163s Get:104 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-310 amd64 1.14.6+repack-2 [1433 kB] 163s Get:105 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-cpp-310 amd64 1.14.6+repack-2 [125 kB] 163s Get:106 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-fortran-310 amd64 1.14.6+repack-2 [106 kB] 163s Get:107 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-310 amd64 1.14.6+repack-2 [59.9 kB] 163s Get:108 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-fortran-310 amd64 1.14.6+repack-2 [32.1 kB] 163s Get:109 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-hl-cpp-310 amd64 1.14.6+repack-2 [11.9 kB] 163s Get:110 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 163s Get:111 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 163s Get:112 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 163s Get:113 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 163s Get:114 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 163s Get:115 http://ftpmaster.internal/ubuntu resolute/universe amd64 libaec-dev amd64 1.1.5-1 [23.5 kB] 163s Get:116 http://ftpmaster.internal/ubuntu resolute/universe amd64 libhdf5-dev amd64 1.14.6+repack-2 [3386 kB] 163s Get:117 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 163s Get:118 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 163s Get:119 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 163s Get:120 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 163s Get:121 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-popper.js all 1.16.1+ds-6build1 [53.8 kB] 163s Get:122 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap4 all 4.6.2+dfsg-1 [532 kB] 163s Get:123 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-d3 all 3.5.17-4build1 [136 kB] 163s Get:124 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-es5-shim all 4.6.7-2 [39.8 kB] 163s Get:125 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 163s Get:126 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 163s Get:127 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 163s Get:128 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-sifter.js all 0.6.0+dfsg-3 [12.6 kB] 163s Get:129 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-microplugin.js all 0.0.3+dfsg-2 [3946 B] 163s Get:130 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-selectize.js all 0.12.6+dfsg-1.1 [51.0 kB] 163s Get:131 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1build1 [251 kB] 163s Get:132 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-json all 0~20221030+~1.0.8-1build1 [20.6 kB] 163s Get:133 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-lunr all 2.3.9~dfsg-2 [66.8 kB] 163s Get:134 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-prettify all 2015.12.04+dfsg-3 [41.4 kB] 163s Get:135 http://ftpmaster.internal/ubuntu resolute/universe amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5build1 [66.0 kB] 163s Get:136 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 163s Get:137 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 163s Get:138 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 163s Get:139 http://ftpmaster.internal/ubuntu resolute/main amd64 liblua5.4-0 amd64 5.4.8-1 [174 kB] 163s Get:140 http://ftpmaster.internal/ubuntu resolute/universe amd64 libmpfi0 amd64 1.5.4+ds-4build1 [36.6 kB] 163s Get:141 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 163s Get:142 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 163s Get:143 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 163s Get:144 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 163s Get:145 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 163s Get:146 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 163s Get:147 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 163s Get:148 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 163s Get:149 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 163s Get:150 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 163s Get:151 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 163s Get:152 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 163s Get:153 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 163s Get:154 http://ftpmaster.internal/ubuntu resolute/universe amd64 libpotrace0 amd64 1.16-2build2 [17.9 kB] 163s Get:155 http://ftpmaster.internal/ubuntu resolute/universe amd64 libptexenc1 amd64 2025.20250727.75242+ds-5build1 [46.4 kB] 163s Get:156 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 163s Get:157 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 163s Get:158 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 163s Get:159 http://ftpmaster.internal/ubuntu resolute/universe amd64 libsynctex2 amd64 2025.20250727.75242+ds-5build1 [62.1 kB] 163s Get:160 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 163s Get:161 http://ftpmaster.internal/ubuntu resolute/universe amd64 libteckit0 amd64 2.5.13+ds-1 [431 kB] 163s Get:162 http://ftpmaster.internal/ubuntu resolute/universe amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5build1 [125 kB] 163s Get:163 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 163s Get:164 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 163s Get:165 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 163s Get:166 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 163s Get:167 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 163s Get:168 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 163s Get:169 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 163s Get:170 http://ftpmaster.internal/ubuntu resolute/main amd64 libxmu6 amd64 2:1.1.3-4 [48.9 kB] 163s Get:171 http://ftpmaster.internal/ubuntu resolute/main amd64 libxpm4 amd64 1:3.5.17-1build3 [37.3 kB] 163s Get:172 http://ftpmaster.internal/ubuntu resolute/main amd64 libxaw7 amd64 2:1.0.16-1build1 [190 kB] 163s Get:173 http://ftpmaster.internal/ubuntu resolute/main amd64 libxi6 amd64 2:1.8.2-2 [33.1 kB] 163s Get:174 http://ftpmaster.internal/ubuntu resolute/universe amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [30.1 kB] 163s Get:175 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-bootstrap-sass all 3.4.3-2 [187 kB] 163s Get:176 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 163s Get:177 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 163s Get:178 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc-data all 3.1.11.1-3build1 [78.8 kB] 163s Get:179 http://ftpmaster.internal/ubuntu resolute/universe amd64 pandoc amd64 3.1.11.1+ds-4 [27.2 MB] 164s Get:180 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 164s Get:181 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 164s Get:182 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 164s Get:183 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 165s Get:184 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 165s Get:185 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 165s Get:186 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 165s Get:187 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 165s Get:188 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocgenerics all 0.52.0-2 [624 kB] 165s Get:189 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biobase amd64 2.66.0-2 [2332 kB] 165s Get:190 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4vectors amd64 0.44.0+dfsg-2 [2065 kB] 165s Get:191 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-iranges amd64 2.40.1-3 [2309 kB] 165s Get:192 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-dbi all 1.2.3-1build1 [855 kB] 165s Get:193 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit amd64 4.6.0+dfsg-1 [466 kB] 165s Get:194 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bit64 amd64 4.6.0-1-4 [491 kB] 165s Get:195 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 165s Get:196 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 165s Get:197 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 165s Get:198 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 165s Get:199 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 165s Get:200 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-blob all 1.3.0-1 [54.1 kB] 165s Get:201 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmap amd64 1.2.0-1 [73.8 kB] 165s Get:202 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cachem amd64 1.1.0-1 [74.1 kB] 165s Get:203 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-memoise all 2.0.1-1build1 [54.5 kB] 165s Get:204 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 165s Get:205 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-plogr all 0.2.0-3build2 [15.8 kB] 165s Get:206 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 165s Get:207 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rsqlite amd64 2.3.9-1 [1467 kB] 165s Get:208 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-curl amd64 7.0.0+dfsg-1 [202 kB] 165s Get:209 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jsonlite amd64 1.9.1+dfsg-1 [447 kB] 165s Get:210 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mime amd64 0.12-2 [35.8 kB] 165s Get:211 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sys amd64 3.4.3-1 [45.3 kB] 165s Get:212 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-askpass amd64 1.2.1-1 [24.9 kB] 165s Get:213 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-openssl amd64 2.3.2+dfsg-1 [407 kB] 165s Get:214 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r6 all 2.6.1-1 [101 kB] 165s Get:215 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httr all 1.4.7+dfsg-1 [459 kB] 165s Get:216 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-png amd64 0.1-8-1build2 [40.6 kB] 165s Get:217 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-zlibbioc all 1.52.0+dfsg-2 [10.2 kB] 165s Get:218 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-xvector amd64 0.46.0-2 [620 kB] 165s Get:219 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-ucsc.utils all 1.2.0+ds-2 [77.2 kB] 165s Get:220 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodbdata all 1.2.13-2 [12.9 MB] 165s Get:221 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomeinfodb all 1.42.3+dfsg-1 [3887 kB] 166s Get:222 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-crayon all 1.5.3-1 [165 kB] 166s Get:223 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biostrings amd64 2.74.1+dfsg-2 [13.3 MB] 166s Get:224 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-keggrest all 1.46.0+dfsg-3 [183 kB] 166s Get:225 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-annotationdbi all 1.68.0-2 [4857 kB] 166s Get:226 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.methodss3 all 1.8.2-1 [84.0 kB] 166s Get:227 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.oo all 1.27.1-1 [978 kB] 166s Get:228 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.utils all 2.13.0-1 [1423 kB] 166s Get:229 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrixstats amd64 1.5.0-1 [542 kB] 166s Get:230 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-aroma.light all 3.36.0-2 [583 kB] 166s Get:231 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocio all 1.16.0+dfsg-2 [209 kB] 166s Get:232 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-formatr all 1.14-2 [152 kB] 166s Get:233 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lambda.r all 1.2.4-2build2 [118 kB] 166s Get:234 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.options all 1.0.1-3build2 [20.5 kB] 166s Get:235 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-futile.logger all 1.4.3-4build2 [98.4 kB] 166s Get:236 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-snow all 1:0.4.4-2build1 [98.7 kB] 166s Get:237 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-codetools all 0.2-20-1build1 [91.1 kB] 166s Get:238 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bh all 1.84.0-1 [5962 B] 166s Get:239 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocparallel amd64 1.40.0-2 [1337 kB] 167s Get:240 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-base64enc amd64 0.1-3-3build1 [28.5 kB] 167s Get:241 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB] 167s Get:242 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-htmltools amd64 0.5.8.1-1 [373 kB] 167s Get:243 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 167s Get:244 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 167s Get:245 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 167s Get:246 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 167s Get:247 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 167s Get:248 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 167s Get:249 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-jquerylib all 0.1.4+dfsg-5 [13.7 kB] 167s Get:250 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fs amd64 1.6.5+dfsg-1 [246 kB] 167s Get:251 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rappdirs amd64 0.3.3-1build1 [49.3 kB] 167s Get:252 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sass amd64 0.4.9+dfsg-1 [1001 kB] 167s Get:253 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bslib all 0.9.0+dfsg-3build1 [4560 kB] 167s Get:254 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fontawesome all 0.5.3-1 [1331 kB] 167s Get:255 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-tinytex all 0.58-1 [148 kB] 167s Get:256 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-modernizr all 3.13.0-0.1build1 [100 kB] 167s Get:257 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 167s Get:258 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 167s Get:259 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 167s Get:260 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-later amd64 1.4.1+dfsg-1 [154 kB] 167s Get:261 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 167s Get:262 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-promises amd64 1.3.2+dfsg-1 [291 kB] 167s Get:263 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-httpuv amd64 1.6.15+dfsg-1 [510 kB] 167s Get:264 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xtable all 1:1.8-4-2build1 [691 kB] 167s Get:265 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-sourcetools amd64 0.1.7-1-1 [48.1 kB] 167s Get:266 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-withr all 3.0.2+dfsg-1 [214 kB] 167s Get:267 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB] 167s Get:268 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-twitter-bootstrap-datepicker all 1.3.1+dfsg1-4.1 [28.5 kB] 167s Get:269 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-shiny all 1.10.0+dfsg-2 [3124 kB] 167s Get:270 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rmarkdown all 2.30+dfsg-1 [1501 kB] 168s Get:271 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bookdown all 0.42+dfsg-1 [1409 kB] 168s Get:272 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-biocmanager all 1.30.25+dfsg-1 [132 kB] 168s Get:273 http://ftpmaster.internal/ubuntu resolute/universe amd64 tex-common all 6.20 [30.0 kB] 168s Get:274 http://ftpmaster.internal/ubuntu resolute/main amd64 t1utils amd64 1.41-4build4 [62.7 kB] 168s Get:275 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-binaries amd64 2025.20250727.75242+ds-5build1 [8747 kB] 168s Get:276 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-base all 2025.20260124-1 [22.8 MB] 168s Get:277 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-latex-base all 2025.20260124-1 [1321 kB] 168s Get:278 http://ftpmaster.internal/ubuntu resolute/universe amd64 texlive-bibtex-extra all 2025.20260124-1 [80.6 MB] 171s Get:279 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocversion all 3.20.0-2 [11.1 kB] 171s Get:280 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-biocstyle all 2.34.0+dfsg-1 [451 kB] 171s Get:281 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicranges amd64 1.58.0+dfsg-2 [2083 kB] 171s Get:282 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml amd64 3.99-0.20-1 [1751 kB] 171s Get:283 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-bitops amd64 1.0-9-1 [30.3 kB] 171s Get:284 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhtslib amd64 3.2.0+dfsg-2 [1499 kB] 171s Get:285 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rsamtools amd64 2.22.0+dfsg-2 [3745 kB] 171s Get:286 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-matrixgenerics all 1.18.1-1 [450 kB] 171s Get:287 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lattice amd64 0.22-7-1 [1367 kB] 171s Get:288 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 171s Get:289 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-abind all 1.4-8-1build1 [67.0 kB] 171s Get:290 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-s4arrays amd64 1.6.0+dfsg-2 [698 kB] 171s Get:291 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-sparsearray amd64 1.6.2+dfsg-2 [1391 kB] 172s Get:292 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-delayedarray amd64 0.32.0+dfsg-2 [2064 kB] 172s Get:293 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-summarizedexperiment all 1.36.0+dfsg-2 [1109 kB] 172s Get:294 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicalignments amd64 1.42.0-2 [2165 kB] 172s Get:295 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcurl amd64 1.98-1.16+dfsg-1 [807 kB] 172s Get:296 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rjson amd64 0.2.23-1 [104 kB] 172s Get:297 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-restfulr amd64 0.0.15-1 [380 kB] 172s Get:298 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rtracklayer amd64 1.66.0-3 [5225 kB] 173s Get:299 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-bsgenome all 1.74.0-2 [7001 kB] 173s Get:300 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-dnacopy amd64 1.80.0-2 [500 kB] 173s Get:301 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-genomicfeatures all 1.58.0+dfsg-2 [937 kB] 173s Get:302 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-org.hs.eg.db all 3.20.0-3 [63.1 MB] 177s Get:303 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-variantannotation amd64 1.52.0-2 [3642 kB] 177s Get:304 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build2 [54.0 kB] 177s Get:305 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-data.table amd64 1.17.0+dfsg-1 [2168 kB] 177s Get:306 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gtable all 0.3.6+dfsg-1 [199 kB] 177s Get:307 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 177s Get:308 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-s7 amd64 0.2.0-1 [328 kB] 177s Get:309 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-farver amd64 2.1.2-1 [1355 kB] 177s Get:310 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 177s Get:311 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-viridislite all 0.4.3-1 [1088 kB] 177s Get:312 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-scales all 1.4.0-1 [725 kB] 178s Get:313 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-ggplot2 all 4.0.2+dfsg-1 [4941 kB] 178s Get:314 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gridextra all 2.3-3build2 [1032 kB] 178s Get:315 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vgam amd64 1.1-13-1 [7789 kB] 178s Get:316 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mclust amd64 6.1.1-1 [3947 kB] 178s Get:317 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhdf5lib amd64 1.28.0+dfsg-3 [97.2 kB] 178s Get:318 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhdf5filters amd64 1.18.1+dfsg-1 [137 kB] 178s Get:319 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-rhdf5 amd64 2.50.2+dfsg-1build1 [822 kB] 178s Get:320 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-bioc-purecn all 2.12.0+dfsg-2 [6054 kB] 178s Get:321 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-brio amd64 1.1.5-1 [39.0 kB] 178s Get:322 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ps amd64 1.9.0-1 [408 kB] 178s Get:323 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-processx amd64 3.8.6-1 [365 kB] 178s Get:324 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-callr all 3.7.6-1 [458 kB] 178s Get:325 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lazyeval amd64 0.2.2-1build2 [146 kB] 178s Get:326 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rex all 1.2.1-1build1 [126 kB] 178s Get:327 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-covr amd64 3.6.4+dfsg-1 [303 kB] 178s Get:328 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-desc all 1.4.3-1 [359 kB] 178s Get:329 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-diffobj amd64 0.3.5-1build1 [1156 kB] 178s Get:330 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-globals all 0.19.0-1 [160 kB] 178s Get:331 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-listenv all 0.10.0+dfsg-1 [113 kB] 178s Get:332 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-parallelly amd64 1.42.0-1 [540 kB] 178s Get:333 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-future all 1.34.0+dfsg-1 [646 kB] 178s Get:334 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-getopt all 1.20.4-1 [38.4 kB] 178s Get:335 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-markdown all 1.13-1 [162 kB] 178s Get:336 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-optparse all 1.7.5-1 [83.6 kB] 178s Get:337 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgbuild all 1.4.8-1 [219 kB] 178s Get:338 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rprojroot all 2.1.1-1 [131 kB] 178s Get:339 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgload all 1.4.1-1 [252 kB] 178s Get:340 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-praise all 1.0.0-4build2 [20.9 kB] 178s Get:341 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-r.cache all 0.17.0-1 [117 kB] 178s Get:342 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pscbs all 0.68.0-1 [4234 kB] 179s Get:343 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-waldo all 0.6.2-1 [153 kB] 179s Get:344 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-testthat amd64 3.2.3-1 [1651 kB] 179s Preconfiguring packages ... 179s Fetched 564 MB in 19s (29.1 MB/s) 179s Selecting previously unselected package libc-dev-bin. 179s (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 ... 125269 files and directories currently installed.) 179s Preparing to unpack .../000-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 179s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 179s Selecting previously unselected package linux-libc-dev:amd64. 179s Preparing to unpack .../001-linux-libc-dev_6.19.0-3.3_amd64.deb ... 179s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 179s Selecting previously unselected package libcrypt-dev:amd64. 179s Preparing to unpack .../002-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 179s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 179s Selecting previously unselected package rpcsvc-proto. 179s Preparing to unpack .../003-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 179s Unpacking rpcsvc-proto (1.4.3-1build1) ... 179s Selecting previously unselected package libc6-dev:amd64. 179s Preparing to unpack .../004-libc6-dev_2.42-2ubuntu4_amd64.deb ... 179s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 179s Selecting previously unselected package libisl23:amd64. 179s Preparing to unpack .../005-libisl23_0.27-1build1_amd64.deb ... 179s Unpacking libisl23:amd64 (0.27-1build1) ... 179s Selecting previously unselected package libmpc3:amd64. 179s Preparing to unpack .../006-libmpc3_1.3.1-2_amd64.deb ... 179s Unpacking libmpc3:amd64 (1.3.1-2) ... 179s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 179s Preparing to unpack .../007-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 179s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package cpp-15. 180s Preparing to unpack .../008-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package cpp-x86-64-linux-gnu. 180s Preparing to unpack .../009-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package cpp. 180s Preparing to unpack .../010-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking cpp (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package libcc1-0:amd64. 180s Preparing to unpack .../011-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libgomp1:amd64. 180s Preparing to unpack .../012-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libitm1:amd64. 180s Preparing to unpack .../013-libitm1_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libasan8:amd64. 180s Preparing to unpack .../014-libasan8_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package liblsan0:amd64. 180s Preparing to unpack .../015-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libtsan2:amd64. 180s Preparing to unpack .../016-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libubsan1:amd64. 180s Preparing to unpack .../017-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libhwasan0:amd64. 180s Preparing to unpack .../018-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libquadmath0:amd64. 180s Preparing to unpack .../019-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 180s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 180s Selecting previously unselected package libgcc-15-dev:amd64. 180s Preparing to unpack .../020-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 180s Preparing to unpack .../021-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package gcc-15. 180s Preparing to unpack .../022-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package gcc-x86-64-linux-gnu. 180s Preparing to unpack .../023-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package gcc. 180s Preparing to unpack .../024-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking gcc (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package libstdc++-15-dev:amd64. 180s Preparing to unpack .../025-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package g++-15-x86-64-linux-gnu. 180s Preparing to unpack .../026-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package g++-15. 180s Preparing to unpack .../027-g++-15_15.2.0-12ubuntu1_amd64.deb ... 180s Unpacking g++-15 (15.2.0-12ubuntu1) ... 180s Selecting previously unselected package g++-x86-64-linux-gnu. 180s Preparing to unpack .../028-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 180s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 180s Selecting previously unselected package g++. 181s Preparing to unpack .../029-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking g++ (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package build-essential. 181s Preparing to unpack .../030-build-essential_12.12ubuntu2_amd64.deb ... 181s Unpacking build-essential (12.12ubuntu2) ... 181s Selecting previously unselected package dctrl-tools. 181s Preparing to unpack .../031-dctrl-tools_2.24-3build4_amd64.deb ... 181s Unpacking dctrl-tools (2.24-3build4) ... 181s Selecting previously unselected package fonts-dejavu-mono. 181s Preparing to unpack .../032-fonts-dejavu-mono_2.37-8build1_all.deb ... 181s Unpacking fonts-dejavu-mono (2.37-8build1) ... 181s Selecting previously unselected package fonts-dejavu-core. 181s Preparing to unpack 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gfortran-15-x86-64-linux-gnu. 181s Preparing to unpack .../043-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gfortran-15. 181s Preparing to unpack .../044-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 181s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 181s Selecting previously unselected package gfortran-x86-64-linux-gnu. 181s Preparing to unpack .../045-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package gfortran. 181s Preparing to unpack .../046-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 181s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 181s Selecting previously unselected package hdf5-helpers. 181s Preparing to unpack .../047-hdf5-helpers_1.14.6+repack-2_amd64.deb ... 181s Unpacking hdf5-helpers (1.14.6+repack-2) ... 181s Selecting previously unselected package icu-devtools. 181s Preparing to unpack .../048-icu-devtools_78.2-1ubuntu1_amd64.deb ... 181s Unpacking icu-devtools (78.2-1ubuntu1) ... 181s Selecting previously unselected package javascript-common. 181s Preparing to unpack .../049-javascript-common_12+nmu1build1_all.deb ... 181s Unpacking javascript-common (12+nmu1build1) ... 181s Selecting previously unselected package comerr-dev:amd64. 181s Preparing to unpack .../050-comerr-dev_2.1-1.47.2-3ubuntu2_amd64.deb ... 181s Unpacking comerr-dev:amd64 (2.1-1.47.2-3ubuntu2) ... 181s Selecting previously unselected package libgssrpc4t64:amd64. 181s Preparing to unpack .../051-libgssrpc4t64_1.22.1-2_amd64.deb ... 181s Unpacking libgssrpc4t64:amd64 (1.22.1-2) ... 181s Selecting previously unselected package libkadm5clnt-mit12:amd64. 181s Preparing to unpack .../052-libkadm5clnt-mit12_1.22.1-2_amd64.deb ... 181s Unpacking libkadm5clnt-mit12:amd64 (1.22.1-2) ... 181s Selecting previously unselected package libkdb5-10t64:amd64. 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Selecting previously unselected package libboost1.90-dev:amd64. 181s Preparing to unpack .../064-libboost1.90-dev_1.90.0-2ubuntu1_amd64.deb ... 181s Unpacking libboost1.90-dev:amd64 (1.90.0-2ubuntu1) ... 182s Selecting previously unselected package libboost-dev:amd64. 182s Preparing to unpack .../065-libboost-dev_1.90.0.0ubuntu3_amd64.deb ... 182s Unpacking libboost-dev:amd64 (1.90.0.0ubuntu3) ... 182s Selecting previously unselected package libbrotli-dev:amd64. 182s Preparing to unpack .../066-libbrotli-dev_1.1.0-2build6_amd64.deb ... 182s Unpacking libbrotli-dev:amd64 (1.1.0-2build6) ... 182s Selecting previously unselected package libbz2-dev:amd64. 182s Preparing to unpack .../067-libbz2-dev_1.0.8-6build2_amd64.deb ... 182s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ... 182s Selecting previously unselected package libpixman-1-0:amd64. 182s Preparing to unpack .../068-libpixman-1-0_0.46.4-1_amd64.deb ... 182s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 182s Selecting previously unselected package libxcb-render0:amd64. 182s Preparing to unpack .../069-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 182s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 182s Selecting previously unselected package libxcb-shm0:amd64. 182s Preparing to unpack .../070-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 182s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 182s Selecting previously unselected package libxrender1:amd64. 182s Preparing to unpack .../071-libxrender1_1%3a0.9.12-1_amd64.deb ... 182s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 182s Selecting previously unselected package libcairo2:amd64. 182s Preparing to unpack .../072-libcairo2_1.18.4-3_amd64.deb ... 182s Unpacking libcairo2:amd64 (1.18.4-3) ... 182s Selecting previously unselected package libidn2-dev:amd64. 182s Preparing to unpack .../073-libidn2-dev_2.3.8-4build1_amd64.deb ... 182s Unpacking libidn2-dev:amd64 (2.3.8-4build1) ... 182s Selecting previously unselected package libkrb5-dev:amd64. 182s Preparing to unpack .../074-libkrb5-dev_1.22.1-2_amd64.deb ... 182s Unpacking libkrb5-dev:amd64 (1.22.1-2) ... 182s Selecting previously unselected package libldap-dev:amd64. 182s Preparing to unpack .../075-libldap-dev_2.6.10+dfsg-1ubuntu5_amd64.deb ... 182s Unpacking libldap-dev:amd64 (2.6.10+dfsg-1ubuntu5) ... 182s Selecting previously unselected package libpkgconf3:amd64. 182s Preparing to unpack .../076-libpkgconf3_1.8.1-4build1_amd64.deb ... 182s Unpacking libpkgconf3:amd64 (1.8.1-4build1) ... 182s Selecting previously unselected package pkgconf-bin. 182s Preparing to unpack .../077-pkgconf-bin_1.8.1-4build1_amd64.deb ... 182s Unpacking pkgconf-bin (1.8.1-4build1) ... 182s Selecting previously unselected package pkgconf:amd64. 182s Preparing to unpack .../078-pkgconf_1.8.1-4build1_amd64.deb ... 182s Unpacking pkgconf:amd64 (1.8.1-4build1) ... 182s Selecting previously unselected package libnghttp2-dev:amd64. 182s Preparing to unpack .../079-libnghttp2-dev_1.64.0-1.1ubuntu1_amd64.deb ... 182s Unpacking libnghttp2-dev:amd64 (1.64.0-1.1ubuntu1) ... 182s Selecting previously unselected package libpsl-dev:amd64. 183s Preparing to unpack .../080-libpsl-dev_0.21.2-1.1build2_amd64.deb ... 183s Unpacking libpsl-dev:amd64 (0.21.2-1.1build2) ... 183s Selecting previously unselected package libgmpxx4ldbl:amd64. 183s Preparing to unpack .../081-libgmpxx4ldbl_2%3a6.3.0+dfsg-5ubuntu1_amd64.deb ... 183s Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5ubuntu1) ... 183s Selecting previously unselected package libgmp-dev:amd64. 183s Preparing to unpack .../082-libgmp-dev_2%3a6.3.0+dfsg-5ubuntu1_amd64.deb ... 183s Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-5ubuntu1) ... 183s Selecting previously unselected package libevent-2.1-7t64:amd64. 183s Preparing to unpack .../083-libevent-2.1-7t64_2.1.12-stable-10build2_amd64.deb ... 183s Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 183s Selecting previously unselected package libunbound8:amd64. 183s Preparing to unpack .../084-libunbound8_1.24.2-1ubuntu1_amd64.deb ... 183s Unpacking libunbound8:amd64 (1.24.2-1ubuntu1) ... 183s Selecting previously unselected package libgnutls-dane0t64:amd64. 183s Preparing to unpack .../085-libgnutls-dane0t64_3.8.10-3ubuntu1_amd64.deb ... 183s Unpacking libgnutls-dane0t64:amd64 (3.8.10-3ubuntu1) ... 183s Selecting previously unselected package libgnutls-openssl27t64:amd64. 183s Preparing to unpack .../086-libgnutls-openssl27t64_3.8.10-3ubuntu1_amd64.deb ... 183s Unpacking libgnutls-openssl27t64:amd64 (3.8.10-3ubuntu1) ... 183s Selecting previously unselected package libp11-kit-dev:amd64. 183s Preparing to unpack .../087-libp11-kit-dev_0.25.10-1_amd64.deb ... 183s Unpacking libp11-kit-dev:amd64 (0.25.10-1) ... 183s Selecting previously unselected package libtasn1-6-dev:amd64. 183s Preparing to unpack .../088-libtasn1-6-dev_4.21.0-2_amd64.deb ... 183s Unpacking libtasn1-6-dev:amd64 (4.21.0-2) ... 183s Selecting previously unselected package nettle-dev:amd64. 183s Preparing to unpack .../089-nettle-dev_3.10.2-1_amd64.deb ... 183s Unpacking nettle-dev:amd64 (3.10.2-1) ... 183s Selecting previously unselected package libgnutls28-dev:amd64. 183s Preparing to unpack .../090-libgnutls28-dev_3.8.10-3ubuntu1_amd64.deb ... 183s Unpacking libgnutls28-dev:amd64 (3.8.10-3ubuntu1) ... 183s Selecting previously unselected package zlib1g-dev:amd64. 183s Preparing to unpack .../091-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_amd64.deb ... 183s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 183s Selecting previously unselected package librtmp-dev:amd64. 183s Preparing to unpack .../092-librtmp-dev_2.4+20151223.gitfa8646d.1-3_amd64.deb ... 183s Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... 183s Selecting previously unselected package libssl-dev:amd64. 183s Preparing to unpack .../093-libssl-dev_3.5.3-1ubuntu2_amd64.deb ... 183s Unpacking libssl-dev:amd64 (3.5.3-1ubuntu2) ... 183s Selecting previously unselected package libssh2-1-dev:amd64. 183s Preparing to unpack .../094-libssh2-1-dev_1.11.1-1build1_amd64.deb ... 183s Unpacking libssh2-1-dev:amd64 (1.11.1-1build1) ... 183s Selecting previously unselected package libzstd-dev:amd64. 183s Preparing to unpack .../095-libzstd-dev_1.5.7+dfsg-3_amd64.deb ... 183s Unpacking libzstd-dev:amd64 (1.5.7+dfsg-3) ... 183s Selecting previously unselected package libcurl4-openssl-dev:amd64. 183s Preparing to unpack .../096-libcurl4-openssl-dev_8.18.0-1ubuntu1_amd64.deb ... 183s Unpacking libcurl4-openssl-dev:amd64 (8.18.0-1ubuntu1) ... 183s Selecting previously unselected package libdatrie1:amd64. 183s Preparing to unpack .../097-libdatrie1_0.2.14-1_amd64.deb ... 183s Unpacking libdatrie1:amd64 (0.2.14-1) ... 183s Selecting previously unselected package libdeflate0:amd64. 183s Preparing to unpack .../098-libdeflate0_1.23-2build1_amd64.deb ... 183s Unpacking libdeflate0:amd64 (1.23-2build1) ... 183s Selecting previously unselected package libdeflate-dev:amd64. 183s Preparing to unpack .../099-libdeflate-dev_1.23-2build1_amd64.deb ... 183s Unpacking libdeflate-dev:amd64 (1.23-2build1) ... 183s Selecting previously unselected package libgraphite2-3:amd64. 183s Preparing to unpack .../100-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 183s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 183s Selecting previously unselected package libharfbuzz0b:amd64. 183s Preparing to unpack .../101-libharfbuzz0b_12.3.2-1_amd64.deb ... 183s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 183s Selecting previously unselected package libsz2:amd64. 183s Preparing to unpack .../102-libsz2_1.1.5-1_amd64.deb ... 183s Unpacking libsz2:amd64 (1.1.5-1) ... 183s Selecting previously unselected package libhdf5-310:amd64. 183s Preparing to unpack .../103-libhdf5-310_1.14.6+repack-2_amd64.deb ... 183s Unpacking libhdf5-310:amd64 (1.14.6+repack-2) ... 183s Selecting previously unselected package libhdf5-cpp-310:amd64. 183s Preparing to unpack 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previously unselected package libjpeg-turbo8:amd64. 183s Preparing to unpack .../109-libjpeg-turbo8_2.1.5-4ubuntu3_amd64.deb ... 183s Unpacking libjpeg-turbo8:amd64 (2.1.5-4ubuntu3) ... 183s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 183s Preparing to unpack .../110-libjpeg-turbo8-dev_2.1.5-4ubuntu3_amd64.deb ... 183s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ... 183s Selecting previously unselected package libjpeg8:amd64. 183s Preparing to unpack .../111-libjpeg8_8c-2ubuntu12_amd64.deb ... 183s Unpacking libjpeg8:amd64 (8c-2ubuntu12) ... 183s Selecting previously unselected package libjpeg8-dev:amd64. 183s Preparing to unpack .../112-libjpeg8-dev_8c-2ubuntu12_amd64.deb ... 183s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu12) ... 183s Selecting previously unselected package libjpeg-dev:amd64. 183s Preparing to unpack .../113-libjpeg-dev_8c-2ubuntu12_amd64.deb ... 183s Unpacking libjpeg-dev:amd64 (8c-2ubuntu12) ... 183s Selecting previously unselected package libaec-dev:amd64. 183s Preparing to unpack .../114-libaec-dev_1.1.5-1_amd64.deb ... 183s Unpacking libaec-dev:amd64 (1.1.5-1) ... 183s Selecting previously unselected package libhdf5-dev. 183s Preparing to unpack .../115-libhdf5-dev_1.14.6+repack-2_amd64.deb ... 183s Unpacking libhdf5-dev (1.14.6+repack-2) ... 183s Selecting previously unselected package x11-common. 183s Preparing to unpack .../116-x11-common_1%3a7.7+24ubuntu1_all.deb ... 183s Unpacking x11-common (1:7.7+24ubuntu1) ... 183s Selecting previously unselected package libice6:amd64. 183s Preparing to unpack .../117-libice6_2%3a1.1.1-1build1_amd64.deb ... 183s Unpacking libice6:amd64 (2:1.1.1-1build1) ... 183s Selecting previously unselected package libicu-dev:amd64. 183s Preparing to unpack .../118-libicu-dev_78.2-1ubuntu1_amd64.deb ... 183s Unpacking libicu-dev:amd64 (78.2-1ubuntu1) ... 183s Selecting previously unselected package libjs-bootstrap. 183s Preparing to unpack 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Selecting previously unselected package libpcre2-posix3:amd64. 184s Preparing to unpack .../150-libpcre2-posix3_10.46-1_amd64.deb ... 184s Unpacking libpcre2-posix3:amd64 (10.46-1) ... 184s Selecting previously unselected package libpcre2-dev:amd64. 184s Preparing to unpack .../151-libpcre2-dev_10.46-1_amd64.deb ... 184s Unpacking libpcre2-dev:amd64 (10.46-1) ... 184s Selecting previously unselected package libpng-dev:amd64. 184s Preparing to unpack .../152-libpng-dev_1.6.54-1_amd64.deb ... 184s Unpacking libpng-dev:amd64 (1.6.54-1) ... 184s Selecting previously unselected package libpotrace0:amd64. 184s Preparing to unpack .../153-libpotrace0_1.16-2build2_amd64.deb ... 184s Unpacking libpotrace0:amd64 (1.16-2build2) ... 184s Selecting previously unselected package libptexenc1:amd64. 184s Preparing to unpack .../154-libptexenc1_2025.20250727.75242+ds-5build1_amd64.deb ... 184s Unpacking libptexenc1:amd64 (2025.20250727.75242+ds-5build1) ... 184s Selecting previously unselected package libreadline-dev:amd64. 184s Preparing to unpack .../155-libreadline-dev_8.3-3_amd64.deb ... 184s Unpacking libreadline-dev:amd64 (8.3-3) ... 184s Selecting previously unselected package libsharpyuv0:amd64. 184s Preparing to unpack .../156-libsharpyuv0_1.5.0-0.1build1_amd64.deb ... 184s Unpacking libsharpyuv0:amd64 (1.5.0-0.1build1) ... 184s Selecting previously unselected package libsm6:amd64. 184s Preparing to unpack .../157-libsm6_2%3a1.2.6-1build1_amd64.deb ... 184s Unpacking libsm6:amd64 (2:1.2.6-1build1) ... 184s Selecting previously unselected package libsynctex2:amd64. 184s Preparing to unpack .../158-libsynctex2_2025.20250727.75242+ds-5build1_amd64.deb ... 184s Unpacking libsynctex2:amd64 (2025.20250727.75242+ds-5build1) ... 184s Selecting previously unselected package libtcl8.6:amd64. 184s Preparing to unpack .../159-libtcl8.6_8.6.17+dfsg-1build1_amd64.deb ... 184s Unpacking libtcl8.6:amd64 (8.6.17+dfsg-1build1) ... 184s Selecting previously unselected package libteckit0:amd64. 185s Preparing to unpack .../160-libteckit0_2.5.13+ds-1_amd64.deb ... 185s Unpacking libteckit0:amd64 (2.5.13+ds-1) ... 185s Selecting previously unselected package libtexlua53-5:amd64. 185s Preparing to unpack .../161-libtexlua53-5_2025.20250727.75242+ds-5build1_amd64.deb ... 185s Unpacking libtexlua53-5:amd64 (2025.20250727.75242+ds-5build1) ... 185s Selecting previously unselected package libjbig0:amd64. 185s Preparing to unpack .../162-libjbig0_2.1-6.1ubuntu3_amd64.deb ... 185s Unpacking libjbig0:amd64 (2.1-6.1ubuntu3) ... 185s Selecting previously unselected package libwebp7:amd64. 185s Preparing to unpack .../163-libwebp7_1.5.0-0.1build1_amd64.deb ... 185s Unpacking libwebp7:amd64 (1.5.0-0.1build1) ... 185s Selecting previously unselected package libtiff6:amd64. 185s Preparing to unpack .../164-libtiff6_4.7.0-3ubuntu3_amd64.deb ... 185s Unpacking libtiff6:amd64 (4.7.0-3ubuntu3) ... 185s Selecting previously unselected package libxft2:amd64. 185s Preparing to unpack .../165-libxft2_2.3.6-1build2_amd64.deb ... 185s Unpacking libxft2:amd64 (2.3.6-1build2) ... 185s Selecting previously unselected package libxss1:amd64. 185s Preparing to unpack .../166-libxss1_1%3a1.2.3-1build4_amd64.deb ... 185s Unpacking libxss1:amd64 (1:1.2.3-1build4) ... 185s Selecting previously unselected package libtk8.6:amd64. 185s Preparing to unpack .../167-libtk8.6_8.6.17-1_amd64.deb ... 185s Unpacking libtk8.6:amd64 (8.6.17-1) ... 185s Selecting previously unselected package libxt6t64:amd64. 185s Preparing to unpack .../168-libxt6t64_1%3a1.2.1-1.3_amd64.deb ... 185s Unpacking libxt6t64:amd64 (1:1.2.1-1.3) ... 185s Selecting previously unselected package libxmu6:amd64. 185s Preparing to unpack .../169-libxmu6_2%3a1.1.3-4_amd64.deb ... 185s Unpacking libxmu6:amd64 (2:1.1.3-4) ... 185s Selecting previously unselected package libxpm4:amd64. 185s Preparing to unpack .../170-libxpm4_1%3a3.5.17-1build3_amd64.deb ... 185s Unpacking libxpm4:amd64 (1:3.5.17-1build3) ... 185s Selecting previously unselected package libxaw7:amd64. 185s Preparing to unpack .../171-libxaw7_2%3a1.0.16-1build1_amd64.deb ... 185s Unpacking libxaw7:amd64 (2:1.0.16-1build1) ... 185s Selecting previously unselected package libxi6:amd64. 185s Preparing to unpack .../172-libxi6_2%3a1.8.2-2_amd64.deb ... 185s Unpacking libxi6:amd64 (2:1.8.2-2) ... 185s Selecting previously unselected package libzzip-0-13t64:amd64. 185s Preparing to unpack .../173-libzzip-0-13t64_0.13.78+dfsg.1-0.2_amd64.deb ... 185s Unpacking libzzip-0-13t64:amd64 (0.13.78+dfsg.1-0.2) ... 185s Selecting previously unselected package node-bootstrap-sass. 185s Preparing to unpack .../174-node-bootstrap-sass_3.4.3-2_all.deb ... 185s Unpacking node-bootstrap-sass (3.4.3-2) ... 185s Selecting previously unselected package node-html5shiv. 185s Preparing to unpack .../175-node-html5shiv_3.7.3+dfsg-5_all.deb ... 185s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 185s Selecting previously unselected package node-normalize.css. 185s Preparing to unpack .../176-node-normalize.css_8.0.1-5.1_all.deb ... 185s Unpacking node-normalize.css (8.0.1-5.1) ... 185s Selecting previously unselected package pandoc-data. 185s Preparing to unpack .../177-pandoc-data_3.1.11.1-3build1_all.deb ... 185s Unpacking pandoc-data (3.1.11.1-3build1) ... 185s Selecting previously unselected package pandoc. 185s Preparing to unpack .../178-pandoc_3.1.11.1+ds-4_amd64.deb ... 185s Unpacking pandoc (3.1.11.1+ds-4) ... 185s Selecting previously unselected package zip. 185s Preparing to unpack .../179-zip_3.0-15ubuntu3_amd64.deb ... 185s Unpacking zip (3.0-15ubuntu3) ... 185s Selecting previously unselected package unzip. 185s Preparing to unpack .../180-unzip_6.0-29ubuntu1_amd64.deb ... 185s Unpacking unzip (6.0-29ubuntu1) ... 185s Selecting previously unselected package xdg-utils. 185s Preparing to unpack .../181-xdg-utils_1.2.1-2ubuntu2_all.deb ... 185s Unpacking xdg-utils (1.2.1-2ubuntu2) ... 185s Selecting previously unselected package r-base-core. 185s Preparing to unpack .../182-r-base-core_4.5.2-1ubuntu2_amd64.deb ... 185s Unpacking r-base-core (4.5.2-1ubuntu2) ... 186s Selecting previously unselected package liblzma-dev:amd64. 186s Preparing to unpack .../183-liblzma-dev_5.8.2-2_amd64.deb ... 186s Unpacking liblzma-dev:amd64 (5.8.2-2) ... 186s Selecting previously unselected package libtirpc-dev:amd64. 186s Preparing to unpack .../184-libtirpc-dev_1.3.6+ds-1_amd64.deb ... 186s Unpacking libtirpc-dev:amd64 (1.3.6+ds-1) ... 186s Selecting previously unselected package r-base-dev. 186s Preparing to unpack .../185-r-base-dev_4.5.2-1ubuntu2_all.deb ... 186s Unpacking r-base-dev (4.5.2-1ubuntu2) ... 186s Selecting previously unselected package pkg-r-autopkgtest. 186s Preparing to unpack .../186-pkg-r-autopkgtest_20250812_all.deb ... 186s Unpacking pkg-r-autopkgtest (20250812) ... 186s Selecting previously unselected package r-bioc-biocgenerics. 186s Preparing to unpack .../187-r-bioc-biocgenerics_0.52.0-2_all.deb ... 186s Unpacking r-bioc-biocgenerics (0.52.0-2) ... 186s Selecting previously unselected package r-bioc-biobase. 186s Preparing to unpack .../188-r-bioc-biobase_2.66.0-2_amd64.deb ... 186s Unpacking r-bioc-biobase (2.66.0-2) ... 186s Selecting previously unselected package r-bioc-s4vectors. 186s Preparing to unpack .../189-r-bioc-s4vectors_0.44.0+dfsg-2_amd64.deb ... 186s Unpacking r-bioc-s4vectors (0.44.0+dfsg-2) ... 186s Selecting previously unselected package r-bioc-iranges. 186s Preparing to unpack .../190-r-bioc-iranges_2.40.1-3_amd64.deb ... 186s Unpacking r-bioc-iranges (2.40.1-3) ... 186s Selecting previously unselected package r-cran-dbi. 186s Preparing to unpack .../191-r-cran-dbi_1.2.3-1build1_all.deb ... 186s Unpacking r-cran-dbi (1.2.3-1build1) ... 186s Selecting previously unselected package r-cran-bit. 186s Preparing to unpack .../192-r-cran-bit_4.6.0+dfsg-1_amd64.deb ... 186s Unpacking r-cran-bit (4.6.0+dfsg-1) ... 186s Selecting previously unselected package r-cran-bit64. 186s Preparing to unpack .../193-r-cran-bit64_4.6.0-1-4_amd64.deb ... 186s Unpacking r-cran-bit64 (4.6.0-1-4) ... 186s Selecting previously unselected package r-cran-rlang. 186s Preparing to unpack .../194-r-cran-rlang_1.1.5-3_amd64.deb ... 186s Unpacking r-cran-rlang (1.1.5-3) ... 186s Selecting previously unselected package r-cran-cli. 186s Preparing to unpack .../195-r-cran-cli_3.6.4-1_amd64.deb ... 186s Unpacking r-cran-cli (3.6.4-1) ... 186s Selecting previously unselected package r-cran-glue. 186s Preparing to unpack .../196-r-cran-glue_1.8.0-1_amd64.deb ... 186s Unpacking r-cran-glue (1.8.0-1) ... 186s Selecting previously unselected package r-cran-lifecycle. 186s Preparing to unpack .../197-r-cran-lifecycle_1.0.5+dfsg-1_all.deb ... 186s Unpacking r-cran-lifecycle (1.0.5+dfsg-1) ... 186s Selecting previously unselected package r-cran-vctrs. 186s Preparing to unpack .../198-r-cran-vctrs_0.6.5-1_amd64.deb ... 186s Unpacking r-cran-vctrs (0.6.5-1) ... 186s Selecting previously unselected package r-cran-blob. 186s Preparing to unpack .../199-r-cran-blob_1.3.0-1_all.deb ... 186s Unpacking r-cran-blob (1.3.0-1) ... 186s Selecting previously unselected package r-cran-fastmap. 186s Preparing to unpack .../200-r-cran-fastmap_1.2.0-1_amd64.deb ... 186s Unpacking r-cran-fastmap (1.2.0-1) ... 186s Selecting previously unselected package r-cran-cachem. 186s Preparing to unpack .../201-r-cran-cachem_1.1.0-1_amd64.deb ... 186s Unpacking r-cran-cachem (1.1.0-1) ... 186s Selecting previously unselected package r-cran-memoise. 186s Preparing to unpack .../202-r-cran-memoise_2.0.1-1build1_all.deb ... 186s Unpacking r-cran-memoise (2.0.1-1build1) ... 186s Selecting previously unselected package r-cran-pkgconfig. 186s Preparing to unpack .../203-r-cran-pkgconfig_2.0.3-2build2_all.deb ... 186s Unpacking r-cran-pkgconfig (2.0.3-2build2) ... 186s Selecting previously unselected package r-cran-plogr. 186s Preparing to unpack .../204-r-cran-plogr_0.2.0-3build2_all.deb ... 186s Unpacking r-cran-plogr (0.2.0-3build2) ... 186s Selecting previously unselected package r-cran-cpp11. 186s Preparing to unpack .../205-r-cran-cpp11_0.5.3-1_all.deb ... 186s Unpacking r-cran-cpp11 (0.5.3-1) ... 186s Selecting previously unselected package r-cran-rsqlite. 186s Preparing to unpack .../206-r-cran-rsqlite_2.3.9-1_amd64.deb ... 186s Unpacking r-cran-rsqlite (2.3.9-1) ... 186s Selecting previously unselected package r-cran-curl. 186s Preparing to unpack .../207-r-cran-curl_7.0.0+dfsg-1_amd64.deb ... 186s Unpacking r-cran-curl (7.0.0+dfsg-1) ... 186s Selecting previously unselected package r-cran-jsonlite. 186s Preparing to unpack .../208-r-cran-jsonlite_1.9.1+dfsg-1_amd64.deb ... 186s Unpacking r-cran-jsonlite (1.9.1+dfsg-1) ... 186s Selecting previously unselected package r-cran-mime. 186s Preparing to unpack .../209-r-cran-mime_0.12-2_amd64.deb ... 186s Unpacking r-cran-mime (0.12-2) ... 186s Selecting previously unselected package r-cran-sys. 186s Preparing to unpack .../210-r-cran-sys_3.4.3-1_amd64.deb ... 186s Unpacking r-cran-sys (3.4.3-1) ... 186s Selecting previously unselected package r-cran-askpass. 186s Preparing to unpack .../211-r-cran-askpass_1.2.1-1_amd64.deb ... 186s Unpacking r-cran-askpass (1.2.1-1) ... 186s Selecting previously unselected package r-cran-openssl. 186s Preparing to unpack .../212-r-cran-openssl_2.3.2+dfsg-1_amd64.deb ... 186s Unpacking r-cran-openssl (2.3.2+dfsg-1) ... 186s Selecting previously unselected package r-cran-r6. 186s Preparing to unpack .../213-r-cran-r6_2.6.1-1_all.deb ... 186s Unpacking r-cran-r6 (2.6.1-1) ... 186s Selecting previously unselected package r-cran-httr. 186s Preparing to unpack .../214-r-cran-httr_1.4.7+dfsg-1_all.deb ... 186s Unpacking r-cran-httr (1.4.7+dfsg-1) ... 186s Selecting previously unselected package r-cran-png. 186s Preparing to unpack .../215-r-cran-png_0.1-8-1build2_amd64.deb ... 186s Unpacking r-cran-png (0.1-8-1build2) ... 186s Selecting previously unselected package r-bioc-zlibbioc. 186s Preparing to unpack .../216-r-bioc-zlibbioc_1.52.0+dfsg-2_all.deb ... 186s Unpacking r-bioc-zlibbioc (1.52.0+dfsg-2) ... 186s Selecting previously unselected package r-bioc-xvector. 186s Preparing to unpack .../217-r-bioc-xvector_0.46.0-2_amd64.deb ... 186s Unpacking r-bioc-xvector (0.46.0-2) ... 186s Selecting previously unselected package r-bioc-ucsc.utils. 186s Preparing to unpack .../218-r-bioc-ucsc.utils_1.2.0+ds-2_all.deb ... 186s Unpacking r-bioc-ucsc.utils (1.2.0+ds-2) ... 186s Selecting previously unselected package r-bioc-genomeinfodbdata. 186s Preparing to unpack .../219-r-bioc-genomeinfodbdata_1.2.13-2_all.deb ... 186s Unpacking r-bioc-genomeinfodbdata (1.2.13-2) ... 186s Selecting previously unselected package r-bioc-genomeinfodb. 186s Preparing to unpack .../220-r-bioc-genomeinfodb_1.42.3+dfsg-1_all.deb ... 186s Unpacking r-bioc-genomeinfodb (1.42.3+dfsg-1) ... 186s Selecting previously unselected package r-cran-crayon. 186s Preparing to unpack .../221-r-cran-crayon_1.5.3-1_all.deb ... 186s Unpacking r-cran-crayon (1.5.3-1) ... 186s Selecting previously unselected package r-bioc-biostrings. 186s Preparing to unpack .../222-r-bioc-biostrings_2.74.1+dfsg-2_amd64.deb ... 186s Unpacking r-bioc-biostrings (2.74.1+dfsg-2) ... 186s Selecting previously unselected package r-bioc-keggrest. 186s Preparing to unpack .../223-r-bioc-keggrest_1.46.0+dfsg-3_all.deb ... 186s Unpacking r-bioc-keggrest (1.46.0+dfsg-3) ... 186s Selecting previously unselected package r-bioc-annotationdbi. 186s Preparing to unpack .../224-r-bioc-annotationdbi_1.68.0-2_all.deb ... 186s Unpacking r-bioc-annotationdbi (1.68.0-2) ... 187s Selecting previously unselected package r-cran-r.methodss3. 187s Preparing to unpack .../225-r-cran-r.methodss3_1.8.2-1_all.deb ... 187s Unpacking r-cran-r.methodss3 (1.8.2-1) ... 187s Selecting previously unselected package r-cran-r.oo. 187s Preparing to unpack .../226-r-cran-r.oo_1.27.1-1_all.deb ... 187s Unpacking r-cran-r.oo (1.27.1-1) ... 187s Selecting previously unselected package r-cran-r.utils. 187s Preparing to unpack .../227-r-cran-r.utils_2.13.0-1_all.deb ... 187s Unpacking r-cran-r.utils (2.13.0-1) ... 187s Selecting previously unselected package r-cran-matrixstats. 187s Preparing to unpack .../228-r-cran-matrixstats_1.5.0-1_amd64.deb ... 187s Unpacking r-cran-matrixstats (1.5.0-1) ... 187s Selecting previously unselected package r-bioc-aroma.light. 187s Preparing to unpack .../229-r-bioc-aroma.light_3.36.0-2_all.deb ... 187s Unpacking r-bioc-aroma.light (3.36.0-2) ... 187s Selecting previously unselected package r-bioc-biocio. 187s Preparing to unpack .../230-r-bioc-biocio_1.16.0+dfsg-2_all.deb ... 187s Unpacking r-bioc-biocio (1.16.0+dfsg-2) ... 187s Selecting previously unselected package r-cran-formatr. 187s Preparing to unpack .../231-r-cran-formatr_1.14-2_all.deb ... 187s Unpacking r-cran-formatr (1.14-2) ... 187s Selecting previously unselected package r-cran-lambda.r. 187s Preparing to unpack .../232-r-cran-lambda.r_1.2.4-2build2_all.deb ... 187s Unpacking r-cran-lambda.r (1.2.4-2build2) ... 187s Selecting previously unselected package r-cran-futile.options. 187s Preparing to unpack .../233-r-cran-futile.options_1.0.1-3build2_all.deb ... 187s Unpacking r-cran-futile.options (1.0.1-3build2) ... 187s Selecting previously unselected package r-cran-futile.logger. 187s Preparing to unpack .../234-r-cran-futile.logger_1.4.3-4build2_all.deb ... 187s Unpacking r-cran-futile.logger (1.4.3-4build2) ... 187s Selecting previously unselected package r-cran-snow. 187s Preparing to unpack .../235-r-cran-snow_1%3a0.4.4-2build1_all.deb ... 187s Unpacking r-cran-snow (1:0.4.4-2build1) ... 187s Selecting previously unselected package r-cran-codetools. 187s Preparing to unpack .../236-r-cran-codetools_0.2-20-1build1_all.deb ... 187s Unpacking r-cran-codetools (0.2-20-1build1) ... 187s Selecting previously unselected package r-cran-bh. 187s Preparing to unpack .../237-r-cran-bh_1.84.0-1_all.deb ... 187s Unpacking r-cran-bh (1.84.0-1) ... 187s Selecting previously unselected package r-bioc-biocparallel. 187s Preparing to unpack .../238-r-bioc-biocparallel_1.40.0-2_amd64.deb ... 187s Unpacking r-bioc-biocparallel (1.40.0-2) ... 187s Selecting previously unselected package r-cran-base64enc. 187s Preparing to unpack .../239-r-cran-base64enc_0.1-3-3build1_amd64.deb ... 187s Unpacking r-cran-base64enc (0.1-3-3build1) ... 187s Selecting previously unselected package r-cran-digest. 187s Preparing to unpack .../240-r-cran-digest_0.6.39-1_amd64.deb ... 187s Unpacking r-cran-digest (0.6.39-1) ... 187s Selecting previously unselected package r-cran-htmltools. 187s Preparing to unpack .../241-r-cran-htmltools_0.5.8.1-1_amd64.deb ... 187s Unpacking r-cran-htmltools (0.5.8.1-1) ... 187s Selecting previously unselected package r-cran-evaluate. 187s Preparing to unpack .../242-r-cran-evaluate_1.0.5-1_all.deb ... 187s Unpacking r-cran-evaluate (1.0.5-1) ... 187s Selecting previously unselected package r-cran-xfun. 187s Preparing to unpack .../243-r-cran-xfun_0.55+dfsg-1_amd64.deb ... 187s Unpacking r-cran-xfun (0.55+dfsg-1) ... 187s Selecting previously unselected package r-cran-highr. 187s Preparing to unpack .../244-r-cran-highr_0.11+dfsg-1_all.deb ... 187s Unpacking r-cran-highr (0.11+dfsg-1) ... 187s Selecting previously unselected package r-cran-yaml. 187s Preparing to unpack .../245-r-cran-yaml_2.3.10-1_amd64.deb ... 187s Unpacking r-cran-yaml (2.3.10-1) ... 187s Selecting previously unselected package libjs-mathjax. 187s Preparing to unpack .../246-libjs-mathjax_2.7.9+dfsg-1build1_all.deb ... 187s Unpacking libjs-mathjax (2.7.9+dfsg-1build1) ... 187s Selecting previously unselected package r-cran-knitr. 187s Preparing to unpack .../247-r-cran-knitr_1.51+dfsg-1_all.deb ... 187s Unpacking r-cran-knitr (1.51+dfsg-1) ... 187s Selecting previously unselected package r-cran-jquerylib. 187s Preparing to unpack .../248-r-cran-jquerylib_0.1.4+dfsg-5_all.deb ... 187s Unpacking r-cran-jquerylib (0.1.4+dfsg-5) ... 187s Selecting previously unselected package r-cran-fs. 187s Preparing to unpack .../249-r-cran-fs_1.6.5+dfsg-1_amd64.deb ... 187s Unpacking r-cran-fs (1.6.5+dfsg-1) ... 187s Selecting previously unselected package r-cran-rappdirs. 187s Preparing to unpack .../250-r-cran-rappdirs_0.3.3-1build1_amd64.deb ... 187s Unpacking r-cran-rappdirs (0.3.3-1build1) ... 187s Selecting previously unselected package r-cran-sass. 187s Preparing to unpack .../251-r-cran-sass_0.4.9+dfsg-1_amd64.deb ... 187s Unpacking r-cran-sass (0.4.9+dfsg-1) ... 187s Selecting previously unselected package r-cran-bslib. 187s Preparing to unpack .../252-r-cran-bslib_0.9.0+dfsg-3build1_all.deb ... 187s Unpacking r-cran-bslib (0.9.0+dfsg-3build1) ... 187s Selecting previously unselected package r-cran-fontawesome. 187s Preparing to unpack .../253-r-cran-fontawesome_0.5.3-1_all.deb ... 187s Unpacking r-cran-fontawesome (0.5.3-1) ... 187s Selecting previously unselected package r-cran-tinytex. 187s Preparing to unpack .../254-r-cran-tinytex_0.58-1_all.deb ... 187s Unpacking r-cran-tinytex (0.58-1) ... 187s Selecting previously unselected package libjs-modernizr. 187s Preparing to unpack .../255-libjs-modernizr_3.13.0-0.1build1_all.deb ... 187s Unpacking libjs-modernizr (3.13.0-0.1build1) ... 187s Selecting previously unselected package r-cran-littler. 187s Preparing to unpack .../256-r-cran-littler_0.3.22-1_amd64.deb ... 187s Unpacking r-cran-littler (0.3.22-1) ... 187s Selecting previously unselected package r-cran-pkgkitten. 187s Preparing to unpack .../257-r-cran-pkgkitten_0.2.4-1_all.deb ... 187s Unpacking r-cran-pkgkitten (0.2.4-1) ... 187s Selecting previously unselected package r-cran-rcpp. 187s Preparing to unpack .../258-r-cran-rcpp_1.1.0-1_amd64.deb ... 187s Unpacking r-cran-rcpp (1.1.0-1) ... 188s Selecting previously unselected package r-cran-later. 188s Preparing to unpack .../259-r-cran-later_1.4.1+dfsg-1_amd64.deb ... 188s Unpacking r-cran-later (1.4.1+dfsg-1) ... 188s Selecting previously unselected package r-cran-magrittr. 188s Preparing to unpack .../260-r-cran-magrittr_2.0.3-1_amd64.deb ... 188s Unpacking r-cran-magrittr (2.0.3-1) ... 188s Selecting previously unselected package r-cran-promises. 188s Preparing to unpack .../261-r-cran-promises_1.3.2+dfsg-1_amd64.deb ... 188s Unpacking r-cran-promises (1.3.2+dfsg-1) ... 188s Selecting previously unselected package r-cran-httpuv. 188s Preparing to unpack .../262-r-cran-httpuv_1.6.15+dfsg-1_amd64.deb ... 188s Unpacking r-cran-httpuv (1.6.15+dfsg-1) ... 188s Selecting previously unselected package r-cran-xtable. 188s Preparing to unpack .../263-r-cran-xtable_1%3a1.8-4-2build1_all.deb ... 188s Unpacking r-cran-xtable (1:1.8-4-2build1) ... 188s Selecting previously unselected package r-cran-sourcetools. 188s Preparing to unpack .../264-r-cran-sourcetools_0.1.7-1-1_amd64.deb ... 188s Unpacking r-cran-sourcetools (0.1.7-1-1) ... 188s Selecting previously unselected package r-cran-withr. 188s Preparing to unpack .../265-r-cran-withr_3.0.2+dfsg-1_all.deb ... 188s Unpacking r-cran-withr (3.0.2+dfsg-1) ... 188s Selecting previously unselected package r-cran-commonmark. 188s Preparing to unpack .../266-r-cran-commonmark_1.9.5-1_amd64.deb ... 188s Unpacking r-cran-commonmark (1.9.5-1) ... 188s Selecting previously unselected package libjs-twitter-bootstrap-datepicker. 188s Preparing to unpack .../267-libjs-twitter-bootstrap-datepicker_1.3.1+dfsg1-4.1_all.deb ... 188s Unpacking libjs-twitter-bootstrap-datepicker (1.3.1+dfsg1-4.1) ... 188s Selecting previously unselected package r-cran-shiny. 188s Preparing to unpack .../268-r-cran-shiny_1.10.0+dfsg-2_all.deb ... 188s Unpacking r-cran-shiny (1.10.0+dfsg-2) ... 188s Selecting previously unselected package r-cran-rmarkdown. 188s Preparing to unpack .../269-r-cran-rmarkdown_2.30+dfsg-1_all.deb ... 188s Unpacking r-cran-rmarkdown (2.30+dfsg-1) ... 188s Selecting previously unselected package r-cran-bookdown. 188s Preparing to unpack .../270-r-cran-bookdown_0.42+dfsg-1_all.deb ... 188s Unpacking r-cran-bookdown (0.42+dfsg-1) ... 188s Selecting previously unselected package r-cran-biocmanager. 188s Preparing to unpack .../271-r-cran-biocmanager_1.30.25+dfsg-1_all.deb ... 188s Unpacking r-cran-biocmanager (1.30.25+dfsg-1) ... 188s Selecting previously unselected package tex-common. 188s Preparing to unpack .../272-tex-common_6.20_all.deb ... 188s Unpacking tex-common (6.20) ... 188s Selecting previously unselected package t1utils. 188s Preparing to unpack .../273-t1utils_1.41-4build4_amd64.deb ... 188s Unpacking t1utils (1.41-4build4) ... 188s Selecting previously unselected package texlive-binaries. 188s Preparing to unpack .../274-texlive-binaries_2025.20250727.75242+ds-5build1_amd64.deb ... 188s Unpacking texlive-binaries (2025.20250727.75242+ds-5build1) ... 188s Selecting previously unselected package texlive-base. 188s Preparing to unpack .../275-texlive-base_2025.20260124-1_all.deb ... 188s Unpacking texlive-base (2025.20260124-1) ... 188s Selecting previously unselected package texlive-latex-base. 188s Preparing to unpack .../276-texlive-latex-base_2025.20260124-1_all.deb ... 188s Unpacking texlive-latex-base (2025.20260124-1) ... 189s Selecting previously unselected package texlive-bibtex-extra. 189s Preparing to unpack .../277-texlive-bibtex-extra_2025.20260124-1_all.deb ... 189s Unpacking texlive-bibtex-extra (2025.20260124-1) ... 190s Selecting previously unselected package r-bioc-biocversion. 190s Preparing to unpack .../278-r-bioc-biocversion_3.20.0-2_all.deb ... 190s Unpacking r-bioc-biocversion (3.20.0-2) ... 190s Selecting previously unselected package r-bioc-biocstyle. 190s Preparing to unpack .../279-r-bioc-biocstyle_2.34.0+dfsg-1_all.deb ... 190s Unpacking r-bioc-biocstyle (2.34.0+dfsg-1) ... 190s Selecting previously unselected package r-bioc-genomicranges. 190s Preparing to unpack .../280-r-bioc-genomicranges_1.58.0+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-genomicranges (1.58.0+dfsg-2) ... 190s Selecting previously unselected package r-cran-xml. 190s Preparing to unpack .../281-r-cran-xml_3.99-0.20-1_amd64.deb ... 190s Unpacking r-cran-xml (3.99-0.20-1) ... 190s Selecting previously unselected package r-cran-bitops. 190s Preparing to unpack .../282-r-cran-bitops_1.0-9-1_amd64.deb ... 190s Unpacking r-cran-bitops (1.0-9-1) ... 190s Selecting previously unselected package r-bioc-rhtslib. 190s Preparing to unpack .../283-r-bioc-rhtslib_3.2.0+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-rhtslib (3.2.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-rsamtools. 190s Preparing to unpack .../284-r-bioc-rsamtools_2.22.0+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-rsamtools (2.22.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-matrixgenerics. 190s Preparing to unpack .../285-r-bioc-matrixgenerics_1.18.1-1_all.deb ... 190s Unpacking r-bioc-matrixgenerics (1.18.1-1) ... 190s Selecting previously unselected package r-cran-lattice. 190s Preparing to unpack .../286-r-cran-lattice_0.22-7-1_amd64.deb ... 190s Unpacking r-cran-lattice (0.22-7-1) ... 190s Selecting previously unselected package r-cran-matrix. 190s Preparing to unpack .../287-r-cran-matrix_1.7-4-1_amd64.deb ... 190s Unpacking r-cran-matrix (1.7-4-1) ... 190s Selecting previously unselected package r-cran-abind. 190s Preparing to unpack .../288-r-cran-abind_1.4-8-1build1_all.deb ... 190s Unpacking r-cran-abind (1.4-8-1build1) ... 190s Selecting previously unselected package r-bioc-s4arrays. 190s Preparing to unpack .../289-r-bioc-s4arrays_1.6.0+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-s4arrays (1.6.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-sparsearray. 190s Preparing to unpack .../290-r-bioc-sparsearray_1.6.2+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-sparsearray (1.6.2+dfsg-2) ... 190s Selecting previously unselected package r-bioc-delayedarray. 190s Preparing to unpack .../291-r-bioc-delayedarray_0.32.0+dfsg-2_amd64.deb ... 190s Unpacking r-bioc-delayedarray (0.32.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-summarizedexperiment. 190s Preparing to unpack .../292-r-bioc-summarizedexperiment_1.36.0+dfsg-2_all.deb ... 190s Unpacking r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-genomicalignments. 190s Preparing to unpack .../293-r-bioc-genomicalignments_1.42.0-2_amd64.deb ... 190s Unpacking r-bioc-genomicalignments (1.42.0-2) ... 190s Selecting previously unselected package r-cran-rcurl. 190s Preparing to unpack .../294-r-cran-rcurl_1.98-1.16+dfsg-1_amd64.deb ... 190s Unpacking r-cran-rcurl (1.98-1.16+dfsg-1) ... 190s Selecting previously unselected package r-cran-rjson. 190s Preparing to unpack .../295-r-cran-rjson_0.2.23-1_amd64.deb ... 190s Unpacking r-cran-rjson (0.2.23-1) ... 190s Selecting previously unselected package r-cran-restfulr. 190s Preparing to unpack .../296-r-cran-restfulr_0.0.15-1_amd64.deb ... 190s Unpacking r-cran-restfulr (0.0.15-1) ... 190s Selecting previously unselected package r-bioc-rtracklayer. 190s Preparing to unpack .../297-r-bioc-rtracklayer_1.66.0-3_amd64.deb ... 190s Unpacking r-bioc-rtracklayer (1.66.0-3) ... 190s Selecting previously unselected package r-bioc-bsgenome. 190s Preparing to unpack .../298-r-bioc-bsgenome_1.74.0-2_all.deb ... 190s Unpacking r-bioc-bsgenome (1.74.0-2) ... 190s Selecting previously unselected package r-bioc-dnacopy. 190s Preparing to unpack .../299-r-bioc-dnacopy_1.80.0-2_amd64.deb ... 190s Unpacking r-bioc-dnacopy (1.80.0-2) ... 190s Selecting previously unselected package r-bioc-genomicfeatures. 190s Preparing to unpack .../300-r-bioc-genomicfeatures_1.58.0+dfsg-2_all.deb ... 190s Unpacking r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 190s Selecting previously unselected package r-bioc-org.hs.eg.db. 190s Preparing to unpack .../301-r-bioc-org.hs.eg.db_3.20.0-3_all.deb ... 190s Unpacking r-bioc-org.hs.eg.db (3.20.0-3) ... 191s Selecting previously unselected package r-bioc-variantannotation. 191s Preparing to unpack .../302-r-bioc-variantannotation_1.52.0-2_amd64.deb ... 191s Unpacking r-bioc-variantannotation (1.52.0-2) ... 191s Selecting previously unselected package r-cran-rcolorbrewer. 191s Preparing to unpack .../303-r-cran-rcolorbrewer_1.1-3-1build2_all.deb ... 191s Unpacking r-cran-rcolorbrewer (1.1-3-1build2) ... 191s Selecting previously unselected package r-cran-data.table. 191s Preparing to unpack .../304-r-cran-data.table_1.17.0+dfsg-1_amd64.deb ... 191s Unpacking r-cran-data.table (1.17.0+dfsg-1) ... 191s Selecting previously unselected package r-cran-gtable. 191s Preparing to unpack .../305-r-cran-gtable_0.3.6+dfsg-1_all.deb ... 191s Unpacking r-cran-gtable (0.3.6+dfsg-1) ... 191s Selecting previously unselected package r-cran-isoband. 191s Preparing to unpack .../306-r-cran-isoband_0.2.7-1_amd64.deb ... 191s Unpacking r-cran-isoband (0.2.7-1) ... 191s Selecting previously unselected package r-cran-s7. 191s Preparing to unpack .../307-r-cran-s7_0.2.0-1_amd64.deb ... 191s Unpacking r-cran-s7 (0.2.0-1) ... 191s Selecting previously unselected package r-cran-farver. 191s Preparing to unpack .../308-r-cran-farver_2.1.2-1_amd64.deb ... 191s Unpacking r-cran-farver (2.1.2-1) ... 191s Selecting previously unselected package r-cran-labeling. 191s Preparing to unpack .../309-r-cran-labeling_0.4.3-1_all.deb ... 191s Unpacking r-cran-labeling (0.4.3-1) ... 191s Selecting previously unselected package r-cran-viridislite. 191s Preparing to unpack .../310-r-cran-viridislite_0.4.3-1_all.deb ... 191s Unpacking r-cran-viridislite (0.4.3-1) ... 191s Selecting previously unselected package r-cran-scales. 192s Preparing to unpack .../311-r-cran-scales_1.4.0-1_all.deb ... 192s Unpacking r-cran-scales (1.4.0-1) ... 192s Selecting previously unselected package r-cran-ggplot2. 192s Preparing to unpack .../312-r-cran-ggplot2_4.0.2+dfsg-1_all.deb ... 192s Unpacking r-cran-ggplot2 (4.0.2+dfsg-1) ... 192s Selecting previously unselected package r-cran-gridextra. 192s Preparing to unpack .../313-r-cran-gridextra_2.3-3build2_all.deb ... 192s Unpacking r-cran-gridextra (2.3-3build2) ... 192s Selecting previously unselected package r-cran-vgam. 192s Preparing to unpack .../314-r-cran-vgam_1.1-13-1_amd64.deb ... 192s Unpacking r-cran-vgam (1.1-13-1) ... 192s Selecting previously unselected package r-cran-mclust. 192s Preparing to unpack .../315-r-cran-mclust_6.1.1-1_amd64.deb ... 192s Unpacking r-cran-mclust (6.1.1-1) ... 192s Selecting previously unselected package r-bioc-rhdf5lib. 192s Preparing to unpack .../316-r-bioc-rhdf5lib_1.28.0+dfsg-3_amd64.deb ... 192s Unpacking r-bioc-rhdf5lib (1.28.0+dfsg-3) ... 192s Selecting previously unselected package r-bioc-rhdf5filters. 192s Preparing to unpack .../317-r-bioc-rhdf5filters_1.18.1+dfsg-1_amd64.deb 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192s Selecting previously unselected package r-cran-globals. 192s Preparing to unpack .../329-r-cran-globals_0.19.0-1_all.deb ... 192s Unpacking r-cran-globals (0.19.0-1) ... 192s Selecting previously unselected package r-cran-listenv. 192s Preparing to unpack .../330-r-cran-listenv_0.10.0+dfsg-1_all.deb ... 192s Unpacking r-cran-listenv (0.10.0+dfsg-1) ... 192s Selecting previously unselected package r-cran-parallelly. 192s Preparing to unpack .../331-r-cran-parallelly_1.42.0-1_amd64.deb ... 192s Unpacking r-cran-parallelly (1.42.0-1) ... 192s Selecting previously unselected package r-cran-future. 192s Preparing to unpack .../332-r-cran-future_1.34.0+dfsg-1_all.deb ... 192s Unpacking r-cran-future (1.34.0+dfsg-1) ... 192s Selecting previously unselected package r-cran-getopt. 192s Preparing to unpack .../333-r-cran-getopt_1.20.4-1_all.deb ... 192s Unpacking r-cran-getopt (1.20.4-1) ... 192s Selecting previously unselected package r-cran-markdown. 192s Preparing to unpack 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... 196s Setting up r-bioc-genomicranges (1.58.0+dfsg-2) ... 196s Setting up r-bioc-biostrings (2.74.1+dfsg-2) ... 196s Setting up r-cran-shiny (1.10.0+dfsg-2) ... 196s Setting up r-cran-pscbs (0.68.0-1) ... 196s Setting up r-cran-rmarkdown (2.30+dfsg-1) ... 196s Setting up r-bioc-rsamtools (2.22.0+dfsg-2) ... 196s Setting up r-cran-bookdown (0.42+dfsg-1) ... 196s Setting up r-bioc-summarizedexperiment (1.36.0+dfsg-2) ... 196s Setting up r-bioc-keggrest (1.46.0+dfsg-3) ... 196s Setting up r-bioc-annotationdbi (1.68.0-2) ... 196s Setting up r-bioc-biocstyle (2.34.0+dfsg-1) ... 196s Setting up r-bioc-genomicalignments (1.42.0-2) ... 196s Setting up r-bioc-org.hs.eg.db (3.20.0-3) ... 196s Setting up r-bioc-rtracklayer (1.66.0-3) ... 196s Setting up r-bioc-genomicfeatures (1.58.0+dfsg-2) ... 196s Setting up r-bioc-bsgenome (1.74.0-2) ... 196s Setting up r-bioc-variantannotation (1.52.0-2) ... 196s Setting up r-bioc-purecn (2.12.0+dfsg-2) ... 196s Processing triggers for libc-bin (2.42-2ubuntu4) ... 196s Processing triggers for man-db (2.13.1-1build1) ... 197s Processing triggers for install-info (7.2-5) ... 198s Processing triggers for tex-common (6.20) ... 198s Running updmap-sys. This may take some time... done. 198s Running mktexlsr /var/lib/texmf ... done. 198s Building format(s) --all. 212s This may take some time... done. 213s autopkgtest [04:20:01]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 213s autopkgtest [04:20:01]: test pkg-r-autopkgtest: [----------------------- 213s Test: Try to load the R library PureCN 213s 213s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 213s Copyright (C) 2025 The R Foundation for Statistical Computing 213s Platform: x86_64-pc-linux-gnu 213s 213s R is free software and comes with ABSOLUTELY NO WARRANTY. 213s You are welcome to redistribute it under certain conditions. 213s Type 'license()' or 'licence()' for distribution details. 213s 213s R is a collaborative project with many contributors. 213s Type 'contributors()' for more information and 213s 'citation()' on how to cite R or R packages in publications. 213s 213s Type 'demo()' for some demos, 'help()' for on-line help, or 213s 'help.start()' for an HTML browser interface to help. 213s Type 'q()' to quit R. 213s 213s > library('PureCN') 213s Loading required package: DNAcopy 213s Loading required package: VariantAnnotation 213s Loading required package: BiocGenerics 213s 213s Attaching package: ‘BiocGenerics’ 213s 213s The following objects are masked from ‘package:stats’: 213s 213s IQR, mad, sd, var, xtabs 213s 213s The following objects are masked from ‘package:base’: 213s 213s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 213s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 213s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 213s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 213s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 213s table, tapply, union, unique, unsplit, which.max, which.min 213s 213s Loading required package: MatrixGenerics 213s Loading required package: matrixStats 213s 213s Attaching package: ‘MatrixGenerics’ 213s 213s The following objects are masked from ‘package:matrixStats’: 213s 213s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 213s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 213s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 213s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 213s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 213s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 213s colWeightedMeans, colWeightedMedians, colWeightedSds, 213s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 213s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 213s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 213s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 213s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 213s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 213s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 213s rowWeightedSds, rowWeightedVars 213s 213s Loading required package: GenomeInfoDb 213s Loading required package: S4Vectors 213s Loading required package: stats4 214s 214s Attaching package: ‘S4Vectors’ 214s 214s The following object is masked from ‘package:utils’: 214s 214s findMatches 214s 214s The following objects are masked from ‘package:base’: 214s 214s expand.grid, I, unname 214s 214s Loading required package: IRanges 214s Loading required package: GenomicRanges 215s Loading required package: SummarizedExperiment 215s Loading required package: Biobase 215s Welcome to Bioconductor 215s 215s Vignettes contain introductory material; view with 215s 'browseVignettes()'. To cite Bioconductor, see 215s 'citation("Biobase")', and for packages 'citation("pkgname")'. 215s 215s 215s Attaching package: ‘Biobase’ 215s 215s The following object is masked from ‘package:MatrixGenerics’: 215s 215s rowMedians 215s 215s The following objects are masked from ‘package:matrixStats’: 215s 215s anyMissing, rowMedians 215s 217s Loading required package: Rsamtools 217s Loading required package: Biostrings 217s Loading required package: XVector 217s 217s Attaching package: ‘Biostrings’ 217s 217s The following object is masked from ‘package:base’: 217s 217s strsplit 217s 220s 220s Attaching package: ‘VariantAnnotation’ 220s 220s The following object is masked from ‘package:base’: 220s 220s tabulate 220s 221s > 221s + cd tests 221s + grep -l genomicsdb testthat/test_adjustLogRatio.R testthat/test_annotateTargets.R testthat/test_bootstrapResults.R testthat/test_calculateBamCoverageByInterval.R testthat/test_calculateLogRatio.R testthat/test_calculatePowerDetectSomatic.R testthat/test_callAlterations.R testthat/test_callAlterationsFromSegmentation.R testthat/test_callAmplificationsInLowPurity.R testthat/test_callCIN.R testthat/test_callLOH.R testthat/test_callMutationBurden.R testthat/test_correctCoverageBias.R testthat/test_createCurationFile.R testthat/test_createNormalDatabase.R testthat/test_filterVcf.R testthat/test_findFocal.R testthat/test_getSexFromCoverage.R testthat/test_getSexFromVcf.R testthat/test_plotAbs.R testthat/test_poolCoverage.R testthat/test_predictSomatic.R testthat/test_preprocessIntervals.R testthat/test_readAllelicCountsFile.R testthat/test_readCoverageFile.R testthat/test_readLogRatioFile.R testthat/test_readSegmentationFile.R testthat/test_runAbsoluteCN.R testthat/test_segmentation.R testthat/test_setMappingBiasVcf.R testthat/test_setPriorVcf.R 221s + rm -f testthat/test_setMappingBiasVcf.R 221s + BEGIN TEST testthat.R 221s rm -f testthat/test_processMultipleSamples.R 221s + grep -Rl TxDb.Hsapiens.UCSC.hg19.knownGene testthat testthat.R 221s + rm -f testthat/test_annotateTargets.R 221s + FAILINGTESTS=test_runAbsoluteCN.R test_calculatePowerDetectSomatic.R test_callAmplificationsInLowPurity.R test_callMutationBurden.R test_correctCoverageBias.R test_createCurationFile.R test_createNormalDatabase.R test_getSexFromVcf.R test_plotAbs.R test_poolCoverage.R test_readLogRatioFile.R test_preprocessIntervals.R 221s + rm -f testthat/test_runAbsoluteCN.R 221s + rm -f testthat/test_calculatePowerDetectSomatic.R 221s + rm -f testthat/test_callAmplificationsInLowPurity.R 221s + rm -f testthat/test_callMutationBurden.R 221s + rm -f testthat/test_correctCoverageBias.R 221s + rm -f testthat/test_createCurationFile.R 221s + rm -f testthat/test_createNormalDatabase.R 221s + rm -f testthat/test_getSexFromVcf.R 221s + rm -f testthat/test_plotAbs.R 221s + rm -f testthat/test_poolCoverage.R 221s + rm -f testthat/test_readLogRatioFile.R 221s + rm -f testthat/test_preprocessIntervals.R 221s + ln -s /usr/lib/R/site-library/PureCN/extdata 221s + echo BEGIN TEST testthat.R 221s + LC_ALL=C.UTF-8 R --no-save 221s 221s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 221s Copyright (C) 2025 The R Foundation for Statistical Computing 221s Platform: x86_64-pc-linux-gnu 221s 221s R is free software and comes with ABSOLUTELY NO WARRANTY. 221s You are welcome to redistribute it under certain conditions. 221s Type 'license()' or 'licence()' for distribution details. 221s 221s R is a collaborative project with many contributors. 221s Type 'contributors()' for more information and 221s 'citation()' on how to cite R or R packages in publications. 221s 221s Type 'demo()' for some demos, 'help()' for on-line help, or 221s 'help.start()' for an HTML browser interface to help. 221s Type 'q()' to quit R. 221s 221s > library(testthat) 221s > library(PureCN) 221s Loading required package: DNAcopy 221s Loading required package: VariantAnnotation 221s Loading required package: BiocGenerics 221s 221s Attaching package: ‘BiocGenerics’ 221s 221s The following objects are masked from ‘package:stats’: 221s 221s IQR, mad, sd, var, xtabs 221s 221s The following objects are masked from ‘package:base’: 221s 221s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 221s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 221s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 221s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 221s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 221s table, tapply, union, unique, unsplit, which.max, which.min 221s 221s Loading required package: MatrixGenerics 221s Loading required package: matrixStats 221s 221s Attaching package: ‘MatrixGenerics’ 221s 221s The following objects are masked from ‘package:matrixStats’: 221s 221s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 221s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 221s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 221s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 221s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 221s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 221s colWeightedMeans, colWeightedMedians, colWeightedSds, 221s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 221s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 221s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 221s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 221s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 221s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 221s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 221s rowWeightedSds, rowWeightedVars 221s 221s Loading required package: GenomeInfoDb 221s Loading required package: S4Vectors 221s Loading required package: stats4 222s 222s Attaching package: ‘S4Vectors’ 222s 222s The following object is masked from ‘package:utils’: 222s 222s findMatches 222s 222s The following objects are masked from ‘package:base’: 222s 222s expand.grid, I, unname 222s 222s Loading required package: IRanges 222s Loading required package: GenomicRanges 222s Loading required package: SummarizedExperiment 222s Loading required package: Biobase 223s Welcome to Bioconductor 223s 223s Vignettes contain introductory material; view with 223s 'browseVignettes()'. To cite Bioconductor, see 223s 'citation("Biobase")', and for packages 'citation("pkgname")'. 223s 223s 223s Attaching package: ‘Biobase’ 223s 223s The following object is masked from ‘package:MatrixGenerics’: 223s 223s rowMedians 223s 223s The following objects are masked from ‘package:matrixStats’: 223s 223s anyMissing, rowMedians 223s 224s Loading required package: Rsamtools 224s Loading required package: Biostrings 224s Loading required package: XVector 225s 225s Attaching package: ‘Biostrings’ 225s 225s The following object is masked from ‘package:base’: 225s 225s strsplit 225s 228s 228s Attaching package: ‘VariantAnnotation’ 228s 228s The following object is masked from ‘package:base’: 228s 228s tabulate 228s 229s > 229s > test_check("PureCN") 231s FATAL [2026-02-10 04:20:18] tumor.coverage.file and interval.file do not align. 231s 231s FATAL [2026-02-10 04:20:18] 231s 231s FATAL [2026-02-10 04:20:18] This is most likely a user error due to invalid input data or 231s 231s FATAL [2026-02-10 04:20:18] parameters (PureCN 2.12.0). 231s 231s WARN [2026-02-10 04:20:18] Cannot find all contig lengths while exporting interval file. 231s INFO [2026-02-10 04:20:19] Processing seq1:1-21 (1/3)... 231s INFO [2026-02-10 04:20:19] Processing seq1:1227-1247 (2/3)... 232s INFO [2026-02-10 04:20:19] Processing seq2:594-614 (3/3)... 232s WARN [2026-02-10 04:20:20] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 235s INFO [2026-02-10 04:20:22] ------------------------------------------------------------ 235s INFO [2026-02-10 04:20:22] PureCN 2.12.0 235s INFO [2026-02-10 04:20:22] ------------------------------------------------------------ 235s INFO [2026-02-10 04:20:22] Loading coverage files... 235s INFO [2026-02-10 04:20:22] Mean target coverages: 112X (tumor) 99X (normal). 235s WARN [2026-02-10 04:20:22] Allosome coverage missing, cannot determine sex. 235s WARN [2026-02-10 04:20:22] Allosome coverage missing, cannot determine sex. 235s INFO [2026-02-10 04:20:22] Removing 228 intervals with missing log.ratio. 235s INFO [2026-02-10 04:20:22] Removing 22 small (< 5bp) intervals. 235s INFO [2026-02-10 04:20:22] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 235s WARN [2026-02-10 04:20:22] No normalDB provided. Provide one for better results. 235s INFO [2026-02-10 04:20:22] Removing 1724 low count (< 100 total reads) intervals. 235s INFO [2026-02-10 04:20:22] Removing 6 low coverage (< 15.0000X) intervals. 235s INFO [2026-02-10 04:20:22] Using 8050 intervals (8050 on-target, 0 off-target). 235s INFO [2026-02-10 04:20:22] No off-target intervals. If this is hybrid-capture data, consider adding them. 235s INFO [2026-02-10 04:20:22] No interval.file provided. Cannot check for any GC-biases. 235s INFO [2026-02-10 04:20:22] Loading VCF... 235s INFO [2026-02-10 04:20:22] Found 127 variants in VCF file. 235s INFO [2026-02-10 04:20:22] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 235s INFO [2026-02-10 04:20:22] LIB-02240e4 is tumor in VCF file. 235s INFO [2026-02-10 04:20:23] No homozygous variants in VCF, provide unfiltered VCF. 235s INFO [2026-02-10 04:20:23] Removing 1 non heterozygous (in matched normal) germline SNPs. 235s INFO [2026-02-10 04:20:23] Removing 0 low quality variants with non-offset BQ < 25. 235s INFO [2026-02-10 04:20:23] Base quality scores range from 29 to 35 (offset by 1) 235s INFO [2026-02-10 04:20:23] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 235s INFO [2026-02-10 04:20:23] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 235s INFO [2026-02-10 04:20:23] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 235s INFO [2026-02-10 04:20:23] 1.2% of targets contain variants. 235s INFO [2026-02-10 04:20:23] Removing 4 variants outside intervals. 235s INFO [2026-02-10 04:20:23] Found SOMATIC annotation in VCF. 235s INFO [2026-02-10 04:20:23] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 235s INFO [2026-02-10 04:20:23] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 235s INFO [2026-02-10 04:20:23] Excluding 0 novel or poor quality variants from segmentation. 236s INFO [2026-02-10 04:20:23] Sample sex: ? 236s INFO [2026-02-10 04:20:23] Segmenting data... 236s INFO [2026-02-10 04:20:23] Loading pre-computed boundaries for DNAcopy... 236s INFO [2026-02-10 04:20:23] Setting undo.SD parameter to 1.000000. 236s INFO [2026-02-10 04:20:24] Setting prune.hclust.h parameter to 0.200000. 236s INFO [2026-02-10 04:20:24] Found 59 segments with median size of 17.67Mb. 236s INFO [2026-02-10 04:20:24] Using 121 variants. 236s INFO [2026-02-10 04:20:24] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 236s INFO [2026-02-10 04:20:24] 2D-grid search of purity and ploidy... 237s INFO [2026-02-10 04:20:24] Local optima: 0.63/1.9, 0.5/2 237s INFO [2026-02-10 04:20:24] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 237s INFO [2026-02-10 04:20:25] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 238s INFO [2026-02-10 04:20:25] Skipping 1 solutions that converged to the same optima. 238s INFO [2026-02-10 04:20:25] Fitting variants with beta model for local optimum 1/2... 238s INFO [2026-02-10 04:20:25] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 239s INFO [2026-02-10 04:20:27] Optimized purity: 0.65 239s INFO [2026-02-10 04:20:27] Done. 239s INFO [2026-02-10 04:20:27] ------------------------------------------------------------ 239s INFO [2026-02-10 04:20:27] Removing 22 non heterozygous (in matched normal) germline SNPs. 239s INFO [2026-02-10 04:20:27] Removing 19 low quality variants with non-offset BQ < 25. 239s INFO [2026-02-10 04:20:27] Base quality scores range from 24 to 35 (offset by 1) 239s INFO [2026-02-10 04:20:27] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 240s INFO [2026-02-10 04:20:27] Initial testing for significant sample cross-contamination: unlikely 240s INFO [2026-02-10 04:20:27] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 240s INFO [2026-02-10 04:20:27] Removing 22 non heterozygous (in matched normal) germline SNPs. 240s INFO [2026-02-10 04:20:27] Removing 19 low quality variants with non-offset BQ < 25. 240s INFO [2026-02-10 04:20:27] Base quality scores range from 24 to 35 (offset by 1) 240s INFO [2026-02-10 04:20:27] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 240s INFO [2026-02-10 04:20:28] Initial testing for significant sample cross-contamination: unlikely 240s INFO [2026-02-10 04:20:28] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 240s INFO [2026-02-10 04:20:28] Removing 6 blacklisted variants. 240s INFO [2026-02-10 04:20:28] Removing 22 non heterozygous (in matched normal) germline SNPs. 240s INFO [2026-02-10 04:20:28] Removing 19 low quality variants with non-offset BQ < 25. 240s INFO [2026-02-10 04:20:28] Base quality scores range from 24 to 35 (offset by 1) 240s INFO [2026-02-10 04:20:28] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 240s INFO [2026-02-10 04:20:28] Initial testing for significant sample cross-contamination: unlikely 240s INFO [2026-02-10 04:20:28] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 240s WARN [2026-02-10 04:20:28] MuTect stats file lacks contig and position columns. 241s INFO [2026-02-10 04:20:28] Removing 22 non heterozygous (in matched normal) germline SNPs. 241s INFO [2026-02-10 04:20:28] Removing 19 low quality variants with non-offset BQ < 25. 241s INFO [2026-02-10 04:20:28] Base quality scores range from 24 to 35 (offset by 1) 241s INFO [2026-02-10 04:20:28] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 241s INFO [2026-02-10 04:20:28] Initial testing for significant sample cross-contamination: unlikely 241s INFO [2026-02-10 04:20:28] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 241s WARN [2026-02-10 04:20:28] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 241s WARN [2026-02-10 04:20:28] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 241s INFO [2026-02-10 04:20:28] Removing 0 non heterozygous (in matched normal) germline SNPs. 241s INFO [2026-02-10 04:20:28] Removing 0 low quality variants with non-offset BQ < 25. 241s INFO [2026-02-10 04:20:28] Base quality scores range from 31 to 33 (offset by 1) 241s INFO [2026-02-10 04:20:28] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 241s INFO [2026-02-10 04:20:29] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 241s INFO [2026-02-10 04:20:29] Removing 22 non heterozygous (in matched normal) germline SNPs. 241s INFO [2026-02-10 04:20:29] Base quality scores range from 7 to 35 (offset by 1) 241s INFO [2026-02-10 04:20:29] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 241s INFO [2026-02-10 04:20:29] Initial testing for significant sample cross-contamination: unlikely 241s INFO [2026-02-10 04:20:29] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 241s INFO [2026-02-10 04:20:29] Removing 22 non heterozygous (in matched normal) germline SNPs. 241s INFO [2026-02-10 04:20:29] Base quality scores range from 7 to 35 (offset by 1) 242s INFO [2026-02-10 04:20:29] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 242s INFO [2026-02-10 04:20:29] Initial testing for significant sample cross-contamination: unlikely 242s INFO [2026-02-10 04:20:29] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 242s INFO [2026-02-10 04:20:29] Removing 22 non heterozygous (in matched normal) germline SNPs. 242s WARN [2026-02-10 04:20:29] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 242s FATAL [2026-02-10 04:20:29] No variants passed filter BQ. 242s 242s FATAL [2026-02-10 04:20:29] 242s 242s FATAL [2026-02-10 04:20:29] This is most likely a user error due to invalid input data or 242s 242s FATAL [2026-02-10 04:20:29] parameters (PureCN 2.12.0). 242s 242s INFO [2026-02-10 04:20:30] Found 11 variants in VCF file. 242s WARN [2026-02-10 04:20:30] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 242s INFO [2026-02-10 04:20:30] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 243s INFO [2026-02-10 04:20:30] Found 11 variants in VCF file. 243s WARN [2026-02-10 04:20:31] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 243s INFO [2026-02-10 04:20:31] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 243s INFO [2026-02-10 04:20:31] Found 11 variants in VCF file. 243s WARN [2026-02-10 04:20:31] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 243s INFO [2026-02-10 04:20:31] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 244s INFO [2026-02-10 04:20:31] Found 1000 variants in VCF file. 244s INFO [2026-02-10 04:20:31] Removing 2 triallelic sites. 244s WARN [2026-02-10 04:20:31] Having trouble guessing SOMATIC status... 244s WARN [2026-02-10 04:20:31] DP FORMAT field contains NAs. Removing 44 variants. 244s INFO [2026-02-10 04:20:31] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 245s INFO [2026-02-10 04:20:32] Found 12 variants in VCF file. 245s INFO [2026-02-10 04:20:32] Removing 1 triallelic sites. 245s WARN [2026-02-10 04:20:32] DP FORMAT field contains NAs. Removing 1 variants. 245s WARN [2026-02-10 04:20:32] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 245s INFO [2026-02-10 04:20:32] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 245s WARN [2026-02-10 04:20:32] BQ FORMAT field contains NAs. 245s INFO [2026-02-10 04:20:33] Found 2331 variants in VCF file. 245s INFO [2026-02-10 04:20:33] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 245s INFO [2026-02-10 04:20:33] Found 2331 variants in VCF file. 245s INFO [2026-02-10 04:20:33] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 245s WARN [2026-02-10 04:20:33] Did not find base quality scores, will use global error rate of 0.0010 instead. 245s INFO [2026-02-10 04:20:33] Removing 21 low quality variants with non-offset BQ < 25. 245s INFO [2026-02-10 04:20:33] Base quality scores range from 24 to 35 (offset by 1) 246s INFO [2026-02-10 04:20:33] Initial testing for significant sample cross-contamination: unlikely 246s INFO [2026-02-10 04:20:33] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 246s INFO [2026-02-10 04:20:33] Found 2331 variants in VCF file. 246s INFO [2026-02-10 04:20:33] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 246s WARN [2026-02-10 04:20:33] BQ FORMAT field contains NAs. 246s WARN [2026-02-10 04:20:34] Allosome coverage missing, cannot determine sex. 247s WARN [2026-02-10 04:20:35] Allosome coverage missing, cannot determine sex. 247s INFO [2026-02-10 04:20:35] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 247s INFO [2026-02-10 04:20:35] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 247s INFO [2026-02-10 04:20:35] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 248s INFO [2026-02-10 04:20:35] Found 20 variants in VCF file. 248s INFO [2026-02-10 04:20:35] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 248s WARN [2026-02-10 04:20:35] Did not find base quality scores, will use global error rate of 0.0010 instead. 248s INFO [2026-02-10 04:20:36] Found 127 variants in VCF file. 248s INFO [2026-02-10 04:20:36] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 248s WARN [2026-02-10 04:20:36] Did not find base quality scores, will use global error rate of 0.0010 instead. 248s INFO [2026-02-10 04:20:36] ------------------------------------------------------------ 248s INFO [2026-02-10 04:20:36] PureCN 2.12.0 248s INFO [2026-02-10 04:20:36] ------------------------------------------------------------ 248s INFO [2026-02-10 04:20:36] Loading coverage files... 249s INFO [2026-02-10 04:20:36] Mean target coverages: 112X (tumor) 99X (normal). 249s WARN [2026-02-10 04:20:36] Allosome coverage missing, cannot determine sex. 249s WARN [2026-02-10 04:20:36] Allosome coverage missing, cannot determine sex. 249s INFO [2026-02-10 04:20:36] Removing 228 intervals with missing log.ratio. 249s INFO [2026-02-10 04:20:36] Removing 22 small (< 5bp) intervals. 249s INFO [2026-02-10 04:20:36] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 249s WARN [2026-02-10 04:20:36] No normalDB provided. Provide one for better results. 249s INFO [2026-02-10 04:20:36] Removing 1724 low count (< 100 total reads) intervals. 249s INFO [2026-02-10 04:20:36] Removing 6 low coverage (< 15.0000X) intervals. 249s INFO [2026-02-10 04:20:36] Using 8050 intervals (8050 on-target, 0 off-target). 249s INFO [2026-02-10 04:20:36] No off-target intervals. If this is hybrid-capture data, consider adding them. 249s INFO [2026-02-10 04:20:36] No interval.file provided. Cannot check for any GC-biases. 249s INFO [2026-02-10 04:20:36] Loading VCF... 249s INFO [2026-02-10 04:20:36] Found 127 variants in VCF file. 249s INFO [2026-02-10 04:20:36] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 249s INFO [2026-02-10 04:20:36] LIB-02240e4 is tumor in VCF file. 249s INFO [2026-02-10 04:20:36] No homozygous variants in VCF, provide unfiltered VCF. 249s INFO [2026-02-10 04:20:37] Removing 1 non heterozygous (in matched normal) germline SNPs. 249s INFO [2026-02-10 04:20:37] Removing 0 low quality variants with non-offset BQ < 25. 249s INFO [2026-02-10 04:20:37] Base quality scores range from 29 to 35 (offset by 1) 249s INFO [2026-02-10 04:20:37] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 249s INFO [2026-02-10 04:20:37] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 249s INFO [2026-02-10 04:20:37] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 249s INFO [2026-02-10 04:20:37] 1.2% of targets contain variants. 249s INFO [2026-02-10 04:20:37] Removing 4 variants outside intervals. 249s INFO [2026-02-10 04:20:37] Found SOMATIC annotation in VCF. 249s INFO [2026-02-10 04:20:37] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 249s INFO [2026-02-10 04:20:37] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 249s INFO [2026-02-10 04:20:37] Excluding 0 novel or poor quality variants from segmentation. 249s INFO [2026-02-10 04:20:37] Sample sex: ? 249s INFO [2026-02-10 04:20:37] Segmenting data... 249s INFO [2026-02-10 04:20:37] Loading pre-computed boundaries for DNAcopy... 249s INFO [2026-02-10 04:20:37] Setting undo.SD parameter to 1.000000. 250s INFO [2026-02-10 04:20:37] Setting prune.hclust.h parameter to 0.200000. 250s INFO [2026-02-10 04:20:37] Found 59 segments with median size of 17.67Mb. 250s INFO [2026-02-10 04:20:37] Using 121 variants. 250s INFO [2026-02-10 04:20:37] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 250s INFO [2026-02-10 04:20:37] 2D-grid search of purity and ploidy... 250s INFO [2026-02-10 04:20:37] Local optima: 0.65/1.8, 0.52/2 250s INFO [2026-02-10 04:20:38] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 250s INFO [2026-02-10 04:20:38] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 251s INFO [2026-02-10 04:20:38] Skipping 1 solutions that converged to the same optima. 251s INFO [2026-02-10 04:20:38] Fitting variants with beta model for local optimum 1/2... 251s INFO [2026-02-10 04:20:38] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 252s INFO [2026-02-10 04:20:40] Optimized purity: 0.65 252s INFO [2026-02-10 04:20:40] Done. 252s INFO [2026-02-10 04:20:40] ------------------------------------------------------------ 253s INFO [2026-02-10 04:20:40] Loaded provided segmentation file example_seg.txt (format DNAcopy). 253s INFO [2026-02-10 04:20:40] Re-centering provided segment means (offset -0.0033). 253s INFO [2026-02-10 04:20:40] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 253s WARN [2026-02-10 04:20:40] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 253s INFO [2026-02-10 04:20:40] Re-centering provided segment means (offset -0.0037). 254s WARN [2026-02-10 04:20:42] Cannot find gatk binary in path. 254s sh: 1: gatk: not found 254s INFO [2026-02-10 04:20:42] ------------------------------------------------------------ 254s INFO [2026-02-10 04:20:42] PureCN 2.12.0 254s INFO [2026-02-10 04:20:42] ------------------------------------------------------------ 254s INFO [2026-02-10 04:20:42] Loading coverage files... 254s INFO [2026-02-10 04:20:42] Mean target coverages: 109X (tumor) 102X (normal). 254s WARN [2026-02-10 04:20:42] Allosome coverage missing, cannot determine sex. 254s WARN [2026-02-10 04:20:42] Allosome coverage missing, cannot determine sex. 254s INFO [2026-02-10 04:20:42] Removing 9 intervals with missing log.ratio. 254s INFO [2026-02-10 04:20:42] Removing 1 small (< 5bp) intervals. 254s INFO [2026-02-10 04:20:42] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 254s WARN [2026-02-10 04:20:42] No normalDB provided. Provide one for better results. 254s INFO [2026-02-10 04:20:42] Removing 73 low count (< 100 total reads) intervals. 254s INFO [2026-02-10 04:20:42] Removing 1 low coverage (< 15.0000X) intervals. 254s INFO [2026-02-10 04:20:42] Using 411 intervals (411 on-target, 0 off-target). 254s INFO [2026-02-10 04:20:42] No off-target intervals. If this is hybrid-capture data, consider adding them. 254s INFO [2026-02-10 04:20:42] No interval.file provided. Cannot check for any GC-biases. 254s INFO [2026-02-10 04:20:42] Sample sex: ? 254s INFO [2026-02-10 04:20:42] Segmenting data... 254s FATAL [2026-02-10 04:20:42] segmentationHclust requires an input segmentation. 254s 254s FATAL [2026-02-10 04:20:42] 254s 254s FATAL [2026-02-10 04:20:42] This is most likely a user error due to invalid input data or 254s 254s FATAL [2026-02-10 04:20:42] parameters (PureCN 2.12.0). 254s 254s INFO [2026-02-10 04:20:42] Loaded provided segmentation file example_seg.txt (format DNAcopy). 254s INFO [2026-02-10 04:20:42] Re-centering provided segment means (offset -0.0033). 254s INFO [2026-02-10 04:20:42] ------------------------------------------------------------ 254s INFO [2026-02-10 04:20:42] PureCN 2.12.0 254s INFO [2026-02-10 04:20:42] ------------------------------------------------------------ 254s INFO [2026-02-10 04:20:42] Loading coverage files... 254s INFO [2026-02-10 04:20:42] Mean target coverages: 109X (tumor) 102X (normal). 255s WARN [2026-02-10 04:20:42] Allosome coverage missing, cannot determine sex. 255s WARN [2026-02-10 04:20:42] Allosome coverage missing, cannot determine sex. 255s INFO [2026-02-10 04:20:42] Removing 9 intervals with missing log.ratio. 255s INFO [2026-02-10 04:20:42] Removing 1 small (< 5bp) intervals. 255s INFO [2026-02-10 04:20:42] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 255s WARN [2026-02-10 04:20:42] No normalDB provided. Provide one for better results. 255s INFO [2026-02-10 04:20:42] Removing 73 low count (< 100 total reads) intervals. 255s INFO [2026-02-10 04:20:42] Removing 1 low coverage (< 15.0000X) intervals. 255s INFO [2026-02-10 04:20:42] Using 411 intervals (411 on-target, 0 off-target). 255s INFO [2026-02-10 04:20:42] No off-target intervals. If this is hybrid-capture data, consider adding them. 255s INFO [2026-02-10 04:20:42] No interval.file provided. Cannot check for any GC-biases. 255s INFO [2026-02-10 04:20:42] Sample sex: ? 255s INFO [2026-02-10 04:20:42] Segmenting data... 255s INFO [2026-02-10 04:20:42] Found SOMATIC annotation in VCF. 255s INFO [2026-02-10 04:20:42] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 255s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 255s 255s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 255s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 255s 255s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 255s > 255s + cd .. 255s + find tests+ -type f -iname *.R 255s wc -l 255s Test: Run tests for PureCN 255s Start: testthat.R 255s + NBTEST=18 255s + [ 18 -gt 0 ] 255s + echo Test: Run tests for PureCN 255s + cd tests 255s + echo Start: testthat.R 255s + R --no-save 255s 255s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 255s Copyright (C) 2025 The R Foundation for Statistical Computing 255s Platform: x86_64-pc-linux-gnu 255s 255s R is free software and comes with ABSOLUTELY NO WARRANTY. 255s You are welcome to redistribute it under certain conditions. 255s Type 'license()' or 'licence()' for distribution details. 255s 255s R is a collaborative project with many contributors. 255s Type 'contributors()' for more information and 255s 'citation()' on how to cite R or R packages in publications. 255s 255s Type 'demo()' for some demos, 'help()' for on-line help, or 255s 'help.start()' for an HTML browser interface to help. 255s Type 'q()' to quit R. 255s 255s > library(testthat) 255s > library(PureCN) 255s Loading required package: DNAcopy 255s Loading required package: VariantAnnotation 255s Loading required package: BiocGenerics 255s 255s Attaching package: ‘BiocGenerics’ 255s 255s The following objects are masked from ‘package:stats’: 255s 255s IQR, mad, sd, var, xtabs 255s 255s The following objects are masked from ‘package:base’: 255s 255s anyDuplicated, aperm, append, as.data.frame, basename, cbind, 255s colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, 255s get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, 255s match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, 255s Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff, 255s table, tapply, union, unique, unsplit, which.max, which.min 255s 255s Loading required package: MatrixGenerics 255s Loading required package: matrixStats 255s 255s Attaching package: ‘MatrixGenerics’ 255s 255s The following objects are masked from ‘package:matrixStats’: 255s 255s colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, 255s colCounts, colCummaxs, colCummins, colCumprods, colCumsums, 255s colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, 255s colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, 255s colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, 255s colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, 255s colWeightedMeans, colWeightedMedians, colWeightedSds, 255s colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, 255s rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, 255s rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, 255s rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, 255s rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, 255s rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, 255s rowWeightedMads, rowWeightedMeans, rowWeightedMedians, 255s rowWeightedSds, rowWeightedVars 255s 255s Loading required package: GenomeInfoDb 255s Loading required package: S4Vectors 255s Loading required package: stats4 256s 256s Attaching package: ‘S4Vectors’ 256s 256s The following object is masked from ‘package:utils’: 256s 256s findMatches 256s 256s The following objects are masked from ‘package:base’: 256s 256s expand.grid, I, unname 256s 256s Loading required package: IRanges 256s Loading required package: GenomicRanges 256s Loading required package: SummarizedExperiment 256s Loading required package: Biobase 257s Welcome to Bioconductor 257s 257s Vignettes contain introductory material; view with 257s 'browseVignettes()'. To cite Bioconductor, see 257s 'citation("Biobase")', and for packages 'citation("pkgname")'. 257s 257s 257s Attaching package: ‘Biobase’ 257s 257s The following object is masked from ‘package:MatrixGenerics’: 257s 257s rowMedians 257s 257s The following objects are masked from ‘package:matrixStats’: 257s 257s anyMissing, rowMedians 257s 258s Loading required package: Rsamtools 258s Loading required package: Biostrings 258s Loading required package: XVector 259s 259s Attaching package: ‘Biostrings’ 259s 259s The following object is masked from ‘package:base’: 259s 259s strsplit 259s 262s 262s Attaching package: ‘VariantAnnotation’ 262s 262s The following object is masked from ‘package:base’: 262s 262s tabulate 262s 263s > 263s > test_check("PureCN") 264s FATAL [2026-02-10 04:20:52] tumor.coverage.file and interval.file do not align. 264s 264s FATAL [2026-02-10 04:20:52] 264s 264s FATAL [2026-02-10 04:20:52] This is most likely a user error due to invalid input data or 264s 264s FATAL [2026-02-10 04:20:52] parameters (PureCN 2.12.0). 264s 264s WARN [2026-02-10 04:20:52] Cannot find all contig lengths while exporting interval file. 265s INFO [2026-02-10 04:20:53] Processing seq1:1-21 (1/3)... 265s INFO [2026-02-10 04:20:53] Processing seq1:1227-1247 (2/3)... 265s INFO [2026-02-10 04:20:53] Processing seq2:594-614 (3/3)... 266s WARN [2026-02-10 04:20:53] Large potential mis-calibration of on- and off-target log2 ratios: 0.26 268s INFO [2026-02-10 04:20:56] ------------------------------------------------------------ 268s INFO [2026-02-10 04:20:56] PureCN 2.12.0 268s INFO [2026-02-10 04:20:56] ------------------------------------------------------------ 268s INFO [2026-02-10 04:20:56] Loading coverage files... 268s INFO [2026-02-10 04:20:56] Mean target coverages: 112X (tumor) 99X (normal). 268s WARN [2026-02-10 04:20:56] Allosome coverage missing, cannot determine sex. 268s WARN [2026-02-10 04:20:56] Allosome coverage missing, cannot determine sex. 268s INFO [2026-02-10 04:20:56] Removing 228 intervals with missing log.ratio. 268s INFO [2026-02-10 04:20:56] Removing 22 small (< 5bp) intervals. 268s INFO [2026-02-10 04:20:56] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 268s WARN [2026-02-10 04:20:56] No normalDB provided. Provide one for better results. 268s INFO [2026-02-10 04:20:56] Removing 1724 low count (< 100 total reads) intervals. 268s INFO [2026-02-10 04:20:56] Removing 6 low coverage (< 15.0000X) intervals. 268s INFO [2026-02-10 04:20:56] Using 8050 intervals (8050 on-target, 0 off-target). 268s INFO [2026-02-10 04:20:56] No off-target intervals. If this is hybrid-capture data, consider adding them. 268s INFO [2026-02-10 04:20:56] No interval.file provided. Cannot check for any GC-biases. 268s INFO [2026-02-10 04:20:56] Loading VCF... 268s INFO [2026-02-10 04:20:56] Found 127 variants in VCF file. 269s INFO [2026-02-10 04:20:56] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 269s INFO [2026-02-10 04:20:56] LIB-02240e4 is tumor in VCF file. 269s INFO [2026-02-10 04:20:56] No homozygous variants in VCF, provide unfiltered VCF. 269s INFO [2026-02-10 04:20:56] Removing 1 non heterozygous (in matched normal) germline SNPs. 269s INFO [2026-02-10 04:20:56] Removing 0 low quality variants with non-offset BQ < 25. 269s INFO [2026-02-10 04:20:56] Base quality scores range from 29 to 35 (offset by 1) 269s INFO [2026-02-10 04:20:56] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 269s INFO [2026-02-10 04:20:56] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 269s INFO [2026-02-10 04:20:56] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 269s INFO [2026-02-10 04:20:57] 1.2% of targets contain variants. 269s INFO [2026-02-10 04:20:57] Removing 4 variants outside intervals. 269s INFO [2026-02-10 04:20:57] Found SOMATIC annotation in VCF. 269s INFO [2026-02-10 04:20:57] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 269s INFO [2026-02-10 04:20:57] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 269s INFO [2026-02-10 04:20:57] Excluding 0 novel or poor quality variants from segmentation. 269s INFO [2026-02-10 04:20:57] Sample sex: ? 269s INFO [2026-02-10 04:20:57] Segmenting data... 269s INFO [2026-02-10 04:20:57] Loading pre-computed boundaries for DNAcopy... 269s INFO [2026-02-10 04:20:57] Setting undo.SD parameter to 1.000000. 270s INFO [2026-02-10 04:20:57] Setting prune.hclust.h parameter to 0.200000. 270s INFO [2026-02-10 04:20:57] Found 59 segments with median size of 17.67Mb. 270s INFO [2026-02-10 04:20:57] Using 121 variants. 270s INFO [2026-02-10 04:20:57] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 270s INFO [2026-02-10 04:20:57] 2D-grid search of purity and ploidy... 270s INFO [2026-02-10 04:20:58] Local optima: 0.63/1.9, 0.5/2 270s INFO [2026-02-10 04:20:58] Testing local optimum 1/2 at purity 0.63 and total ploidy 1.90... 271s INFO [2026-02-10 04:20:58] Testing local optimum 2/2 at purity 0.50 and total ploidy 2.00... 271s INFO [2026-02-10 04:20:59] Skipping 1 solutions that converged to the same optima. 271s INFO [2026-02-10 04:20:59] Fitting variants with beta model for local optimum 1/2... 271s INFO [2026-02-10 04:20:59] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 273s INFO [2026-02-10 04:21:00] Optimized purity: 0.65 273s INFO [2026-02-10 04:21:00] Done. 273s INFO [2026-02-10 04:21:00] ------------------------------------------------------------ 273s INFO [2026-02-10 04:21:01] Removing 22 non heterozygous (in matched normal) germline SNPs. 273s INFO [2026-02-10 04:21:01] Removing 19 low quality variants with non-offset BQ < 25. 273s INFO [2026-02-10 04:21:01] Base quality scores range from 24 to 35 (offset by 1) 273s INFO [2026-02-10 04:21:01] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 273s INFO [2026-02-10 04:21:01] Initial testing for significant sample cross-contamination: unlikely 273s INFO [2026-02-10 04:21:01] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 273s INFO [2026-02-10 04:21:01] Removing 22 non heterozygous (in matched normal) germline SNPs. 273s INFO [2026-02-10 04:21:01] Removing 19 low quality variants with non-offset BQ < 25. 273s INFO [2026-02-10 04:21:01] Base quality scores range from 24 to 35 (offset by 1) 273s INFO [2026-02-10 04:21:01] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 274s INFO [2026-02-10 04:21:01] Initial testing for significant sample cross-contamination: unlikely 274s INFO [2026-02-10 04:21:01] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 274s INFO [2026-02-10 04:21:01] Removing 6 blacklisted variants. 274s INFO [2026-02-10 04:21:01] Removing 22 non heterozygous (in matched normal) germline SNPs. 274s INFO [2026-02-10 04:21:01] Removing 19 low quality variants with non-offset BQ < 25. 274s INFO [2026-02-10 04:21:01] Base quality scores range from 24 to 35 (offset by 1) 274s INFO [2026-02-10 04:21:01] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 274s INFO [2026-02-10 04:21:02] Initial testing for significant sample cross-contamination: unlikely 274s INFO [2026-02-10 04:21:02] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 274s WARN [2026-02-10 04:21:02] MuTect stats file lacks contig and position columns. 274s INFO [2026-02-10 04:21:02] Removing 22 non heterozygous (in matched normal) germline SNPs. 274s INFO [2026-02-10 04:21:02] Removing 19 low quality variants with non-offset BQ < 25. 274s INFO [2026-02-10 04:21:02] Base quality scores range from 24 to 35 (offset by 1) 274s INFO [2026-02-10 04:21:02] Minimum number of supporting reads ranges from 2 to 9, depending on coverage and BQS. 274s INFO [2026-02-10 04:21:02] Initial testing for significant sample cross-contamination: unlikely 274s INFO [2026-02-10 04:21:02] Removing 45 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 275s WARN [2026-02-10 04:21:02] MuTect stats file and VCF file do not align perfectly. Will remove 2325 unmatched variants. 275s WARN [2026-02-10 04:21:02] MuTect stats file lacks failure_reasons column. Keeping all variants listed in stats file. 275s INFO [2026-02-10 04:21:02] Removing 0 non heterozygous (in matched normal) germline SNPs. 275s INFO [2026-02-10 04:21:02] Removing 0 low quality variants with non-offset BQ < 25. 275s INFO [2026-02-10 04:21:02] Base quality scores range from 31 to 33 (offset by 1) 275s INFO [2026-02-10 04:21:02] Minimum number of supporting reads ranges from 3 to 4, depending on coverage and BQS. 275s INFO [2026-02-10 04:21:02] Removing 0 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 275s INFO [2026-02-10 04:21:02] Removing 22 non heterozygous (in matched normal) germline SNPs. 275s INFO [2026-02-10 04:21:02] Base quality scores range from 7 to 35 (offset by 1) 275s INFO [2026-02-10 04:21:02] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 275s INFO [2026-02-10 04:21:03] Initial testing for significant sample cross-contamination: unlikely 275s INFO [2026-02-10 04:21:03] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 275s INFO [2026-02-10 04:21:03] Removing 22 non heterozygous (in matched normal) germline SNPs. 275s INFO [2026-02-10 04:21:03] Base quality scores range from 7 to 35 (offset by 1) 275s INFO [2026-02-10 04:21:03] Minimum number of supporting reads ranges from 1 to 41, depending on coverage and BQS. 275s INFO [2026-02-10 04:21:03] Initial testing for significant sample cross-contamination: unlikely 275s INFO [2026-02-10 04:21:03] Removing 49 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 275s INFO [2026-02-10 04:21:03] Removing 22 non heterozygous (in matched normal) germline SNPs. 275s WARN [2026-02-10 04:21:03] Many variants removed by min.base.quality (50) filter. You might want to lower the cutoff. 275s FATAL [2026-02-10 04:21:03] No variants passed filter BQ. 275s 275s FATAL [2026-02-10 04:21:03] 275s 275s FATAL [2026-02-10 04:21:03] This is most likely a user error due to invalid input data or 275s 275s FATAL [2026-02-10 04:21:03] parameters (PureCN 2.12.0). 275s 276s INFO [2026-02-10 04:21:03] Found 11 variants in VCF file. 276s WARN [2026-02-10 04:21:03] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 276s INFO [2026-02-10 04:21:03] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 277s INFO [2026-02-10 04:21:04] Found 11 variants in VCF file. 277s WARN [2026-02-10 04:21:04] vcf.file has no DB info field for membership in germline databases. Found and used valid population allele frequency > 0.001000 instead. 277s INFO [2026-02-10 04:21:04] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 277s INFO [2026-02-10 04:21:05] Found 11 variants in VCF file. 277s WARN [2026-02-10 04:21:05] vcf.file has no DB or POP_AF info field for membership in germline databases. Guessing it based on available dbSNP ID. 277s INFO [2026-02-10 04:21:05] 1 (9.1%) variants annotated as likely germline (DB INFO flag). 277s INFO [2026-02-10 04:21:05] Found 1000 variants in VCF file. 277s INFO [2026-02-10 04:21:05] Removing 2 triallelic sites. 277s WARN [2026-02-10 04:21:05] Having trouble guessing SOMATIC status... 277s WARN [2026-02-10 04:21:05] DP FORMAT field contains NAs. Removing 44 variants. 278s INFO [2026-02-10 04:21:05] 954 (100.0%) variants annotated as likely germline (DB INFO flag). 278s INFO [2026-02-10 04:21:06] Found 12 variants in VCF file. 278s INFO [2026-02-10 04:21:06] Removing 1 triallelic sites. 278s WARN [2026-02-10 04:21:06] DP FORMAT field contains NAs. Removing 1 variants. 278s WARN [2026-02-10 04:21:06] vcf.file has no DB info field for membership in germline databases. Found and used somatic status instead. 278s INFO [2026-02-10 04:21:06] 8 (80.0%) variants annotated as likely germline (DB INFO flag). 279s WARN [2026-02-10 04:21:06] BQ FORMAT field contains NAs. 279s INFO [2026-02-10 04:21:06] Found 2331 variants in VCF file. 279s INFO [2026-02-10 04:21:06] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 279s INFO [2026-02-10 04:21:07] Found 2331 variants in VCF file. 279s INFO [2026-02-10 04:21:07] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 279s WARN [2026-02-10 04:21:07] Did not find base quality scores, will use global error rate of 0.0010 instead. 279s INFO [2026-02-10 04:21:07] Removing 21 low quality variants with non-offset BQ < 25. 279s INFO [2026-02-10 04:21:07] Base quality scores range from 24 to 35 (offset by 1) 279s INFO [2026-02-10 04:21:07] Initial testing for significant sample cross-contamination: unlikely 279s INFO [2026-02-10 04:21:07] Removing 89 variants with AF < 0.030 or AF >= 0.970 or insufficient supporting reads or depth < 15. 279s INFO [2026-02-10 04:21:07] Found 2331 variants in VCF file. 279s INFO [2026-02-10 04:21:07] 2282 (97.9%) variants annotated as likely germline (DB INFO flag). 280s WARN [2026-02-10 04:21:07] BQ FORMAT field contains NAs. 280s WARN [2026-02-10 04:21:08] Allosome coverage missing, cannot determine sex. 281s WARN [2026-02-10 04:21:09] Allosome coverage missing, cannot determine sex. 281s INFO [2026-02-10 04:21:09] Mean coverages: chrX: 108.58, chrY: 108.58, chr1-22: 104.87. 281s INFO [2026-02-10 04:21:09] Mean coverages: chrX: 108.58, chrY: 2.17, chr1-22: 104.87. 281s INFO [2026-02-10 04:21:09] Mean coverages: chrX: 108.58, chrY: 5.17, chr1-22: 104.87. 282s INFO [2026-02-10 04:21:09] Found 20 variants in VCF file. 282s INFO [2026-02-10 04:21:09] 20 (100.0%) variants annotated as likely germline (DB INFO flag). 282s WARN [2026-02-10 04:21:09] Did not find base quality scores, will use global error rate of 0.0010 instead. 282s INFO [2026-02-10 04:21:10] Found 127 variants in VCF file. 282s INFO [2026-02-10 04:21:10] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 282s WARN [2026-02-10 04:21:10] Did not find base quality scores, will use global error rate of 0.0010 instead. 282s INFO [2026-02-10 04:21:10] ------------------------------------------------------------ 282s INFO [2026-02-10 04:21:10] PureCN 2.12.0 282s INFO [2026-02-10 04:21:10] ------------------------------------------------------------ 282s INFO [2026-02-10 04:21:10] Loading coverage files... 283s INFO [2026-02-10 04:21:10] Mean target coverages: 112X (tumor) 99X (normal). 283s WARN [2026-02-10 04:21:10] Allosome coverage missing, cannot determine sex. 283s WARN [2026-02-10 04:21:10] Allosome coverage missing, cannot determine sex. 283s INFO [2026-02-10 04:21:10] Removing 228 intervals with missing log.ratio. 283s INFO [2026-02-10 04:21:10] Removing 22 small (< 5bp) intervals. 283s INFO [2026-02-10 04:21:10] Removing 19 intervals with low total coverage in normal (< 150.00 reads). 283s WARN [2026-02-10 04:21:10] No normalDB provided. Provide one for better results. 283s INFO [2026-02-10 04:21:10] Removing 1724 low count (< 100 total reads) intervals. 283s INFO [2026-02-10 04:21:10] Removing 6 low coverage (< 15.0000X) intervals. 283s INFO [2026-02-10 04:21:10] Using 8050 intervals (8050 on-target, 0 off-target). 283s INFO [2026-02-10 04:21:10] No off-target intervals. If this is hybrid-capture data, consider adding them. 283s INFO [2026-02-10 04:21:10] No interval.file provided. Cannot check for any GC-biases. 283s INFO [2026-02-10 04:21:10] Loading VCF... 283s INFO [2026-02-10 04:21:10] Found 127 variants in VCF file. 283s INFO [2026-02-10 04:21:10] 127 (100.0%) variants annotated as likely germline (DB INFO flag). 283s INFO [2026-02-10 04:21:10] LIB-02240e4 is tumor in VCF file. 283s INFO [2026-02-10 04:21:10] No homozygous variants in VCF, provide unfiltered VCF. 283s INFO [2026-02-10 04:21:10] Removing 1 non heterozygous (in matched normal) germline SNPs. 283s INFO [2026-02-10 04:21:10] Removing 0 low quality variants with non-offset BQ < 25. 283s INFO [2026-02-10 04:21:10] Base quality scores range from 29 to 35 (offset by 1) 283s INFO [2026-02-10 04:21:10] Minimum number of supporting reads ranges from 2 to 5, depending on coverage and BQS. 283s INFO [2026-02-10 04:21:11] Removing 1 variants with AF < 0.030 or AF >= 1.000 or insufficient supporting reads or depth < 15. 283s INFO [2026-02-10 04:21:11] Total size of targeted genomic region: 1.53Mb (2.33Mb with 50bp padding). 283s INFO [2026-02-10 04:21:11] 1.2% of targets contain variants. 283s INFO [2026-02-10 04:21:11] Removing 4 variants outside intervals. 283s INFO [2026-02-10 04:21:11] Found SOMATIC annotation in VCF. 283s INFO [2026-02-10 04:21:11] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 283s INFO [2026-02-10 04:21:11] Found SOMATIC annotation in VCF. Setting mapping bias to 0.972. 283s INFO [2026-02-10 04:21:11] Excluding 0 novel or poor quality variants from segmentation. 283s INFO [2026-02-10 04:21:11] Sample sex: ? 283s INFO [2026-02-10 04:21:11] Segmenting data... 283s INFO [2026-02-10 04:21:11] Loading pre-computed boundaries for DNAcopy... 283s INFO [2026-02-10 04:21:11] Setting undo.SD parameter to 1.000000. 284s INFO [2026-02-10 04:21:11] Setting prune.hclust.h parameter to 0.200000. 284s INFO [2026-02-10 04:21:11] Found 59 segments with median size of 17.67Mb. 284s INFO [2026-02-10 04:21:12] Using 121 variants. 284s INFO [2026-02-10 04:21:12] Mean standard deviation of log-ratios: 0.34 (MAPD: 0.30) 284s INFO [2026-02-10 04:21:12] 2D-grid search of purity and ploidy... 284s INFO [2026-02-10 04:21:12] Local optima: 0.65/1.8, 0.52/2 284s INFO [2026-02-10 04:21:12] Testing local optimum 1/2 at purity 0.65 and total ploidy 1.80... 285s INFO [2026-02-10 04:21:12] Testing local optimum 2/2 at purity 0.52 and total ploidy 2.00... 285s INFO [2026-02-10 04:21:13] Skipping 1 solutions that converged to the same optima. 285s INFO [2026-02-10 04:21:13] Fitting variants with beta model for local optimum 1/2... 285s INFO [2026-02-10 04:21:13] Fitting variants for purity 0.65, tumor ploidy 1.75 and contamination 0.01. 286s INFO [2026-02-10 04:21:14] Optimized purity: 0.65 286s INFO [2026-02-10 04:21:14] Done. 286s INFO [2026-02-10 04:21:14] ------------------------------------------------------------ 287s INFO [2026-02-10 04:21:14] Loaded provided segmentation file example_seg.txt (format DNAcopy). 287s INFO [2026-02-10 04:21:14] Re-centering provided segment means (offset -0.0033). 287s INFO [2026-02-10 04:21:14] Loaded provided segmentation file example_gatk4_modelfinal.seg.gz (format GATK4). 287s WARN [2026-02-10 04:21:14] Expecting numeric chromosome names in seg.file, assuming file is properly sorted. 287s INFO [2026-02-10 04:21:14] Re-centering provided segment means (offset -0.0037). 288s sh: 1: gatk: not found 288s WARN [2026-02-10 04:21:16] Cannot find gatk binary in path. 288s INFO [2026-02-10 04:21:16] ------------------------------------------------------------ 288s INFO [2026-02-10 04:21:16] PureCN 2.12.0 288s INFO [2026-02-10 04:21:16] ------------------------------------------------------------ 288s INFO [2026-02-10 04:21:16] Loading coverage files... 288s INFO [2026-02-10 04:21:16] Mean target coverages: 109X (tumor) 102X (normal). 288s WARN [2026-02-10 04:21:16] Allosome coverage missing, cannot determine sex. 288s WARN [2026-02-10 04:21:16] Allosome coverage missing, cannot determine sex. 288s INFO [2026-02-10 04:21:16] Removing 9 intervals with missing log.ratio. 288s INFO [2026-02-10 04:21:16] Removing 1 small (< 5bp) intervals. 288s INFO [2026-02-10 04:21:16] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 288s WARN [2026-02-10 04:21:16] No normalDB provided. Provide one for better results. 288s INFO [2026-02-10 04:21:16] Removing 73 low count (< 100 total reads) intervals. 288s INFO [2026-02-10 04:21:16] Removing 1 low coverage (< 15.0000X) intervals. 288s INFO [2026-02-10 04:21:16] Using 411 intervals (411 on-target, 0 off-target). 288s INFO [2026-02-10 04:21:16] No off-target intervals. If this is hybrid-capture data, consider adding them. 288s INFO [2026-02-10 04:21:16] No interval.file provided. Cannot check for any GC-biases. 288s INFO [2026-02-10 04:21:16] Sample sex: ? 288s INFO [2026-02-10 04:21:16] Segmenting data... 288s FATAL [2026-02-10 04:21:16] segmentationHclust requires an input segmentation. 288s 288s FATAL [2026-02-10 04:21:16] 288s 288s FATAL [2026-02-10 04:21:16] This is most likely a user error due to invalid input data or 288s 288s FATAL [2026-02-10 04:21:16] parameters (PureCN 2.12.0). 288s 288s INFO [2026-02-10 04:21:16] Loaded provided segmentation file example_seg.txt (format DNAcopy). 288s INFO [2026-02-10 04:21:16] Re-centering provided segment means (offset -0.0033). 288s INFO [2026-02-10 04:21:16] ------------------------------------------------------------ 288s INFO [2026-02-10 04:21:16] PureCN 2.12.0 288s INFO [2026-02-10 04:21:16] ------------------------------------------------------------ 288s INFO [2026-02-10 04:21:16] Loading coverage files... 289s INFO [2026-02-10 04:21:16] Mean target coverages: 109X (tumor) 102X (normal). 289s WARN [2026-02-10 04:21:16] Allosome coverage missing, cannot determine sex. 289s WARN [2026-02-10 04:21:16] Allosome coverage missing, cannot determine sex. 289s INFO [2026-02-10 04:21:16] Removing 9 intervals with missing log.ratio. 289s INFO [2026-02-10 04:21:16] Removing 1 small (< 5bp) intervals. 289s INFO [2026-02-10 04:21:16] Removing 1 intervals with low total coverage in normal (< 150.00 reads). 289s WARN [2026-02-10 04:21:16] No normalDB provided. Provide one for better results. 289s INFO [2026-02-10 04:21:16] Removing 73 low count (< 100 total reads) intervals. 289s INFO [2026-02-10 04:21:16] Removing 1 low coverage (< 15.0000X) intervals. 289s INFO [2026-02-10 04:21:16] Using 411 intervals (411 on-target, 0 off-target). 289s INFO [2026-02-10 04:21:16] No off-target intervals. If this is hybrid-capture data, consider adding them. 289s INFO [2026-02-10 04:21:16] No interval.file provided. Cannot check for any GC-biases. 289s INFO [2026-02-10 04:21:16] Sample sex: ? 289s INFO [2026-02-10 04:21:16] Segmenting data... 289s INFO [2026-02-10 04:21:16] Found SOMATIC annotation in VCF. 289s INFO [2026-02-10 04:21:16] Setting somatic prior probabilities for somatic variants to 0.999000 or to 0.000100 otherwise. 289s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 289s 289s ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ 289s • gatk binary > 4.1.7.0 required (1): 'test_segmentation.R:25:4' 289s 289s [ FAIL 0 | WARN 1 | SKIP 1 | PASS 150 ] 289s > 289s + exit 0 289s autopkgtest [04:21:17]: test pkg-r-autopkgtest: -----------------------] 290s pkg-r-autopkgtest PASS 290s autopkgtest [04:21:18]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 290s autopkgtest [04:21:18]: @@@@@@@@@@@@@@@@@@@@ summary 290s pkg-r-autopkgtest PASS