0s autopkgtest [01:51:35]: starting date and time: 2026-02-10 01:51:35+0000 0s autopkgtest [01:51:35]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [01:51:35]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v5y3yi9k/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-ape --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-23.secgroup --name adt-resolute-amd64-r-cran-ape-20260210-015135-juju-7f2275-prod-proposed-migration-environment-15-56afed14-7941-413a-92f8-dae8c6f965ab --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-r-cran-ape-20260210-015135-juju-7f2275-prod-proposed-migration-environment-15-56afed14-7941-413a-92f8-dae8c6f965ab from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 76s autopkgtest [01:52:51]: testbed dpkg architecture: amd64 76s autopkgtest [01:52:51]: testbed apt version: 3.1.14 76s autopkgtest [01:52:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s autopkgtest [01:52:51]: testbed release detected to be: None 77s autopkgtest [01:52:52]: updating testbed package index (apt update) 77s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 77s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 77s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 77s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB] 78s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB] 78s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB] 78s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B] 78s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B] 78s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB] 78s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB] 78s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB] 78s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB] 78s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 78s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 79s Fetched 4710 kB in 1s (4392 kB/s) 79s Reading package lists... 80s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 80s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 81s Reading package lists... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 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] 82s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 82s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 82s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 82s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 82s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 82s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 82s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 82s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 82s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 82s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 82s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 82s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 82s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 82s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 82s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 82s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 82s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 82s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 82s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 82s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 82s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 82s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 82s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 82s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 82s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 82s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 82s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 82s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 82s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 82s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 82s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 82s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 82s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 82s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 82s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 82s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 82s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 82s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 82s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 82s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 82s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 82s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 82s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 82s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 82s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 82s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 82s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 82s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 82s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 82s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 82s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 82s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 82s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 82s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 82s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 82s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 82s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 82s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 82s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 82s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 82s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 82s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 82s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 82s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 82s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 82s 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] 85s 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] 86s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 86s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 86s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 86s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 86s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 86s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 86s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 86s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 86s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 86s 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 5s (45.0 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 ... 87s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 87s Setting up findutils (4.10.0-3build2) ... 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 .../sed_4.9-2build3_amd64.deb ... 87s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 87s Setting up sed (4.9-2build3) ... 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 .../tar_1.35+dfsg-3.1build2_amd64.deb ... 87s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 87s Setting up tar (1.35+dfsg-3.1build2) ... 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 .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 87s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 87s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 87s Selecting previously unselected package gcc-16-base:amd64. 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 .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 87s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 87s 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 96s 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) ... 108s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 108s Setting up libwrap0:amd64 (7.6.q-36build2) ... 108s 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) ... 110s Setting up linux-headers-generic (6.19.0-3.3) ... 110s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 110s Setting up hwdata (0.394-1build1) ... 110s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 110s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 110s No schema files found: doing nothing. 110s Setting up dbus (1.16.2-2ubuntu3) ... 110s A reboot is required to replace the running dbus-daemon. 110s Please reboot the system when convenient. 110s Setting up shared-mime-info (2.4-5build3) ... 111s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 111s Setting up pciutils (1:3.14.0-1build2) ... 111s Setting up python3-markdown-it (3.0.0-3build1) ... 111s Setting up libdrm2:amd64 (2.4.131-1) ... 111s Setting up libpython3.14:amd64 (3.14.2-1) ... 111s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 111s Setting up linux-tools-common (6.19.0-3.3) ... 111s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 111s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 111s 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) ... 112s Processing triggers for install-info (7.2-5) ... 112s Processing triggers for initramfs-tools (0.150ubuntu7) ... 112s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 116s Processing triggers for libc-bin (2.42-2ubuntu4) ... 116s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 117s /etc/kernel/postinst.d/initramfs-tools: 117s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 120s /etc/kernel/postinst.d/zz-update-grub: 120s Sourcing file `/etc/default/grub' 120s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 120s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 120s Generating grub configuration file ... 122s Found linux image: /boot/vmlinuz-6.19.0-3-generic 122s autopkgtest [01:53:36]: upgrading testbed (apt dist-upgrade and autopurge) 122s Found initrd image: /boot/initrd.img-6.19.0-3-generic 122s Found linux image: /boot/vmlinuz-6.18.0-9-generic 122s Found initrd image: /boot/initrd.img-6.18.0-9-generic 122s Warning: os-prober will not be executed to detect other bootable partitions. 122s Systems on them will not be added to the GRUB boot configuration. 122s Check GRUB_DISABLE_OS_PROBER documentation entry. 122s Adding boot menu entry for UEFI Firmware Settings ... 122s done 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Calculating upgrade... 122s The following package was automatically installed and is no longer required: 122s libpython3.13 122s Use 'sudo apt autoremove' to remove it. 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 122s Solving dependencies... 123s The following packages will be REMOVED: 123s libpython3.13* 123s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 123s After this operation, 7599 kB disk space will be freed. 123s (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.) 123s Removing libpython3.13:amd64 (3.13.11-1) ... 123s Processing triggers for libc-bin (2.42-2ubuntu4) ... 123s autopkgtest [01:53:38]: rebooting testbed after setup commands that affected boot 153s autopkgtest [01:54:08]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 155s autopkgtest [01:54:10]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 157s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 157s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-ape 5.8-1-1 (diff) [5600 B] 157s gpgv: Signature made Wed Jan 22 08:35:21 2025 UTC 157s gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 157s gpgv: issuer "plessy@debian.org" 157s gpgv: Can't check signature: No public key 157s dpkg-source: warning: cannot verify inline signature for ./r-cran-ape_5.8-1-1.dsc: no acceptable signature found 157s autopkgtest [01:54:12]: testing package r-cran-ape version 5.8-1-1 157s autopkgtest [01:54:12]: build not needed 160s autopkgtest [01:54:15]: test run-unit-test: preparing testbed 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 161s Solving dependencies... 161s The following NEW packages will be installed: 161s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 161s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 161s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 161s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 161s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 161s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 161s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 161s libxss1 libxt6t64 r-base-core r-cran-ape r-cran-cli r-cran-cpp11 161s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 161s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 161s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 161s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 161s xdg-utils zip 161s 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. 161s Need to get 66.2 MB of archives. 161s After this operation, 128 MB of additional disk space will be used. 161s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 161s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 161s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 161s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 161s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 161s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 161s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libsuitesparseconfig7 amd64 1:7.12.1+dfsg-1 [22.0 kB] 161s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 libamd3 amd64 1:7.12.1+dfsg-1 [35.8 kB] 161s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 161s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 161s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 161s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 161s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 161s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 161s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libcolamd3 amd64 1:7.12.1+dfsg-1 [27.4 kB] 161s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 161s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 161s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 161s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libltdl7 amd64 2.5.4-9 [43.7 kB] 161s Get:20 http://ftpmaster.internal/ubuntu resolute/universe amd64 libglpk40 amd64 5.0-2 [380 kB] 161s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 161s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 161s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 161s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 161s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 161s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 161s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 162s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 162s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 162s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 162s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 162s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 162s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 162s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 162s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 162s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 162s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 162s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 162s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 162s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 162s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 162s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 162s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 162s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 162s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 162s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 162s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 162s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 162s Get:49 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 163s Get:50 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB] 163s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 163s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-littler amd64 0.3.22-1 [85.5 kB] 163s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 163s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rcpp amd64 1.1.0-1 [2021 kB] 163s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-digest amd64 0.6.39-1 [203 kB] 163s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-ape amd64 5.8-1-1 [2918 kB] 163s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 163s Get:58 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cpp11 all 0.5.3-1 [242 kB] 163s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-fastmatch amd64 1.1-6-1 [37.0 kB] 163s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-generics all 0.1.4-1 [84.0 kB] 163s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 163s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-rlang amd64 1.1.5-3 [1721 kB] 163s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-lifecycle all 1.0.5+dfsg-1 [120 kB] 163s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 164s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 164s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-pkgconfig all 2.0.3-2build2 [20.4 kB] 164s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 164s Get:68 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-igraph amd64 2.1.4-1build1 [5218 kB] 164s Get:69 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-quadprog amd64 1.5-8-1build2 [32.6 kB] 164s Get:70 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-phangorn amd64 2.12.1+dfsg-1 [1831 kB] 164s Preconfiguring packages ... 164s Fetched 66.2 MB in 3s (20.8 MB/s) 164s Selecting previously unselected package fonts-dejavu-mono. 164s (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.) 164s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 164s Unpacking fonts-dejavu-mono (2.37-8build1) ... 164s Selecting previously unselected package fonts-dejavu-core. 164s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 164s Unpacking fonts-dejavu-core (2.37-8build1) ... 164s Selecting previously unselected package fontconfig-config. 164s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 164s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 164s Selecting previously unselected package libfontconfig1:amd64. 164s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 164s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 164s Selecting previously unselected package fontconfig. 164s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 164s Unpacking fontconfig (2.17.1-3ubuntu1) ... 164s Selecting previously unselected package libgomp1:amd64. 164s Preparing to unpack .../05-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 164s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 164s Selecting previously unselected package libsuitesparseconfig7:amd64. 164s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.12.1+dfsg-1_amd64.deb ... 164s Unpacking libsuitesparseconfig7:amd64 (1:7.12.1+dfsg-1) ... 165s Selecting previously unselected package libamd3:amd64. 165s Preparing to unpack .../07-libamd3_1%3a7.12.1+dfsg-1_amd64.deb ... 165s Unpacking libamd3:amd64 (1:7.12.1+dfsg-1) ... 165s Selecting previously unselected package libblas3:amd64. 165s Preparing to unpack .../08-libblas3_3.12.1-7ubuntu1_amd64.deb ... 165s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 165s Selecting previously unselected package libpixman-1-0:amd64. 165s Preparing to unpack .../09-libpixman-1-0_0.46.4-1_amd64.deb ... 165s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 165s Selecting previously unselected package libxcb-render0:amd64. 165s Preparing to unpack .../10-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 165s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 165s Selecting previously unselected package libxcb-shm0:amd64. 165s Preparing to unpack .../11-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 165s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 165s Selecting previously unselected package libxrender1:amd64. 165s Preparing to unpack .../12-libxrender1_1%3a0.9.12-1_amd64.deb ... 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previously unselected package libltdl7:amd64. 165s Preparing to unpack .../18-libltdl7_2.5.4-9_amd64.deb ... 165s Unpacking libltdl7:amd64 (2.5.4-9) ... 165s Selecting previously unselected package libglpk40:amd64. 165s Preparing to unpack .../19-libglpk40_5.0-2_amd64.deb ... 165s Unpacking libglpk40:amd64 (5.0-2) ... 165s Selecting previously unselected package libgraphite2-3:amd64. 165s Preparing to unpack .../20-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 165s Unpacking libgraphite2-3:amd64 (1.3.14-11ubuntu1) ... 165s Selecting previously unselected package libharfbuzz0b:amd64. 165s Preparing to unpack .../21-libharfbuzz0b_12.3.2-1_amd64.deb ... 165s Unpacking libharfbuzz0b:amd64 (12.3.2-1) ... 165s Selecting previously unselected package x11-common. 165s Preparing to unpack .../22-x11-common_1%3a7.7+24ubuntu1_all.deb ... 165s Unpacking x11-common (1:7.7+24ubuntu1) ... 165s Selecting previously unselected package libice6:amd64. 165s Preparing to unpack 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Regenerating fonts cache... done. 168s Setting up libxft2:amd64 (2.3.6-1build2) ... 168s Setting up libtk8.6:amd64 (8.6.17-1) ... 168s Setting up libpango-1.0-0:amd64 (1.57.0-1) ... 168s Setting up libcairo2:amd64 (1.18.4-3) ... 168s Setting up libxt6t64:amd64 (1:1.2.1-1.3) ... 168s Setting up libpangoft2-1.0-0:amd64 (1.57.0-1) ... 168s Setting up libpangocairo-1.0-0:amd64 (1.57.0-1) ... 168s Setting up r-base-core (4.5.2-1ubuntu2) ... 168s Creating config file /etc/R/Renviron with new version 168s Setting up r-cran-fastmatch (1.1-6-1) ... 168s Setting up r-cran-lattice (0.22-9-1) ... 168s Setting up r-cran-nlme (3.1.168-1) ... 168s Setting up r-cran-pkgkitten (0.2.4-1) ... 168s Setting up r-cran-magrittr (2.0.3-1) ... 168s Setting up r-cran-quadprog (1.5-8-1build2) ... 168s Setting up r-cran-littler (0.3.22-1) ... 168s Setting up r-cran-rcpp (1.1.0-1) ... 168s Setting up r-cran-rlang (1.1.5-3) ... 168s Setting up r-cran-generics (0.1.4-1) ... 168s Setting up r-cran-digest (0.6.39-1) ... 168s Setting up r-cran-ape (5.8-1-1) ... 168s Setting up r-cran-glue (1.8.0-1) ... 168s Setting up r-cran-cli (3.6.4-1) ... 168s Setting up r-cran-lifecycle (1.0.5+dfsg-1) ... 168s Setting up r-cran-pkgconfig (2.0.3-2build2) ... 168s Setting up r-cran-cpp11 (0.5.3-1) ... 168s Setting up r-cran-matrix (1.7-4-1) ... 168s Setting up r-cran-vctrs (0.6.5-1) ... 168s Setting up r-cran-igraph (2.1.4-1build1) ... 168s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 168s Processing triggers for libc-bin (2.42-2ubuntu4) ... 168s Processing triggers for man-db (2.13.1-1build1) ... 169s Processing triggers for install-info (7.2-5) ... 170s autopkgtest [01:54:25]: test run-unit-test: [----------------------- 170s 170s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 170s Copyright (C) 2025 The R Foundation for Statistical Computing 170s Platform: x86_64-pc-linux-gnu 170s 170s R is free software and comes with ABSOLUTELY NO WARRANTY. 170s You are welcome to redistribute it under certain conditions. 170s Type 'license()' or 'licence()' for distribution details. 170s 170s R is a collaborative project with many contributors. 170s Type 'contributors()' for more information and 170s 'citation()' on how to cite R or R packages in publications. 170s 170s Type 'demo()' for some demos, 'help()' for on-line help, or 170s 'help.start()' for an HTML browser interface to help. 170s Type 'q()' to quit R. 170s 170s > Stangle("DrawingPhylogenies.Rnw") 170s Writing to file DrawingPhylogenies.R 170s > source("DrawingPhylogenies.R", echo=TRUE) 170s 170s > options(width = 80, prompt = "> ") 170s 170s > library(ape) 170s 170s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 170s 170s > foo <- function() { 170s + col <- "green" 170s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 170s + las = 1) 170s + box(lty .... [TRUNCATED] 170s 170s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 170s 170s > plot(mytr) 170s 170s > foo() 170s 170s > plot(mytr, "c", FALSE) 170s 170s > foo() 170s 170s > plot(mytr, "u") 170s 170s > foo() 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, "f") 170s 170s > foo() 170s 170s > box("outer") 170s 170s > tr <- compute.brlen(stree(8, "l"), 0.1) 170s 170s > tr$tip.label[] <- "" 170s 170s > foo <- function() { 170s + col <- "green" 170s + axis(1, col = col, col.ticks = col, col.axis = col) 170s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 170s 170s > layout(matrix(1:12, 6, 2)) 170s 170s > par(mar = c(2, 2, 0.3, 0)) 170s 170s > for (type in c("p", "c")) { 170s + plot(tr, type) 170s + foo() 170s + plot(tr, type, node.pos = 2) 170s + foo() 170s + plot(tr, type, FALSE) 170s + foo() 170s .... [TRUNCATED] 170s 170s > foo <- function() { 170s + col <- "green" 170s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 170s + las = 1) 170s + box(lty .... [TRUNCATED] 170s 170s > layout(matrix(1:4, 2, 2)) 170s 170s > par(las = 1) 170s 170s > plot(tr, "u") 170s 170s > foo() 170s 170s > plot(tr, "u", FALSE) 170s 170s > foo() 170s 170s > plot(tr, "f") 170s 170s > foo() 170s 170s > plot(tr, "f", FALSE) 170s 170s > foo() 170s 170s > args(node.depth.edgelength) 170s function (phy) 170s NULL 170s 170s > args(node.depth) 170s function (phy, method = 1) 170s NULL 170s 170s > args(node.height) 170s function (phy, clado.style = FALSE) 170s NULL 170s 170s > args(unrooted.xy) 170s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 170s NULL 170s 170s > args(phylogram.plot) 170s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 170s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 170s node.lty = NULL) 170s NULL 170s 170s > args(cladogram.plot) 170s function (edge, xx, yy, edge.color, edge.width, edge.lty) 170s NULL 170s 170s > args(circular.plot) 170s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 170s edge.lty) 170s NULL 170s 170s > args(plot.phylo) 170s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 170s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 170s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 170s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 170s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 170s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 170s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 170s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 170s ...) 170s NULL 170s 170s > geo <- factor(c("Africa", "World", "Africa")) 170s 170s > (mycol <- c("blue", "red")[geo]) 170s [1] "blue" "red" "blue" 170s 170s > plot(mytr, tip.color = mycol) 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 170s 170s > args(def) 170s function (x, ..., default = NULL, regexp = FALSE) 170s NULL 170s 170s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 170s 170s > identical(mycol, mycol2) 170s [1] TRUE 170s 170s > (i <- which.edge(mytr, c("Homo", "Pan"))) 170s [1] 2 3 170s 170s > co <- rep("black", Nedge(mytr)) 170s 170s > co[i] <- "blue" 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr, edge.col = co) 170s 170s > edgelabels() 170s 170s > args(axisPhylo) 170s function (side = NULL, root.time = NULL, backward = TRUE, ...) 170s NULL 170s 170s > args(add.scale.bar) 170s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 170s ...) 170s NULL 170s 170s > plot(mytr) 170s 170s > add.scale.bar() 170s 170s > axisPhylo() 170s 170s > axis(3) 170s 170s > args(nodelabels) 170s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 170s ...) 170s NULL 170s 170s > args(tiplabels) 170s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 170s offset = 0, ...) 170s NULL 170s 170s > args(edgelabels) 170s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 170s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 170s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 170s date = NULL, ...) 170s NULL 170s 170s > par(xpd = TRUE) 170s 170s > plot(mytr) 170s 170s > nodelabels() 170s 170s > tiplabels() 170s 170s > edgelabels() 170s 170s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 170s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 170s 170s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 170s 170s > v <- c(0, 0.5, 1) 170s 170s > layout(matrix(1:9, 3, 3)) 170s 170s > par(mar = c(3, 3, 3, 0), las = 1) 170s 170s > for (i in v) { 170s + for (j in v) { 170s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 170s + ")")) 170s + abline(v = 0, h = .... [TRUNCATED] 170s 170s > plot(rep(0, 3), 0:2, "n", las = 1) 170s 170s > abline(v = 0, h = 0:2, lty = 3) 170s 170s > text(0, 0:2, mytr$tip.label, adj = -1) 170s 170s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 170s 170s > args(phydataplot) 170s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 170s width = NULL, legend = "below", funcol = rainbow, ...) 170s NULL 170s 170s > args(ring) 170s function (x, phy, style = "ring", offset = 1, ...) 170s NULL 170s 170s > x <- matrix(1:6, 3, 10) 170s 170s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 170s 170s > x 170s A B C D E F G H I J 170s Homo 1 4 1 4 1 4 1 4 1 4 170s Gorilla 2 5 2 5 2 5 2 5 2 5 170s Pan 3 6 3 6 3 6 3 6 3 6 170s 170s > mytr$tip.label 170s [1] "Pan" "Homo" "Gorilla" 170s 170s > par(mar = c(10, 2, 5, 5)) 170s 170s > plot(mytr, x.lim = 30) 170s 170s > phydataplot(x, mytr, "m", border = "white", offset = 2, 170s + width = 1) 170s 170s > phydataplot(x, mytr, "m", border = "white", offset = 15, 170s + width = 1, continuous = 2) 170s 170s > n <- 100 170s 170s > p <- 3 170s 170s > set.seed(3) 170s 170s > tr <- rcoal(n) 170s 170s > x <- matrix(runif(p * n), n, p) 170s 170s > rownames(x) <- tr$tip.label 170s 170s > COL <- c("red", "green", "blue") 170s 170s > par(xpd = TRUE) 170s 170s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 170s + no.margin = TRUE) 170s 170s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 170s + col = COL[j]) 171s 171s > tree <- rtree(10) 171s 171s > tree$edge.length[1] <- 1000 171s 171s > layout(matrix(1:2, 1)) 171s 171s > plot(tree) 171s 171s > axisPhylo() 171s 171s > plotBreakLongEdges(tree) 171s 171s > axisPhylo() 171s 171s > el <- tree$edge.length 171s 171s > sum(el > mean(el) + 2 * sd(el)) 171s [1] 1 171s 171s > tree$edge.length[8] <- 1000 171s 171s > el <- tree$edge.length 171s 171s > sum(el > mean(el) + 2 * sd(el)) 171s [1] 2 171s 171s > layout(matrix(1:2, 1)) 171s 171s > plotBreakLongEdges(tree) 171s 171s > plotBreakLongEdges(tree, n = 2) 171s 171s > TR <- replicate(10, rcoal(sample(11:20, size = 1)), 171s + simplify = FALSE) 171s 171s > kronoviz(TR, type = "c", show.tip.label = FALSE) 171s 171s > dates <- as.Date(.leap.seconds) 171s 171s > tr <- rcoal(length(dates)) 171s 171s > plotTreeTime(tr, dates) 171s 171s > par(oma = rep(2, 4)) 171s 171s > plot(mytr) 171s 171s > box(lty = 3) 171s 171s > box("figure", col = "blue") 171s 171s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 171s + font = 2, col = "blue") 171s 171s > box("outer") 171s 171s > layout(matrix(1:4, 2, 2)) 171s 171s > par(oma = rep(2, 4)) 171s 171s > for (i in 1:4) { 171s + par(mar = rep(i, 4)) 171s + plot(mytr) 171s + box(lty = 3) 171s + box("figure", col = "blue") 171s + } 171s 171s > for (i in 1:4) mtext("Outer margin", i, 0.5, outer = TRUE, 171s + font = 2, col = "blue") 171s 171s > box("outer") 171s 171s > layout(matrix(c(1, 2, 1, 3), 2, 2)) 171s 171s > for (i in 1:3) plot(rtree(5)) 171s 171s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 171s $type 171s [1] "phylogram" 171s 171s $use.edge.length 171s [1] TRUE 171s 171s $node.pos 171s [1] 1 171s 171s $node.depth 171s [1] 1 171s 171s $show.tip.label 171s [1] TRUE 171s 171s $show.node.label 171s [1] FALSE 171s 171s $font 171s [1] 3 171s 171s $cex 171s [1] 0.83 171s 171s $adj 171s [1] 0 171s 171s $srt 171s [1] 0 171s 171s $no.margin 171s [1] FALSE 171s 171s $label.offset 171s [1] 0 171s 171s $x.lim 171s [1] 0.00000 3.13046 171s 171s $y.lim 171s [1] 1 5 171s 171s $direction 171s [1] "rightwards" 171s 171s $tip.color 171s [1] "black" 171s 171s $Ntip 171s [1] 5 171s 171s $Nnode 171s [1] 4 171s 171s $root.time 171s NULL 171s 171s $align.tip.label 171s [1] FALSE 171s 171s $edge 171s [,1] [,2] 171s [1,] 6 1 171s [2,] 6 7 171s [3,] 7 2 171s [4,] 7 8 171s [5,] 8 3 171s [6,] 8 9 171s [7,] 9 4 171s [8,] 9 5 171s 171s $xx 171s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 171s [8] 1.3631198 1.9857132 171s 171s $yy 171s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 171s 171s 171s > layout(matrix(1:2, 2)) 171s 171s > plot(rtree(4)) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > x <- pp$xx[1] 171s 171s > y <- pp$yy[1] 171s 171s > (pu <- par("usr")) 171s [1] -0.06364557 1.65478492 0.88000000 4.12000000 171s 171s > (x - pu[1])/(pu[2] - pu[1]) 171s [1] 0.9349839 171s 171s > (y - pu[3])/(pu[4] - pu[3]) 171s [1] 0.03703704 171s 171s > pi <- par("pin") 171s 171s > mi <- par("mai") 171s 171s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 171s 171s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 171s 171s > plot(rtree(4)) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > x <- pp$xx[5] 171s 171s > y <- pp$yy[5] 171s 171s > pu <- par("usr") 171s 171s > pi <- par("pin") 171s 171s > mi <- par("mai") 171s 171s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 171s 171s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 171s 171s > yi1 <- yi1 + par("fin")[2] 171s 171s > di <- par("din") 171s 171s > layout(1) 171s 171s > par(new = TRUE, mai = rep(0, 4)) 171s 171s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 171s + ylim = 0:1, xaxs = "i", yaxs = "i") 171s 171s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 171s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 171s 171s > foo <- function(phy1, phy2, from) { 171s + layout(matrix(1:2, 2)) 171s + plot(phy1, font = 1) 171s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 171s 171s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 171s 171s > par(xpd = TRUE) 171s 171s > foo(trb, mytr, "Primates") 171s 171s > plot(mytr, plot = FALSE) 171s 171s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 171s 171s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 171s + pp$yy[2] + 0.1, col = "yellow", border = NA) 171s 171s > par(new = TRUE) 171s 171s > plot(mytr) 171s > 171s 171s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > Stangle("MoranI.Rnw") 171s Writing to file MoranI.R 171s > source("MoranI.R", echo=TRUE) 171s 171s > options(width = 80, prompt = "> ") 171s 171s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 171s 171s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 171s 171s > names(body) <- names(longevity) <- c("Homo", "Pongo", 171s + "Macaca", "Ateles", "Galago") 171s 171s > library(ape) 171s 171s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 171s 171s > trnwk[2] <- ":0.38,Galago:1.00);" 171s 171s > tr <- read.tree(text = trnwk) 171s 171s > plot(tr) 171s 171s > axisPhylo() 171s 171s > w <- 1/cophenetic(tr) 171s 171s > w 171s Homo Pongo Macaca Ateles Galago 171s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 171s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 171s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 171s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 171s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 171s 171s > diag(w) <- 0 171s 171s > Moran.I(body, w) 171s $observed 171s [1] -0.07312179 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.08910814 171s 171s $p.value 171s [1] 0.04714628 171s 171s 171s > Moran.I(body, w, alt = "greater") 171s $observed 171s [1] -0.07312179 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.08910814 171s 171s $p.value 171s [1] 0.02357314 171s 171s 171s > Moran.I(longevity, w) 171s $observed 171s [1] -0.1837739 171s 171s $expected 171s [1] -0.25 171s 171s $sd 171s [1] 0.09114549 171s 171s $p.value 171s [1] 0.4674727 171s 171s 171s > data(carnivora) 171s 171s > carnivora$log10SW <- log10(carnivora$SW) 171s 171s > carnivora$log10FW <- log10(carnivora$FW) 171s 171s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 171s 171s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 171s 171s > plot(co1) 171s 171s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 171s 171s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 171s 171s > print(plot(co2)) 171s 171s > plot(co2, FALSE) 171s > 171s 171s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > Stangle("RandomTopologies.Rnw") 171s Writing to file RandomTopologies.R 171s > source("RandomTopologies.R", echo=TRUE) 171s 171s > options(width = 80, prompt = "> ") 171s 171s > library(ape) 171s 171s > n <- 1:10 171s 171s > data.frame(N.topo = sapply(n, howmanytrees)) 171s N.topo 171s 1 1 171s 2 1 171s 3 3 171s 4 15 171s 5 105 171s 6 945 171s 7 10395 171s 8 135135 171s 9 2027025 171s 10 34459425 171s 171s > howmanytrees(25) 171s [1] 1.192568e+30 171s 171s > howmanytrees(25) * 0.21 171s [1] 2.504393e+29 171s 171s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 171s N.topo 171s 1 1 171s 2 1 171s 3 1 171s 4 2 171s 5 3 171s 6 6 171s 7 11 171s 8 23 171s 9 46 171s 10 98 171s 171s > n2 <- c(50, 100, 200) 171s 171s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 171s + row.names = n2) 171s N.topo 171s 50 5.150149e+16 171s 100 1.019560e+36 171s 200 1.141703e+75 171s 171s > 1/howmanytrees(50) 171s [1] 3.632505e-77 171s 171s > 1/sapply(n, howmanytrees) 171s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 171s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 171s 171s > 1/sapply(n, howmanytrees, labeled = FALSE) 171s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 171s [7] 0.09090909 0.04347826 0.02173913 0.01020408 171s 171s > library(phangorn) 172s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 172s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 172s 172s > TR <- allTrees(4, rooted = TRUE) 172s 172s > TR 172s 15 phylogenetic trees 172s 172s > layout(matrix(1:15, 3, 5)) 172s 172s > par(mar = rep(1.5, 4), xpd = TRUE) 172s 172s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 172s 172s > K <- 100 172s 172s > n <- 50 172s 172s > N <- howmanytrees(n, labeled = FALSE) 172s 172s > p <- 1/N 172s 172s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 172s [1] 0 172s 172s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 172s [1] -5.431212e-17 172s 172s > f <- function(n, K) { 172s + N <- howmanytrees(n, labeled = FALSE) 172s + p <- 1/N 172s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 172s + } 172s 172s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 172s + 10000)) 172s 172s > DF$P <- mapply(f, n = DF$n, K = DF$K) 172s 172s > library(lattice) 172s 172s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 172s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 172s 172s > subset(DF, n == 20) 172s n K P 172s 17 20 2 1.160494e-11 172s 34 20 5 1.160491e-10 172s 51 20 10 5.222149e-10 172s 68 20 100 5.743191e-08 172s 85 20 1000 5.783570e-06 172s 102 20 10000 5.671842e-04 172s 172s > f(20, 1e+05) 172s [1] 0.04638755 172s 172s > f(30, 1e+06) 172s [1] 2.525152e-07 172s 172s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 172s 172s > TR5 <- read.tree(text = txt) 172s 172s > layout(matrix(1:3, 1)) 172s 172s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 172s 172s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 172s + labeled = FALSE) 172s [1] 2 172s 172s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 172s + labeled = FALSE) 172s [1] 1 172s 172s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 172s + labeled = FALSE) 172s [1] Inf 172s 172s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 172s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 172s 172s > foo.test <- function(x, labeled = TRUE) { 172s + uTR <- unique(x, use.tip.label = labeled) 172s + f <- integer(length(uTR)) 172s + for (j in seq_along( .... [TRUNCATED] 172s 172s > lapply(TR, foo.test) 174s [1] 61 73 81 76 81 63 51 76 76 54 49 56 75 71 57 176s [1] 50 99 51 52 55 61 58 113 47 119 56 64 60 61 54 177s [1] 51 162 37 161 39 40 163 47 41 46 45 39 41 44 44 177s [[1]] 177s 177s Chi-squared test for given probabilities 177s 177s data: f 177s X-squared = 26.57, df = 14, p-value = 0.02189 177s 177s 177s [[2]] 177s 177s Chi-squared test for given probabilities 177s 177s data: f 177s X-squared = 114.86, df = 14, p-value < 2.2e-16 177s 177s 177s [[3]] 177s 177s Chi-squared test for given probabilities 177s 177s data: f 177s X-squared = 513.95, df = 14, p-value < 2.2e-16 177s 177s 177s 177s > lapply(TR, foo.test, labeled = FALSE) 177s [1] 209 791 178s [1] 669 331 178s [1] 514 486 178s [[1]] 178s 178s Chi-squared test for given probabilities 178s 178s data: f 178s X-squared = 338.72, df = 1, p-value < 2.2e-16 178s 178s 178s [[2]] 178s 178s Chi-squared test for given probabilities 178s 178s data: f 178s X-squared = 114.24, df = 1, p-value < 2.2e-16 178s 178s 178s [[3]] 178s 178s Chi-squared test for given probabilities 178s 178s data: f 178s X-squared = 0.784, df = 1, p-value = 0.3759 178s 178s 178s 178s > .Machine$double.xmax 178s [1] 1.797693e+308 178s 178s > howmanytrees(151) 178s [1] 3.753274e+306 178s 178s > howmanytrees(792, labeled = FALSE) 178s [1] 1.029038e+308 178s 178s > (N <- howmanytrees(2e+06)) 178s approximately 3.692364 * 10^12335524 178s 178s > N[2] + 1 178s n 178s 12335525 178s 178s > ceiling((N[2] + 1)/3000) 178s n 178s 4112 178s 178s > n <- 1:792 178s 178s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 178s 178s > lN <- log10(N) 178s 178s > summary(lm(lN ~ n)) 178s 178s Call: 178s lm(formula = lN ~ n) 178s 178s Residuals: 178s Min 1Q Median 3Q Max 178s -0.25968 -0.21424 -0.08311 0.12406 2.82605 178s 178s Coefficients: 178s Estimate Std. Error t value Pr(>|t|) 178s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 178s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 178s --- 178s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 178s 178s Residual standard error: 0.3175 on 790 degrees of freedom 178s Multiple R-squared: 1, Adjusted R-squared: 1 178s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 178s 178s 178s > s <- n > 700 178s 178s > summary(lm(lN[s] ~ n[s])) 178s 178s Call: 178s lm(formula = lN[s] ~ n[s]) 178s 178s Residuals: 178s Min 1Q Median 3Q Max 178s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 178s 178s Coefficients: 178s Estimate Std. Error t value Pr(>|t|) 178s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 178s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 178s --- 178s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 178s 178s Residual standard error: 0.0003738 on 90 degrees of freedom 178s Multiple R-squared: 1, Adjusted R-squared: 1 178s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 178s 178s 178s > n <- 788:792 178s 178s > log10(sapply(n, howmanytrees, labeled = FALSE)) 178s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 178s 178s > 0.3941 * n - 4.153 178s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 178s 178s > xi <- 2.477993 178s 178s > lxi <- log10(xi) 178s 178s > n <- 1000 178s 178s > (n - 1) * lxi 178s [1] 393.706 178s 178s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 178s + 1))))) 178s [1] 393.8532 178s [1] 393.9009 178s [1] 393.9187 178s [1] 393.9257 178s [1] 393.9285 178s [1] 393.9296 178s [1] 393.9301 178s [1] 393.9303 178s [1] 393.9304 178s [1] 393.9304 178s > 178s autopkgtest [01:54:33]: test run-unit-test: -----------------------] 179s run-unit-test PASS 179s autopkgtest [01:54:34]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 179s autopkgtest [01:54:34]: test pkg-r-autopkgtest: preparing testbed 179s Reading package lists... 179s Building dependency tree... 179s Reading state information... 179s Solving dependencies... 180s The following NEW packages will be installed: 180s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 180s dctrl-tools g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 180s gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 180s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 180s libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 180s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 180s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjs-jquery 180s liblapack-dev liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 180s libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev 180s libquadmath0 libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 180s libubsan1 libzstd-dev linux-libc-dev node-html5shiv pkg-r-autopkgtest 180s pkgconf pkgconf-bin r-base-dev r-cran-expm r-cran-gee r-cran-xml2 180s rpcsvc-proto zlib1g-dev 180s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 180s Need to get 113 MB of archives. 180s After this operation, 404 MB of additional disk space will be used. 180s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 180s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 180s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 180s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 180s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 180s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 180s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 180s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 180s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 180s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 180s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 180s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 180s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 180s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 180s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 180s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 181s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 181s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 181s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 181s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 181s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 181s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 181s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 181s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 181s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 181s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 181s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 181s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 181s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 181s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 181s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 181s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 181s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 182s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 182s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 182s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 182s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 182s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 182s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 182s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 182s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 182s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 182s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 182s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 182s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 182s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 182s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 182s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 182s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 182s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 182s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 182s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 182s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 182s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 182s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 182s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 182s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 182s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 182s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 182s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 182s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 182s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 182s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 182s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-expm amd64 1.0-0-1 [226 kB] 182s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-gee amd64 4.13-29-1 [84.2 kB] 182s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xml2 amd64 1.4.1-1 [329 kB] 182s Fetched 113 MB in 3s (44.2 MB/s) 182s Selecting previously unselected package libc-dev-bin. 182s (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 ... 130378 files and directories currently installed.) 182s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 182s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 182s Selecting previously unselected package linux-libc-dev:amd64. 182s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_amd64.deb ... 182s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 183s Selecting previously unselected package libcrypt-dev:amd64. 183s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 183s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 183s Selecting previously unselected package rpcsvc-proto. 183s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 183s Unpacking rpcsvc-proto (1.4.3-1build1) ... 183s Selecting previously unselected package libc6-dev:amd64. 183s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_amd64.deb ... 183s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 183s Selecting previously unselected package libisl23:amd64. 183s Preparing to unpack .../05-libisl23_0.27-1build1_amd64.deb ... 183s Unpacking libisl23:amd64 (0.27-1build1) ... 183s Selecting previously unselected package libmpc3:amd64. 183s Preparing to unpack .../06-libmpc3_1.3.1-2_amd64.deb ... 183s Unpacking libmpc3:amd64 (1.3.1-2) ... 183s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 183s Preparing to unpack .../07-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 183s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package cpp-15. 183s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 183s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 183s Selecting previously unselected package cpp-x86-64-linux-gnu. 183s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 183s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 183s Selecting previously unselected package cpp. 183s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 183s Unpacking cpp (4:15.2.0-4ubuntu1) ... 183s Selecting previously unselected package libcc1-0:amd64. 183s Preparing to unpack .../11-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libitm1:amd64. 183s Preparing to unpack .../12-libitm1_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libasan8:amd64. 183s Preparing to unpack .../13-libasan8_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package liblsan0:amd64. 183s Preparing to unpack .../14-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libtsan2:amd64. 183s Preparing to unpack .../15-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libubsan1:amd64. 183s Preparing to unpack .../16-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libhwasan0:amd64. 183s Preparing to unpack .../17-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 183s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 183s Selecting previously unselected package libquadmath0:amd64. 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skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 185s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 185s update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist 185s Setting up g++ (4:15.2.0-4ubuntu1) ... 185s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 185s Setting up build-essential (12.12ubuntu2) ... 185s Setting up r-base-dev (4.5.2-1ubuntu2) ... 185s Setting up pkg-r-autopkgtest (20250812) ... 185s Processing triggers for libc-bin (2.42-2ubuntu4) ... 185s Processing triggers for man-db (2.13.1-1build1) ... 186s Processing triggers for install-info (7.2-5) ... 186s autopkgtest [01:54:41]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 186s autopkgtest [01:54:41]: test pkg-r-autopkgtest: [----------------------- 187s Test: Try to load the R library ape 187s 187s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 187s Copyright (C) 2025 The R Foundation for Statistical Computing 187s Platform: x86_64-pc-linux-gnu 187s 187s R is free software and comes with ABSOLUTELY NO WARRANTY. 187s You are welcome to redistribute it under certain conditions. 187s Type 'license()' or 'licence()' for distribution details. 187s 187s R is a collaborative project with many contributors. 187s Type 'contributors()' for more information and 187s 'citation()' on how to cite R or R packages in publications. 187s 187s Type 'demo()' for some demos, 'help()' for on-line help, or 187s 'help.start()' for an HTML browser interface to help. 187s Type 'q()' to quit R. 187s 187s > library('ape') 187s > 187s autopkgtest [01:54:42]: test pkg-r-autopkgtest: -----------------------] 187s autopkgtest [01:54:42]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 187s pkg-r-autopkgtest PASS 188s autopkgtest [01:54:43]: @@@@@@@@@@@@@@@@@@@@ summary 188s run-unit-test PASS 188s pkg-r-autopkgtest PASS