0s autopkgtest [22:02:32]: starting date and time: 2025-03-15 22:02:32+0000 0s autopkgtest [22:02:32]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:02:32]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.i5vyorz2/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade r-cran-ape --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-71.secgroup --name adt-plucky-amd64-r-cran-ape-20250315-220232-juju-7f2275-prod-proposed-migration-environment-2-c4e0bceb-0c8b-4609-9ce6-517bbd795cd0 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [22:03:21]: testbed dpkg architecture: amd64 49s autopkgtest [22:03:21]: testbed apt version: 2.9.31ubuntu1 49s autopkgtest [22:03:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 49s autopkgtest [22:03:21]: testbed release detected to be: None 49s autopkgtest [22:03:21]: updating testbed package index (apt update) 50s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 50s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 50s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 50s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 50s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 50s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 50s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 50s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 50s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 50s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 50s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 50s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 50s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 50s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 50s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 50s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 50s Fetched 1265 kB in 0s (5391 kB/s) 51s Reading package lists... 51s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s Calculating upgrade... 52s The following package was automatically installed and is no longer required: 52s libnl-genl-3-200 52s Use 'sudo apt autoremove' to remove it. 52s The following NEW packages will be installed: 52s bpftool libdebuginfod-common libdebuginfod1t64 linux-headers-6.14.0-10 52s linux-headers-6.14.0-10-generic linux-image-6.14.0-10-generic 52s linux-modules-6.14.0-10-generic linux-modules-extra-6.14.0-10-generic 52s linux-perf linux-tools-6.14.0-10 linux-tools-6.14.0-10-generic pnp.ids 52s The following packages will be upgraded: 52s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 52s cloud-init cloud-init-base curl dosfstools fwupd gir1.2-girepository-2.0 52s gir1.2-glib-2.0 htop hwdata libapparmor1 libapt-pkg7.0 libaudit-common 52s libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 libctf0 52s libcurl3t64-gnutls libcurl4t64 libestr0 libfwupd3 libgirepository-1.0-1 52s libglib2.0-0t64 libglib2.0-data libgprofng0 libjemalloc2 liblz4-1 liblzma5 52s libmm-glib0 libncurses6 libncursesw6 libnl-3-200 libnl-genl-3-200 52s libnl-route-3-200 libpci3 libpython3-stdlib libpython3.13 52s libpython3.13-minimal libpython3.13-stdlib libselinux1 libsframe1 52s libsqlite3-0 libtinfo6 libxml2 linux-firmware linux-generic 52s linux-headers-generic linux-headers-virtual linux-image-generic 52s linux-image-virtual linux-libc-dev linux-tools-common linux-virtual 52s media-types ncurses-base ncurses-bin ncurses-term pci.ids pciutils 52s pinentry-curses python-apt-common python3 python3-apt python3-cffi-backend 52s python3-dbus python3-gi python3-jinja2 python3-lazr.uri python3-markupsafe 52s python3-minimal python3-systemd python3-yaml python3.13 python3.13-gdbm 52s python3.13-minimal rsync rsyslog strace xz-utils 52s 86 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 52s Need to get 807 MB of archives. 52s After this operation, 326 MB of additional disk space will be used. 52s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 52s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 52s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 52s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 52s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 52s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 52s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 53s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 53s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 53s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 53s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 53s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 53s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 53s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 53s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 53s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 53s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 53s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 53s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 53s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 53s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 53s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 53s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 53s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 53s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 53s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 53s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 53s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 53s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 53s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 53s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 53s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 53s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 53s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 53s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 53s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 53s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 53s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 53s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 53s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 53s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 53s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 53s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 53s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 53s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 53s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 53s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 53s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 53s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 53s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 53s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 53s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 53s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 53s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 53s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 53s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 53s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 53s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 53s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 53s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 53s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 53s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 53s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 53s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 53s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 53s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 53s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 53s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 53s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 53s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 53s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 53s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 53s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 53s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 53s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 53s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 53s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 53s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 57s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 57s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 57s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 58s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 58s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 58s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 58s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 58s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 58s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 58s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 58s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 58s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 58s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 58s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 58s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 58s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 58s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 58s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 58s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 58s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 59s Preconfiguring packages ... 59s Fetched 807 MB in 6s (133 MB/s) 59s (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 ... 109138 files and directories currently installed.) 59s Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ... 59s Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ... 59s Setting up ncurses-bin (6.5+20250216-2) ... 59s (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 ... 109138 files and directories currently installed.) 59s Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... 59s Unpacking ncurses-base (6.5+20250216-2) over (6.5+20250216-1) ... 60s Setting up ncurses-base (6.5+20250216-2) ... 60s (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 ... 109138 files and directories currently installed.) 60s Preparing to unpack .../ncurses-term_6.5+20250216-2_all.deb ... 60s Unpacking ncurses-term (6.5+20250216-2) over (6.5+20250216-1) ... 60s Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ... 60s Unpacking liblz4-1:amd64 (1.10.0-4) over (1.10.0-3) ... 60s Setting up liblz4-1:amd64 (1.10.0-4) ... 60s (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 ... 109138 files and directories currently installed.) 60s Preparing to unpack .../liblzma5_5.6.4-1_amd64.deb ... 60s Unpacking liblzma5:amd64 (5.6.4-1) over (5.6.3-1) ... 60s Setting up liblzma5:amd64 (5.6.4-1) ... 60s (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 ... 109138 files and directories currently installed.) 60s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 60s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 60s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 61s (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 ... 109138 files and directories currently installed.) 61s Preparing to unpack .../archives/apt_2.9.33_amd64.deb ... 61s Unpacking apt (2.9.33) over (2.9.31ubuntu1) ... 61s Setting up apt (2.9.33) ... 61s (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 ... 109138 files and directories currently installed.) 61s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 61s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 62s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 62s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 62s Setting up python3-minimal (3.13.2-2) ... 62s (Reading database ... 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64s Unpacking python3-apt (2.9.9build1) over (2.9.9) ... 64s Preparing to unpack .../10-python3-cffi-backend_1.17.1-2build2_amd64.deb ... 64s Unpacking python3-cffi-backend:amd64 (1.17.1-2build2) over (1.17.1-2build1) ... 64s Preparing to unpack .../11-python3-dbus_1.3.2-5build5_amd64.deb ... 64s Unpacking python3-dbus (1.3.2-5build5) over (1.3.2-5build4) ... 64s Preparing to unpack .../12-python3-gi_3.50.0-4build1_amd64.deb ... 64s Unpacking python3-gi (3.50.0-4build1) over (3.50.0-4) ... 64s Preparing to unpack .../13-python3-yaml_6.0.2-1build2_amd64.deb ... 64s Unpacking python3-yaml (6.0.2-1build2) over (6.0.2-1build1) ... 64s Preparing to unpack .../14-rsyslog_8.2412.0-2ubuntu2_amd64.deb ... 64s Unpacking rsyslog (8.2412.0-2ubuntu2) over (8.2412.0-2ubuntu1) ... 64s Preparing to unpack .../15-apparmor_4.1.0~beta5-0ubuntu8_amd64.deb ... 65s Unpacking apparmor (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu6) ... 66s Preparing to unpack .../16-dosfstools_4.2-1.2_amd64.deb ... 66s 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Preparing to unpack .../68-python3-systemd_235-1build6_amd64.deb ... 78s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 78s Preparing to unpack .../69-python3.13-gdbm_3.13.2-2_amd64.deb ... 78s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 78s Preparing to unpack .../70-cloud-init_25.1-0ubuntu3_all.deb ... 78s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 78s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 78s Setting up media-types (13.0.0) ... 78s Installing new version of config file /etc/mime.types ... 78s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 78s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 78s Setting up pci.ids (0.0~2025.03.09-1) ... 78s Setting up apt-utils (2.9.33) ... 78s Setting up libdebuginfod-common (0.192-4) ... 78s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 78s Setting up bpftool (7.6.0+6.14.0-10.10) ... 78s Setting up libestr0:amd64 (0.1.11-2) ... 78s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 78s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 78s Setting up dosfstools (4.2-1.2) ... 78s Setting up rsyslog (8.2412.0-2ubuntu2) ... 78s info: The user `syslog' is already a member of `adm'. 79s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 79s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 79s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 79s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 79s Setting up linux-headers-generic (6.14.0-10.10) ... 79s Setting up libjemalloc2:amd64 (5.3.0-3) ... 79s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 79s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 79s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 79s Installing new version of config file /etc/apparmor.d/openvpn ... 80s Reloading AppArmor profiles 82s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 82s No schema files found: doing nothing. 82s Setting up libglib2.0-data (2.84.0-1) ... 82s Setting up libncurses6:amd64 (6.5+20250216-2) ... 82s Setting up strace (6.13+ds-1ubuntu1) ... 82s Setting up xz-utils (5.6.4-1) ... 82s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 82s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 84s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 84s Setting up libpci3:amd64 (1:3.13.0-2) ... 84s Setting up python-apt-common (2.9.9build1) ... 84s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 84s Setting up pnp.ids (0.393-3) ... 84s Setting up libnl-3-200:amd64 (3.7.0-1) ... 84s Setting up python3.13-minimal (3.13.2-2) ... 85s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 85s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 85s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 85s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 85s Setting up rsync (3.4.1+ds1-3) ... 86s rsync.service is a disabled or a static unit not running, not starting it. 86s Setting up python3.13-gdbm (3.13.2-2) ... 86s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 86s Setting up ncurses-term (6.5+20250216-2) ... 86s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 86s Setting up libpython3.13:amd64 (3.13.2-2) ... 86s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 86s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 86s Setting up linux-headers-virtual (6.14.0-10.10) ... 86s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 86s Setting up python3.13 (3.13.2-2) ... 87s Setting up htop (3.4.0-2) ... 87s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 89s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 89s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 89s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 89s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 89s Setting up libfwupd3:amd64 (2.0.6-4) ... 89s Setting up python3 (3.13.2-2) ... 89s Setting up python3-markupsafe (2.1.5-1build4) ... 89s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 91s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 91s Setting up hwdata (0.393-3) ... 91s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 92s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 92s Setting up linux-perf (6.14.0-10.10) ... 92s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 92s Setting up python3-gi (3.50.0-4build1) ... 92s Setting up pciutils (1:3.13.0-2) ... 92s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 92s Setting up curl (8.12.1-3ubuntu1) ... 92s Setting up linux-image-virtual (6.14.0-10.10) ... 92s Setting up linux-tools-common (6.14.0-10.10) ... 92s Setting up fwupd (2.0.6-4) ... 92s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 92s fwupd.service is a disabled or a static unit not running, not starting it. 92s Setting up python3-systemd (235-1build6) ... 92s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 92s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 92s Setting up linux-image-generic (6.14.0-10.10) ... 92s Setting up python3-dbus (1.3.2-5build5) ... 93s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 93s Setting up linux-generic (6.14.0-10.10) ... 93s Setting up python3-apt (2.9.9build1) ... 93s Setting up python3-yaml (6.0.2-1build2) ... 93s Setting up python3-lazr.uri (1.0.6-6) ... 93s Setting up binutils (2.44-3ubuntu1) ... 93s Setting up cloud-init-base (25.1-0ubuntu3) ... 94s Setting up linux-virtual (6.14.0-10.10) ... 94s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 94s Setting up cloud-init (25.1-0ubuntu3) ... 94s Processing triggers for systemd (257.3-1ubuntu3) ... 95s Processing triggers for man-db (2.13.0-1) ... 96s Processing triggers for dbus (1.16.2-1ubuntu1) ... 96s Processing triggers for libc-bin (2.41-1ubuntu1) ... 96s Processing triggers for initramfs-tools (0.146ubuntu1) ... 96s update-initramfs: Generating /boot/initrd.img-6.12.0-16-generic 96s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 108s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 108s /etc/kernel/postinst.d/initramfs-tools: 108s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 108s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 118s /etc/kernel/postinst.d/zz-update-grub: 118s Sourcing file `/etc/default/grub' 118s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 118s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 118s Generating grub configuration file ... 118s Found linux image: /boot/vmlinuz-6.14.0-10-generic 118s Found initrd image: /boot/initrd.img-6.14.0-10-generic 118s Found linux image: /boot/vmlinuz-6.12.0-16-generic 118s Found initrd image: /boot/initrd.img-6.12.0-16-generic 118s Found linux image: /boot/vmlinuz-6.11.0-8-generic 118s Found initrd image: /boot/initrd.img-6.11.0-8-generic 118s Warning: os-prober will not be executed to detect other bootable partitions. 118s Systems on them will not be added to the GRUB boot configuration. 118s Check GRUB_DISABLE_OS_PROBER documentation entry. 118s Adding boot menu entry for UEFI Firmware Settings ... 118s done 120s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Solving dependencies... 120s The following packages will be REMOVED: 120s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 120s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 120s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 120s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 120s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 120s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 120s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 120s linux-tools-6.12.0-16-generic* 121s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 121s After this operation, 545 MB disk space will be freed. 121s (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 ... 148643 files and directories currently installed.) 121s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 121s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 121s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 121s Removing libpython3.12t64:amd64 (3.12.9-1) ... 121s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 121s Removing libnsl2:amd64 (1.3.0-3build3) ... 121s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 121s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 122s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 124s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 125s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 127s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 127s /etc/kernel/postrm.d/initramfs-tools: 127s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 127s /etc/kernel/postrm.d/zz-update-grub: 127s Sourcing file `/etc/default/grub' 127s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 127s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 127s Generating grub configuration file ... 127s Found linux image: /boot/vmlinuz-6.14.0-10-generic 127s Found initrd image: /boot/initrd.img-6.14.0-10-generic 127s Found linux image: /boot/vmlinuz-6.12.0-16-generic 127s Found initrd image: /boot/initrd.img-6.12.0-16-generic 128s Warning: os-prober will not be executed to detect other bootable partitions. 128s Systems on them will not be added to the GRUB boot configuration. 128s Check GRUB_DISABLE_OS_PROBER documentation entry. 128s Adding boot menu entry for UEFI Firmware Settings ... 128s done 128s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 128s W: Removing the running kernel 128s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 128s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 128s /etc/kernel/postrm.d/initramfs-tools: 128s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 128s /etc/kernel/postrm.d/zz-update-grub: 128s Sourcing file `/etc/default/grub' 128s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 128s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 128s Generating grub configuration file ... 128s Found linux image: /boot/vmlinuz-6.14.0-10-generic 128s Found initrd image: /boot/initrd.img-6.14.0-10-generic 128s Warning: os-prober will not be executed to detect other bootable partitions. 128s Systems on them will not be added to the GRUB boot configuration. 128s Check GRUB_DISABLE_OS_PROBER documentation entry. 128s Adding boot menu entry for UEFI Firmware Settings ... 128s done 128s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 129s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 130s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 130s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 130s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 130s Processing triggers for libc-bin (2.41-1ubuntu1) ... 130s (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 ... 76972 files and directories currently installed.) 130s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 131s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 131s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 131s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 131s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 131s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 131s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 131s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 131s autopkgtest [22:04:43]: upgrading testbed (apt dist-upgrade and autopurge) 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 132s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 132s Starting 2 pkgProblemResolver with broken count: 0 132s Done 132s Entering ResolveByKeep 133s 133s Calculating upgrade... 133s The following packages will be upgraded: 133s libc-bin libc-dev-bin libc6 libc6-dev locales 133s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 10.5 MB of archives. 133s After this operation, 1024 B of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 133s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 133s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 133s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 133s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 134s Preconfiguring packages ... 134s Fetched 10.5 MB in 0s (44.7 MB/s) 134s (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 ... 76968 files and directories currently installed.) 134s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 134s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 134s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 134s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 134s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 134s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 134s Setting up libc6:amd64 (2.41-1ubuntu2) ... 135s (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 ... 76968 files and directories currently installed.) 135s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 135s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 135s Setting up libc-bin (2.41-1ubuntu2) ... 135s (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 ... 76968 files and directories currently installed.) 135s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 135s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 135s Setting up locales (2.41-1ubuntu2) ... 136s Generating locales (this might take a while)... 137s en_US.UTF-8... done 137s Generation complete. 137s Setting up libc-dev-bin (2.41-1ubuntu2) ... 137s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 137s Processing triggers for man-db (2.13.0-1) ... 138s Processing triggers for systemd (257.3-1ubuntu3) ... 139s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 140s Solving dependencies... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 140s autopkgtest [22:04:52]: rebooting testbed after setup commands that affected boot 144s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 155s autopkgtest [22:05:07]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 156s autopkgtest [22:05:08]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-ape 157s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (dsc) [2114 B] 157s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-ape 5.8-1-1 (tar) [1425 kB] 157s Get:3 http://ftpmaster.internal/ubuntu plucky/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 [22:05:09]: testing package r-cran-ape version 5.8-1-1 158s autopkgtest [22:05:10]: build not needed 159s autopkgtest [22:05:11]: test run-unit-test: preparing testbed 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Starting pkgProblemResolver with broken count: 0 160s Starting 2 pkgProblemResolver with broken count: 0 160s Done 160s The following NEW packages will be installed: 160s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libamd3 160s libblas3 libcairo2 libcolamd3 libdatrie1 libdeflate0 libfontconfig1 160s libgfortran5 libglpk40 libgomp1 libgraphite2-3 libharfbuzz0b libice6 160s libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 libltdl7 libpango-1.0-0 160s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper2 libpixman-1-0 160s libsharpyuv0 libsm6 libsuitesparseconfig7 libtcl8.6 libthai-data libthai0 160s libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 libxft2 libxrender1 160s libxss1 libxt6t64 littler r-base-core r-cran-ape r-cran-cli r-cran-cpp11 160s r-cran-digest r-cran-fastmatch r-cran-generics r-cran-glue r-cran-igraph 160s r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-matrix 160s r-cran-nlme r-cran-phangorn r-cran-pkgconfig r-cran-pkgkitten 160s r-cran-quadprog r-cran-rcpp r-cran-rlang r-cran-vctrs unzip x11-common 160s xdg-utils zip 160s 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. 160s Need to get 67.5 MB of archives. 160s After this operation, 136 MB of additional disk space will be used. 160s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 160s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 161s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 161s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 161s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 161s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 161s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libsuitesparseconfig7 amd64 1:7.8.3+dfsg-3 [13.5 kB] 161s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd3 amd64 1:7.8.3+dfsg-3 [31.0 kB] 161s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 161s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 161s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 161s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 161s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 161s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 161s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libcolamd3 amd64 1:7.8.3+dfsg-3 [19.5 kB] 161s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 161s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 161s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 161s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libltdl7 amd64 2.5.4-4 [46.5 kB] 161s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 libglpk40 amd64 5.0-1build2 [369 kB] 161s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 161s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 161s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 161s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 161s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 161s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 161s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 161s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 161s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 161s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 161s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 161s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 161s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 161s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 161s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 161s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 161s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 161s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 161s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 161s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 161s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 161s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 161s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 161s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 161s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 161s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 161s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 161s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 161s Get:49 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 161s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-littler amd64 0.3.20-2 [96.6 kB] 161s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 littler all 0.3.20-2 [2554 B] 161s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 161s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 161s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgkitten all 0.2.4-1 [27.2 kB] 161s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rcpp amd64 1.0.14-1 [1998 kB] 162s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-digest amd64 0.6.37-1 [200 kB] 162s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-ape amd64 5.8-1-1 [2918 kB] 162s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cli amd64 3.6.4-1 [1394 kB] 162s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cpp11 all 0.5.2-1 [233 kB] 162s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-fastmatch amd64 1.1-6-1 [37.0 kB] 162s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-generics all 0.1.3-1 [81.3 kB] 162s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-glue amd64 1.8.0-1 [164 kB] 162s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-rlang amd64 1.1.5-1 [1719 kB] 162s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 162s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 162s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 162s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 162s Get:68 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 162s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-igraph amd64 2.1.4-1 [5357 kB] 162s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-quadprog amd64 1.5-8-1build1 [30.9 kB] 162s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-phangorn amd64 2.12.1+dfsg-1 [1831 kB] 162s Preconfiguring packages ... 162s Fetched 67.5 MB in 1s (45.8 MB/s) 162s Selecting previously unselected package fonts-dejavu-mono. 162s (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 ... 76968 files and directories currently installed.) 162s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 162s Unpacking fonts-dejavu-mono (2.37-8) ... 163s Selecting previously unselected package fonts-dejavu-core. 163s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 163s Unpacking fonts-dejavu-core (2.37-8) ... 163s Selecting previously unselected package fontconfig-config. 163s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 163s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 163s Selecting previously unselected package libfontconfig1:amd64. 163s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 163s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 163s Selecting previously unselected package fontconfig. 163s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 163s Unpacking fontconfig (2.15.0-2ubuntu1) ... 163s Selecting previously unselected package libgomp1:amd64. 163s Preparing to unpack .../05-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 163s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 163s Selecting previously unselected package libsuitesparseconfig7:amd64. 163s Preparing to unpack .../06-libsuitesparseconfig7_1%3a7.8.3+dfsg-3_amd64.deb ... 163s Unpacking libsuitesparseconfig7:amd64 (1:7.8.3+dfsg-3) ... 163s Selecting previously unselected package libamd3:amd64. 163s Preparing to unpack .../07-libamd3_1%3a7.8.3+dfsg-3_amd64.deb ... 163s Unpacking libamd3:amd64 (1:7.8.3+dfsg-3) ... 163s Selecting previously unselected package libblas3:amd64. 163s Preparing to unpack .../08-libblas3_3.12.1-2_amd64.deb ... 163s Unpacking libblas3:amd64 (3.12.1-2) ... 163s Selecting previously unselected package libpixman-1-0:amd64. 163s Preparing to unpack .../09-libpixman-1-0_0.44.0-3_amd64.deb ... 163s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 163s Selecting previously unselected package libxcb-render0:amd64. 163s Preparing to unpack .../10-libxcb-render0_1.17.0-2_amd64.deb ... 163s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 163s Selecting previously unselected package libxcb-shm0:amd64. 163s Preparing to unpack .../11-libxcb-shm0_1.17.0-2_amd64.deb ... 163s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 163s Selecting previously unselected package libxrender1:amd64. 163s Preparing to unpack .../12-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 163s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 163s Selecting previously unselected package libcairo2:amd64. 163s Preparing to unpack .../13-libcairo2_1.18.2-2_amd64.deb ... 163s Unpacking libcairo2:amd64 (1.18.2-2) ... 163s Selecting previously unselected package libcolamd3:amd64. 163s Preparing to unpack .../14-libcolamd3_1%3a7.8.3+dfsg-3_amd64.deb ... 163s Unpacking libcolamd3:amd64 (1:7.8.3+dfsg-3) ... 163s Selecting previously unselected package libdatrie1:amd64. 163s Preparing to unpack .../15-libdatrie1_0.2.13-3build1_amd64.deb ... 163s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 163s Selecting previously unselected package libdeflate0:amd64. 163s Preparing to unpack .../16-libdeflate0_1.23-1_amd64.deb ... 163s Unpacking libdeflate0:amd64 (1.23-1) ... 163s Selecting previously unselected package libgfortran5:amd64. 163s Preparing to unpack .../17-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 163s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 163s Selecting previously unselected package libltdl7:amd64. 163s Preparing to unpack .../18-libltdl7_2.5.4-4_amd64.deb ... 163s Unpacking libltdl7:amd64 (2.5.4-4) ... 163s Selecting previously unselected package libglpk40:amd64. 163s Preparing to unpack .../19-libglpk40_5.0-1build2_amd64.deb ... 163s Unpacking libglpk40:amd64 (5.0-1build2) ... 163s Selecting previously unselected package libgraphite2-3:amd64. 163s Preparing to unpack .../20-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 163s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 163s Selecting previously unselected package libharfbuzz0b:amd64. 164s Preparing to unpack .../21-libharfbuzz0b_10.2.0-1_amd64.deb ... 164s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 164s Selecting previously unselected package x11-common. 164s Preparing to unpack .../22-x11-common_1%3a7.7+23ubuntu3_all.deb ... 164s Unpacking x11-common (1:7.7+23ubuntu3) ... 164s Selecting previously unselected package libice6:amd64. 164s Preparing to unpack .../23-libice6_2%3a1.1.1-1_amd64.deb ... 164s Unpacking libice6:amd64 (2:1.1.1-1) ... 164s Selecting previously unselected package libjpeg-turbo8:amd64. 164s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 164s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 164s Selecting previously unselected package libjpeg8:amd64. 164s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_amd64.deb ... 164s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 164s Selecting previously unselected package liblapack3:amd64. 164s Preparing to unpack .../26-liblapack3_3.12.1-2_amd64.deb ... 164s Unpacking liblapack3:amd64 (3.12.1-2) ... 164s Selecting previously unselected package liblerc4:amd64. 164s Preparing to unpack .../27-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 164s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 164s Selecting previously unselected package libthai-data. 164s Preparing to unpack .../28-libthai-data_0.1.29-2build1_all.deb ... 164s Unpacking libthai-data (0.1.29-2build1) ... 164s Selecting previously unselected package libthai0:amd64. 164s Preparing to unpack .../29-libthai0_0.1.29-2build1_amd64.deb ... 164s Unpacking libthai0:amd64 (0.1.29-2build1) ... 164s Selecting previously unselected package libpango-1.0-0:amd64. 164s Preparing to unpack .../30-libpango-1.0-0_1.56.2-1_amd64.deb ... 164s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 164s Selecting previously unselected package libpangoft2-1.0-0:amd64. 164s Preparing to unpack .../31-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 164s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 164s Selecting previously unselected package libpangocairo-1.0-0:amd64. 164s Preparing to unpack .../32-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 164s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 164s Selecting previously unselected package libpaper2:amd64. 164s Preparing to unpack .../33-libpaper2_2.2.5-0.3_amd64.deb ... 164s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 164s Selecting previously unselected package libpaper-utils. 164s Preparing to unpack .../34-libpaper-utils_2.2.5-0.3_amd64.deb ... 164s Unpacking libpaper-utils (2.2.5-0.3) ... 164s Selecting previously unselected package libsharpyuv0:amd64. 164s Preparing to unpack .../35-libsharpyuv0_1.5.0-0.1_amd64.deb ... 164s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 164s Selecting previously unselected package libsm6:amd64. 164s Preparing to unpack .../36-libsm6_2%3a1.2.4-1_amd64.deb ... 164s Unpacking libsm6:amd64 (2:1.2.4-1) ... 164s Selecting previously unselected package libtcl8.6:amd64. 164s Preparing to unpack .../37-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 164s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 164s Selecting previously unselected package libjbig0:amd64. 164s Preparing to unpack .../38-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 164s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 164s Selecting previously unselected package libwebp7:amd64. 164s Preparing to unpack .../39-libwebp7_1.5.0-0.1_amd64.deb ... 164s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 164s Selecting previously unselected package libtiff6:amd64. 164s Preparing to unpack .../40-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 164s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 164s Selecting previously unselected package libxft2:amd64. 164s Preparing to unpack .../41-libxft2_2.3.6-1build1_amd64.deb ... 164s Unpacking libxft2:amd64 (2.3.6-1build1) ... 164s Selecting previously unselected package libxss1:amd64. 164s Preparing to unpack .../42-libxss1_1%3a1.2.3-1build3_amd64.deb ... 164s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 164s Selecting previously unselected package libtk8.6:amd64. 164s Preparing to unpack .../43-libtk8.6_8.6.16-1_amd64.deb ... 164s Unpacking libtk8.6:amd64 (8.6.16-1) ... 164s Selecting previously unselected package libxt6t64:amd64. 164s Preparing to unpack .../44-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 164s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 164s Selecting previously unselected package zip. 164s Preparing to unpack .../45-zip_3.0-14ubuntu2_amd64.deb ... 164s Unpacking zip (3.0-14ubuntu2) ... 164s Selecting previously unselected package unzip. 164s Preparing to unpack .../46-unzip_6.0-28ubuntu6_amd64.deb ... 164s Unpacking unzip (6.0-28ubuntu6) ... 164s Selecting previously unselected package xdg-utils. 164s Preparing to unpack .../47-xdg-utils_1.2.1-2ubuntu1_all.deb ... 164s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 164s Selecting previously unselected package r-base-core. 164s Preparing to unpack .../48-r-base-core_4.4.3-1_amd64.deb ... 164s Unpacking r-base-core (4.4.3-1) ... 165s Selecting previously unselected package r-cran-littler. 165s Preparing to unpack .../49-r-cran-littler_0.3.20-2_amd64.deb ... 165s Unpacking r-cran-littler (0.3.20-2) ... 165s Selecting previously unselected package littler. 165s Preparing to unpack .../50-littler_0.3.20-2_all.deb ... 165s Unpacking littler (0.3.20-2) ... 165s Selecting previously unselected package r-cran-lattice. 165s Preparing to unpack .../51-r-cran-lattice_0.22-6-1_amd64.deb ... 165s Unpacking r-cran-lattice (0.22-6-1) ... 165s Selecting previously unselected package r-cran-nlme. 165s Preparing to unpack .../52-r-cran-nlme_3.1.167-1_amd64.deb ... 165s Unpacking r-cran-nlme (3.1.167-1) ... 165s Selecting previously unselected package r-cran-pkgkitten. 165s Preparing to unpack .../53-r-cran-pkgkitten_0.2.4-1_all.deb ... 165s Unpacking r-cran-pkgkitten (0.2.4-1) ... 165s Selecting previously unselected package r-cran-rcpp. 165s Preparing to unpack .../54-r-cran-rcpp_1.0.14-1_amd64.deb ... 165s Unpacking r-cran-rcpp (1.0.14-1) ... 165s Selecting previously unselected package r-cran-digest. 165s Preparing to unpack .../55-r-cran-digest_0.6.37-1_amd64.deb ... 165s Unpacking r-cran-digest (0.6.37-1) ... 165s Selecting previously unselected package r-cran-ape. 165s Preparing to unpack .../56-r-cran-ape_5.8-1-1_amd64.deb ... 165s Unpacking r-cran-ape (5.8-1-1) ... 165s Selecting previously unselected package r-cran-cli. 165s Preparing to unpack .../57-r-cran-cli_3.6.4-1_amd64.deb ... 165s Unpacking r-cran-cli (3.6.4-1) ... 165s Selecting previously unselected package r-cran-cpp11. 165s Preparing to unpack .../58-r-cran-cpp11_0.5.2-1_all.deb ... 165s Unpacking r-cran-cpp11 (0.5.2-1) ... 165s Selecting previously unselected package r-cran-fastmatch. 165s Preparing to unpack .../59-r-cran-fastmatch_1.1-6-1_amd64.deb ... 165s Unpacking r-cran-fastmatch (1.1-6-1) ... 165s Selecting previously unselected package r-cran-generics. 165s Preparing to unpack .../60-r-cran-generics_0.1.3-1_all.deb ... 165s Unpacking r-cran-generics (0.1.3-1) ... 165s Selecting previously unselected package r-cran-glue. 165s Preparing to unpack .../61-r-cran-glue_1.8.0-1_amd64.deb ... 165s Unpacking r-cran-glue (1.8.0-1) ... 165s Selecting previously unselected package r-cran-rlang. 165s Preparing to unpack .../62-r-cran-rlang_1.1.5-1_amd64.deb ... 165s Unpacking r-cran-rlang (1.1.5-1) ... 165s Selecting previously unselected package 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(0.6.37-1) ... 169s Setting up r-cran-ape (5.8-1-1) ... 169s Setting up r-cran-glue (1.8.0-1) ... 169s Setting up r-cran-cli (3.6.4-1) ... 169s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 169s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 169s Setting up r-cran-cpp11 (0.5.2-1) ... 169s Setting up r-cran-matrix (1.7-3-1) ... 169s Setting up r-cran-vctrs (0.6.5-1) ... 169s Setting up r-cran-igraph (2.1.4-1) ... 169s Setting up r-cran-phangorn (2.12.1+dfsg-1) ... 169s Processing triggers for libc-bin (2.41-1ubuntu2) ... 169s Processing triggers for man-db (2.13.0-1) ... 170s Processing triggers for install-info (7.1.1-1) ... 171s autopkgtest [22:05:23]: test run-unit-test: [----------------------- 171s 171s R version 4.4.3 (2025-02-28) -- "Trophy Case" 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("DrawingPhylogenies.Rnw") 171s Writing to file DrawingPhylogenies.R 171s > source("DrawingPhylogenies.R", echo=TRUE) 171s 171s > options(width = 80, prompt = "> ") 171s 171s > library(ape) 171s 171s > mytr <- read.tree(text = "((Pan:5,Homo:5):2,Gorilla:7);") 171s 171s > foo <- function() { 171s + col <- "green" 171s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 171s + las = 1) 171s + box(lty .... [TRUNCATED] 171s 171s > layout(matrix(1:4, 2, 2, byrow = TRUE)) 171s 171s > plot(mytr) 171s 171s > foo() 171s 171s > plot(mytr, "c", FALSE) 171s 171s > foo() 171s 171s > plot(mytr, "u") 171s 171s > foo() 171s 171s > par(xpd = TRUE) 171s 171s > plot(mytr, "f") 171s 171s > foo() 171s 171s > box("outer") 171s 171s > tr <- compute.brlen(stree(8, "l"), 0.1) 171s 171s > tr$tip.label[] <- "" 171s 171s > foo <- function() { 171s + col <- "green" 171s + axis(1, col = col, col.ticks = col, col.axis = col) 171s + axis(2, col = col, col.ticks = col, col.axi .... [TRUNCATED] 171s 171s > layout(matrix(1:12, 6, 2)) 171s 171s > par(mar = c(2, 2, 0.3, 0)) 171s 171s > for (type in c("p", "c")) { 171s + plot(tr, type) 171s + foo() 171s + plot(tr, type, node.pos = 2) 171s + foo() 171s + plot(tr, type, FALSE) 171s + foo() 171s .... [TRUNCATED] 171s 171s > foo <- function() { 171s + col <- "green" 171s + for (i in 1:2) axis(i, col = col, col.ticks = col, col.axis = col, 171s + las = 1) 171s + box(lty .... [TRUNCATED] 171s 171s > layout(matrix(1:4, 2, 2)) 171s 171s > par(las = 1) 171s 171s > plot(tr, "u") 171s 171s > foo() 171s 171s > plot(tr, "u", FALSE) 171s 171s > foo() 171s 171s > plot(tr, "f") 171s 171s > foo() 171s 171s > plot(tr, "f", FALSE) 171s 171s > foo() 171s 171s > args(node.depth.edgelength) 171s function (phy) 171s NULL 171s 171s > args(node.depth) 171s function (phy, method = 1) 171s NULL 171s 171s > args(node.height) 171s function (phy, clado.style = FALSE) 171s NULL 171s 171s > args(unrooted.xy) 171s function (Ntip, Nnode, edge, edge.length, nb.sp, rotate.tree) 171s NULL 171s 171s > args(phylogram.plot) 171s function (edge, Ntip, Nnode, xx, yy, horizontal, edge.color = NULL, 171s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 171s node.lty = NULL) 171s NULL 171s 171s > args(cladogram.plot) 171s function (edge, xx, yy, edge.color, edge.width, edge.lty) 171s NULL 171s 171s > args(circular.plot) 171s function (edge, Ntip, Nnode, xx, yy, theta, r, edge.color, edge.width, 171s edge.lty) 171s NULL 171s 171s > args(plot.phylo) 171s function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL, 171s show.tip.label = TRUE, show.node.label = FALSE, edge.color = NULL, 171s edge.width = NULL, edge.lty = NULL, node.color = NULL, node.width = NULL, 171s node.lty = NULL, font = 3, cex = par("cex"), adj = NULL, 171s srt = 0, no.margin = FALSE, root.edge = FALSE, label.offset = 0, 171s underscore = FALSE, x.lim = NULL, y.lim = NULL, direction = "rightwards", 171s lab4ut = NULL, tip.color = par("col"), plot = TRUE, rotate.tree = 0, 171s open.angle = 0, node.depth = 1, align.tip.label = FALSE, 171s ...) 171s NULL 171s 171s > geo <- factor(c("Africa", "World", "Africa")) 171s 171s > (mycol <- c("blue", "red")[geo]) 171s [1] "blue" "red" "blue" 171s 171s > plot(mytr, tip.color = mycol) 171s 171s > par(xpd = TRUE) 171s 171s > plot(mytr, tip.color = mycol, cex = c(1, 1, 1.5)) 171s 171s > args(def) 171s function (x, ..., default = NULL, regexp = FALSE) 171s NULL 171s 171s > mycol2 <- def(mytr$tip.label, Homo = "red", default = "blue") 171s 171s > identical(mycol, mycol2) 171s [1] TRUE 171s 171s > (i <- which.edge(mytr, c("Homo", "Pan"))) 171s [1] 2 3 171s 171s > co <- rep("black", Nedge(mytr)) 171s 171s > co[i] <- "blue" 171s 171s > par(xpd = TRUE) 171s 171s > plot(mytr, edge.col = co) 171s 171s > edgelabels() 171s 171s > args(axisPhylo) 171s function (side = NULL, root.time = NULL, backward = TRUE, ...) 171s NULL 171s 171s > args(add.scale.bar) 171s function (x, y, length = NULL, ask = FALSE, lwd = 1, lcol = "black", 171s ...) 171s NULL 171s 171s > plot(mytr) 171s 171s > add.scale.bar() 171s 171s > axisPhylo() 171s 171s > axis(3) 171s 171s > args(nodelabels) 171s function (text, node, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 171s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 171s bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, 171s ...) 171s NULL 171s 171s > args(tiplabels) 171s function (text, tip, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 171s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 171s bg = "yellow", horiz = FALSE, width = NULL, height = NULL, 171s offset = 0, ...) 171s NULL 171s 171s > args(edgelabels) 171s function (text, edge, adj = c(0.5, 0.5), frame = "rect", pch = NULL, 171s thermo = NULL, pie = NULL, piecol = NULL, col = "black", 171s bg = "lightgreen", horiz = FALSE, width = NULL, height = NULL, 171s date = NULL, ...) 171s NULL 171s 171s > par(xpd = TRUE) 171s 171s > plot(mytr) 171s 171s > nodelabels() 171s 171s > tiplabels() 171s 171s > edgelabels() 171s 171s > plot(rep(1:5, 5), rep(1:5, each = 5), pch = 1:25, 171s + xlim = c(1, 5.2), col = "blue", bg = "yellow", cex = 2) 171s 171s > text(rep(1:5, 5) + 0.2, rep(1:5, each = 5), 1:25) 171s 171s > v <- c(0, 0.5, 1) 171s 171s > layout(matrix(1:9, 3, 3)) 171s 171s > par(mar = c(3, 3, 3, 0), las = 1) 171s 171s > for (i in v) { 171s + for (j in v) { 171s + plot(0, 0, "n", main = paste0("adj = c(", i, ", ", j, 171s + ")")) 171s + abline(v = 0, h = .... [TRUNCATED] 171s 171s > plot(rep(0, 3), 0:2, "n", las = 1) 171s 171s > abline(v = 0, h = 0:2, lty = 3) 171s 171s > text(0, 0:2, mytr$tip.label, adj = -1) 171s 171s > text(0, 0:2, mytr$tip.label, adj = 2, font = 2) 171s 171s > args(phydataplot) 171s function (x, phy, style = "bars", offset = 1, scaling = 1, continuous = FALSE, 171s width = NULL, legend = "below", funcol = rainbow, ...) 171s NULL 171s 171s > args(ring) 171s function (x, phy, style = "ring", offset = 1, ...) 171s NULL 171s 171s > x <- matrix(1:6, 3, 10) 171s 171s > dimnames(x) <- list(c("Homo", "Gorilla", "Pan"), LETTERS[1:ncol(x)]) 171s 171s > x 171s A B C D E F G H I J 171s Homo 1 4 1 4 1 4 1 4 1 4 171s Gorilla 2 5 2 5 2 5 2 5 2 5 171s Pan 3 6 3 6 3 6 3 6 3 6 171s 171s > mytr$tip.label 171s [1] "Pan" "Homo" "Gorilla" 171s 171s > par(mar = c(10, 2, 5, 5)) 171s 171s > plot(mytr, x.lim = 30) 171s 171s > phydataplot(x, mytr, "m", border = "white", offset = 2, 171s + width = 1) 171s 171s > phydataplot(x, mytr, "m", border = "white", offset = 15, 171s + width = 1, continuous = 2) 171s 171s > n <- 100 171s 171s > p <- 3 171s 171s > set.seed(3) 171s 171s > tr <- rcoal(n) 171s 171s > x <- matrix(runif(p * n), n, p) 171s 171s > rownames(x) <- tr$tip.label 171s 171s > COL <- c("red", "green", "blue") 171s 171s > par(xpd = TRUE) 171s 171s > plot(tr, "f", x.lim = c(-5, 5), show.tip.label = FALSE, 171s + no.margin = TRUE) 171s 171s > for (j in 1:p) ring(x[, j], tr, offset = j - 1 + 0.1, 171s + 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)) 172s 172s > (pp <- get("last_plot.phylo", envir = .PlotPhyloEnv)) 172s $type 172s [1] "phylogram" 172s 172s $use.edge.length 172s [1] TRUE 172s 172s $node.pos 172s [1] 1 172s 172s $node.depth 172s [1] 1 172s 172s $show.tip.label 172s [1] TRUE 172s 172s $show.node.label 172s [1] FALSE 172s 172s $font 172s [1] 3 172s 172s $cex 172s [1] 0.83 172s 172s $adj 172s [1] 0 172s 172s $srt 172s [1] 0 172s 172s $no.margin 172s [1] FALSE 172s 172s $label.offset 172s [1] 0 172s 172s $x.lim 172s [1] 0.00000 3.13046 172s 172s $y.lim 172s [1] 1 5 172s 172s $direction 172s [1] "rightwards" 172s 172s $tip.color 172s [1] "black" 172s 172s $Ntip 172s [1] 5 172s 172s $Nnode 172s [1] 4 172s 172s $root.time 172s NULL 172s 172s $align.tip.label 172s [1] FALSE 172s 172s $edge 172s [,1] [,2] 172s [1,] 6 1 172s [2,] 6 7 172s [3,] 7 2 172s [4,] 7 8 172s [5,] 8 3 172s [6,] 8 9 172s [7,] 9 4 172s [8,] 9 5 172s 172s $xx 172s [1] 0.3967457 1.7260289 2.2158455 2.9728029 2.8310192 0.0000000 0.8134181 172s [8] 1.3631198 1.9857132 172s 172s $yy 172s [1] 1.0000 2.0000 3.0000 4.0000 5.0000 1.9375 2.8750 3.7500 4.5000 172s 172s 172s > layout(matrix(1:2, 2)) 172s 172s > plot(rtree(4)) 172s 172s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 172s 172s > x <- pp$xx[1] 172s 172s > y <- pp$yy[1] 172s 172s > (pu <- par("usr")) 172s [1] -0.06364557 1.65478492 0.88000000 4.12000000 172s 172s > (x - pu[1])/(pu[2] - pu[1]) 172s [1] 0.9349839 172s 172s > (y - pu[3])/(pu[4] - pu[3]) 172s [1] 0.03703704 172s 172s > pi <- par("pin") 172s 172s > mi <- par("mai") 172s 172s > xi1 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 172s 172s > yi1 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 172s 172s > plot(rtree(4)) 172s 172s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 172s 172s > x <- pp$xx[5] 172s 172s > y <- pp$yy[5] 172s 172s > pu <- par("usr") 172s 172s > pi <- par("pin") 172s 172s > mi <- par("mai") 172s 172s > xi2 <- (x - pu[1])/(pu[2] - pu[1]) * pi[1] + mi[2] 172s 172s > yi2 <- (y - pu[3])/(pu[4] - pu[3]) * pi[2] + mi[1] 172s 172s > yi1 <- yi1 + par("fin")[2] 172s 172s > di <- par("din") 172s 172s > layout(1) 172s 172s > par(new = TRUE, mai = rep(0, 4)) 172s 172s > plot(NA, type = "n", ann = FALSE, axes = FALSE, xlim = 0:1, 172s + ylim = 0:1, xaxs = "i", yaxs = "i") 172s 172s > fancyarrows(xi1/di[1], yi1/di[2], xi2/di[1], yi2/di[2], 172s + 1, lwd = 10, col = rgb(1, 0.5, 0, 0.5), type = "h") 172s 172s > foo <- function(phy1, phy2, from) { 172s + layout(matrix(1:2, 2)) 172s + plot(phy1, font = 1) 172s + pp <- get("last_plot.phylo", envir = .PlotPhyloEnv .... [TRUNCATED] 172s 172s > trb <- read.tree(text = "((Primates,Carnivora),Monotremata);") 172s 172s > par(xpd = TRUE) 172s 172s > foo(trb, mytr, "Primates") 172s 172s > plot(mytr, plot = FALSE) 172s 172s > pp <- get("last_plot.phylo", envir = .PlotPhyloEnv) 172s 172s > rect(pp$xx[5] - 0.1, pp$yy[1] - 0.1, pp$xx[1] + 2, 172s + pp$yy[2] + 0.1, col = "yellow", border = NA) 172s 172s > par(new = TRUE) 172s 172s > plot(mytr) 172s > 172s 172s R version 4.4.3 (2025-02-28) -- "Trophy Case" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > Stangle("MoranI.Rnw") 172s Writing to file MoranI.R 172s > source("MoranI.R", echo=TRUE) 172s 172s > options(width = 80, prompt = "> ") 172s 172s > body <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 172s 172s > longevity <- c(4.74493, 3.3322, 3.3673, 2.89037, 2.30259) 172s 172s > names(body) <- names(longevity) <- c("Homo", "Pongo", 172s + "Macaca", "Ateles", "Galago") 172s 172s > library(ape) 172s 172s > trnwk <- "((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62)" 172s 172s > trnwk[2] <- ":0.38,Galago:1.00);" 172s 172s > tr <- read.tree(text = trnwk) 172s 172s > plot(tr) 172s 172s > axisPhylo() 172s 172s > w <- 1/cophenetic(tr) 172s 172s > w 172s Homo Pongo Macaca Ateles Galago 172s Homo Inf 2.3809524 1.0204082 0.8064516 0.5 172s Pongo 2.3809524 Inf 1.0204082 0.8064516 0.5 172s Macaca 1.0204082 1.0204082 Inf 0.8064516 0.5 172s Ateles 0.8064516 0.8064516 0.8064516 Inf 0.5 172s Galago 0.5000000 0.5000000 0.5000000 0.5000000 Inf 172s 172s > diag(w) <- 0 172s 172s > Moran.I(body, w) 172s $observed 172s [1] -0.07312179 172s 172s $expected 172s [1] -0.25 172s 172s $sd 172s [1] 0.08910814 172s 172s $p.value 172s [1] 0.04714628 172s 172s 172s > Moran.I(body, w, alt = "greater") 172s $observed 172s [1] -0.07312179 172s 172s $expected 172s [1] -0.25 172s 172s $sd 172s [1] 0.08910814 172s 172s $p.value 172s [1] 0.02357314 172s 172s 172s > Moran.I(longevity, w) 172s $observed 172s [1] -0.1837739 172s 172s $expected 172s [1] -0.25 172s 172s $sd 172s [1] 0.09114549 172s 172s $p.value 172s [1] 0.4674727 172s 172s 172s > data(carnivora) 172s 172s > carnivora$log10SW <- log10(carnivora$SW) 172s 172s > carnivora$log10FW <- log10(carnivora$FW) 172s 172s > fm1.carn <- log10SW ~ Order/SuperFamily/Family/Genus 172s 172s > co1 <- correlogram.formula(fm1.carn, data = carnivora) 172s 172s > plot(co1) 172s 172s > fm2.carn <- log10SW + log10FW ~ Order/SuperFamily/Family/Genus 172s 172s > co2 <- correlogram.formula(fm2.carn, data = carnivora) 172s 172s > print(plot(co2)) 172s 172s > plot(co2, FALSE) 172s > 172s 172s R version 4.4.3 (2025-02-28) -- "Trophy Case" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > Stangle("RandomTopologies.Rnw") 172s Writing to file RandomTopologies.R 172s > source("RandomTopologies.R", echo=TRUE) 172s 172s > options(width = 80, prompt = "> ") 172s 172s > library(ape) 172s 172s > n <- 1:10 172s 172s > data.frame(N.topo = sapply(n, howmanytrees)) 172s N.topo 172s 1 1 172s 2 1 172s 3 3 172s 4 15 172s 5 105 172s 6 945 172s 7 10395 172s 8 135135 172s 9 2027025 172s 10 34459425 172s 172s > howmanytrees(25) 172s [1] 1.192568e+30 172s 172s > howmanytrees(25) * 0.21 172s [1] 2.504393e+29 172s 172s > data.frame(N.topo = sapply(n, howmanytrees, labeled = FALSE)) 172s N.topo 172s 1 1 172s 2 1 172s 3 1 172s 4 2 172s 5 3 172s 6 6 172s 7 11 172s 8 23 172s 9 46 172s 10 98 172s 172s > n2 <- c(50, 100, 200) 172s 172s > data.frame(N.topo = sapply(n2, howmanytrees, labeled = FALSE), 172s + row.names = n2) 172s N.topo 172s 50 5.150149e+16 172s 100 1.019560e+36 172s 200 1.141703e+75 172s 172s > 1/howmanytrees(50) 172s [1] 3.632505e-77 172s 172s > 1/sapply(n, howmanytrees) 172s [1] 1.000000e+00 1.000000e+00 3.333333e-01 6.666667e-02 9.523810e-03 172s [6] 1.058201e-03 9.620010e-05 7.400007e-06 4.933338e-07 2.901964e-08 172s 172s > 1/sapply(n, howmanytrees, labeled = FALSE) 172s [1] 1.00000000 1.00000000 1.00000000 0.50000000 0.33333333 0.16666667 172s [7] 0.09090909 0.04347826 0.02173913 0.01020408 172s 172s > library(phangorn) 174s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 174s code for methods in class "Rcpp_Fitch" was not checked for suspicious field assignments (recommended package 'codetools' not available?) 174s 174s > TR <- allTrees(4, rooted = TRUE) 174s 174s > TR 174s 15 phylogenetic trees 174s 174s > layout(matrix(1:15, 3, 5)) 174s 174s > par(mar = rep(1.5, 4), xpd = TRUE) 174s 174s > for (i in 1:15) plot(TR[[i]], "c", cex = 1.2, font = 1) 174s 174s > K <- 100 174s 174s > n <- 50 174s 174s > N <- howmanytrees(n, labeled = FALSE) 174s 174s > p <- 1/N 174s 174s > 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 174s [1] 0 174s 174s > 1 - dbinom(0, K, p) - dbinom(1, K, p) 174s [1] -5.431212e-17 174s 174s > f <- function(n, K) { 174s + N <- howmanytrees(n, labeled = FALSE) 174s + p <- 1/N 174s + 1 - (dbinom(0, K, p) + dbinom(1, K, p)) 174s + } 174s 174s > DF <- expand.grid(n = 4:20, K = c(2, 5, 10, 100, 1000, 174s + 10000)) 174s 174s > DF$P <- mapply(f, n = DF$n, K = DF$K) 174s 174s > library(lattice) 174s 174s > xyplot(P ~ n, DF, groups = K, panel = panel.superpose, 174s + type = "b", auto.key = list(x = 0.8, y = 0.9, title = "K")) 174s 174s > subset(DF, n == 20) 174s n K P 174s 17 20 2 1.160494e-11 174s 34 20 5 1.160491e-10 174s 51 20 10 5.222149e-10 174s 68 20 100 5.743191e-08 174s 85 20 1000 5.783570e-06 174s 102 20 10000 5.671842e-04 174s 174s > f(20, 1e+05) 174s [1] 0.04638755 174s 174s > f(30, 1e+06) 174s [1] 2.525152e-07 174s 174s > txt <- c("((,),((,),));", "(((,),(,)),);", "((((,),),),);") 174s 174s > TR5 <- read.tree(text = txt) 174s 174s > layout(matrix(1:3, 1)) 174s 174s > for (i in 1:3) plot(TR5[[i]], "c", cex = 1.2, main = LETTERS[i]) 174s 174s > howmanytrees(1, labeled = FALSE) * howmanytrees(4, 174s + labeled = FALSE) 174s [1] 2 174s 174s > howmanytrees(2, labeled = FALSE) * howmanytrees(3, 174s + labeled = FALSE) 174s [1] 1 174s 174s > howmanytrees(400, labeled = FALSE) * howmanytrees(403, 174s + labeled = FALSE) 174s [1] Inf 174s 174s > TR <- list(rmtopology(1000, 4, TRUE, br = NULL), rmtree(1000, 174s + 4, TRUE, br = NULL), rmtree(1000, 4, TRUE, br = NULL, equiprob = TRUE)) 174s 174s > foo.test <- function(x, labeled = TRUE) { 174s + uTR <- unique(x, use.tip.label = labeled) 174s + f <- integer(length(uTR)) 174s + for (j in seq_along( .... [TRUNCATED] 174s 174s > lapply(TR, foo.test) 177s [1] 59 70 82 61 67 56 77 66 66 61 57 80 64 68 66 180s [1] 62 53 116 114 51 59 60 48 57 123 60 49 58 44 46 182s [1] 169 51 49 46 53 31 162 166 51 37 49 30 35 39 32 182s [[1]] 182s 182s Chi-squared test for given probabilities 182s 182s data: f 182s X-squared = 13.07, df = 14, p-value = 0.521 182s 182s 182s [[2]] 182s 182s Chi-squared test for given probabilities 182s 182s data: f 182s X-squared = 153.29, df = 14, p-value < 2.2e-16 182s 182s 182s [[3]] 182s 182s Chi-squared test for given probabilities 182s 182s data: f 182s X-squared = 564.35, df = 14, p-value < 2.2e-16 182s 182s 182s 182s > lapply(TR, foo.test, labeled = FALSE) 183s [1] 184 816 184s [1] 647 353 184s [1] 497 503 184s [[1]] 184s 184s Chi-squared test for given probabilities 184s 184s data: f 184s X-squared = 399.42, df = 1, p-value < 2.2e-16 184s 184s 184s [[2]] 184s 184s Chi-squared test for given probabilities 184s 184s data: f 184s X-squared = 86.436, df = 1, p-value < 2.2e-16 184s 184s 184s [[3]] 184s 184s Chi-squared test for given probabilities 184s 184s data: f 184s X-squared = 0.036, df = 1, p-value = 0.8495 184s 184s 184s 184s > .Machine$double.xmax 184s [1] 1.797693e+308 184s 184s > howmanytrees(151) 184s [1] 3.753274e+306 184s 184s > howmanytrees(792, labeled = FALSE) 184s [1] 1.029038e+308 184s 184s > (N <- howmanytrees(2e+06)) 184s approximately 3.692364 * 10^12335524 184s 184s > N[2] + 1 184s n 184s 12335525 184s 184s > ceiling((N[2] + 1)/3000) 184s n 184s 4112 184s 184s > n <- 1:792 184s 184s > N <- howmanytrees(792, labeled = FALSE, detail = TRUE) 184s 184s > lN <- log10(N) 184s 184s > summary(lm(lN ~ n)) 184s 184s Call: 184s lm(formula = lN ~ n) 184s 184s Residuals: 184s Min 1Q Median 3Q Max 184s -0.25968 -0.21424 -0.08311 0.12406 2.82605 184s 184s Coefficients: 184s Estimate Std. Error t value Pr(>|t|) 184s (Intercept) -3.219e+00 2.258e-02 -142.5 <2e-16 *** 184s n 3.926e-01 4.934e-05 7956.3 <2e-16 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s 184s Residual standard error: 0.3175 on 790 degrees of freedom 184s Multiple R-squared: 1, Adjusted R-squared: 1 184s F-statistic: 6.33e+07 on 1 and 790 DF, p-value: < 2.2e-16 184s 184s 184s > s <- n > 700 184s 184s > summary(lm(lN[s] ~ n[s])) 184s 184s Call: 184s lm(formula = lN[s] ~ n[s]) 184s 184s Residuals: 184s Min 1Q Median 3Q Max 184s -0.0004133 -0.0003323 -0.0001032 0.0002834 0.0008197 184s 184s Coefficients: 184s Estimate Std. Error t value Pr(>|t|) 184s (Intercept) -4.153e+00 1.096e-03 -3788 <2e-16 *** 184s n[s] 3.941e-01 1.468e-06 268567 <2e-16 *** 184s --- 184s Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 184s 184s Residual standard error: 0.0003738 on 90 degrees of freedom 184s Multiple R-squared: 1, Adjusted R-squared: 1 184s F-statistic: 7.213e+10 on 1 and 90 DF, p-value: < 2.2e-16 184s 184s 184s > n <- 788:792 184s 184s > log10(sapply(n, howmanytrees, labeled = FALSE)) 184s [1] 306.4356 306.8298 307.2240 307.6182 308.0124 184s 184s > 0.3941 * n - 4.153 184s [1] 306.3978 306.7919 307.1860 307.5801 307.9742 184s 184s > xi <- 2.477993 184s 184s > lxi <- log10(xi) 184s 184s > n <- 1000 184s 184s > (n - 1) * lxi 184s [1] 393.706 184s 184s > for (k in 2:11) print((n - k) * lxi + log10(sum(xi^(0:(k - 184s + 1))))) 184s [1] 393.8532 184s [1] 393.9009 184s [1] 393.9187 184s [1] 393.9257 184s [1] 393.9285 184s [1] 393.9296 184s [1] 393.9301 184s [1] 393.9303 184s [1] 393.9304 184s [1] 393.9304 184s > 184s autopkgtest [22:05:36]: test run-unit-test: -----------------------] 185s autopkgtest [22:05:37]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 185s run-unit-test PASS 185s autopkgtest [22:05:37]: test pkg-r-autopkgtest: preparing testbed 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 186s Starting pkgProblemResolver with broken count: 0 186s Starting 2 pkgProblemResolver with broken count: 0 186s Done 186s The following NEW packages will be installed: 186s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 186s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 186s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 186s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 186s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 186s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 186s libjpeg-turbo8-dev libjpeg8-dev libjs-jquery liblapack-dev liblsan0 186s liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev 186s libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 libreadline-dev 186s libstdc++-14-dev libtirpc-dev libtsan2 libubsan1 node-html5shiv 186s pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev r-cran-expm r-cran-gee 186s r-cran-xml2 zlib1g-dev 186s 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 186s Need to get 104 MB of archives. 186s After this operation, 365 MB of additional disk space will be used. 186s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 186s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 186s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 186s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 186s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 186s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 186s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 186s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 186s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 186s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 186s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 186s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 186s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 186s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 186s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 186s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 187s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 187s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 187s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 187s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 187s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 187s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 187s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 187s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 187s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 187s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 187s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 187s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 187s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 187s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 187s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 187s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 187s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 187s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 187s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 187s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 187s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 187s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 187s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 187s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 187s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 187s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 187s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 187s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 187s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 187s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 187s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 187s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 187s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 187s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 187s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-html5shiv all 3.7.3+dfsg-5 [13.5 kB] 187s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 187s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 187s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 187s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 187s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 187s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 187s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-expm amd64 1.0-0-1 [226 kB] 187s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-gee amd64 4.13-29-1 [84.2 kB] 187s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xml2 amd64 1.3.7-1 [334 kB] 187s Fetched 104 MB in 1s (97.8 MB/s) 188s Selecting previously unselected package libisl23:amd64. 188s (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 ... 82075 files and directories currently installed.) 188s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 188s Unpacking libisl23:amd64 (0.27-1) ... 188s Selecting previously unselected package libmpc3:amd64. 188s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 188s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 188s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 188s Preparing to unpack .../02-cpp-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 188s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 188s Selecting previously unselected package cpp-14. 188s Preparing to unpack .../03-cpp-14_14.2.0-17ubuntu3_amd64.deb ... 188s Unpacking cpp-14 (14.2.0-17ubuntu3) ... 188s Selecting previously unselected package cpp-x86-64-linux-gnu. 188s Preparing to unpack .../04-cpp-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 188s Unpacking cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 188s Selecting previously unselected package cpp. 188s Preparing to unpack .../05-cpp_4%3a14.2.0-1ubuntu1_amd64.deb ... 188s Unpacking cpp (4:14.2.0-1ubuntu1) ... 188s Selecting previously unselected package libcc1-0:amd64. 188s Preparing to unpack .../06-libcc1-0_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libcc1-0:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libitm1:amd64. 188s Preparing to unpack .../07-libitm1_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libitm1:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libasan8:amd64. 188s Preparing to unpack .../08-libasan8_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libasan8:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package liblsan0:amd64. 188s Preparing to unpack .../09-liblsan0_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking liblsan0:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libtsan2:amd64. 188s Preparing to unpack .../10-libtsan2_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libtsan2:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libubsan1:amd64. 188s Preparing to unpack .../11-libubsan1_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libubsan1:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libhwasan0:amd64. 188s Preparing to unpack .../12-libhwasan0_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libhwasan0:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libquadmath0:amd64. 188s Preparing to unpack .../13-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 188s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 188s Selecting previously unselected package libgcc-14-dev:amd64. 188s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 188s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 189s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 189s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package gcc-14. 189s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 189s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package gcc-x86-64-linux-gnu. 189s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 189s Unpacking gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 189s Selecting previously unselected package gcc. 189s Preparing to unpack .../18-gcc_4%3a14.2.0-1ubuntu1_amd64.deb ... 189s Unpacking gcc (4:14.2.0-1ubuntu1) ... 189s Selecting previously unselected package libstdc++-14-dev:amd64. 189s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-17ubuntu3_amd64.deb ... 189s Unpacking libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package g++-14-x86-64-linux-gnu. 189s Preparing to unpack .../20-g++-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 189s Unpacking g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package g++-14. 189s Preparing to unpack .../21-g++-14_14.2.0-17ubuntu3_amd64.deb ... 189s Unpacking g++-14 (14.2.0-17ubuntu3) ... 189s Selecting previously unselected package g++-x86-64-linux-gnu. 189s Preparing to unpack .../22-g++-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 189s Unpacking g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 189s Selecting previously unselected package g++. 189s Preparing to unpack .../23-g++_4%3a14.2.0-1ubuntu1_amd64.deb ... 189s Unpacking g++ (4:14.2.0-1ubuntu1) ... 189s Selecting previously unselected package build-essential. 189s Preparing to unpack .../24-build-essential_12.10ubuntu1_amd64.deb ... 189s Unpacking build-essential (12.10ubuntu1) ... 190s Selecting previously unselected package dctrl-tools. 190s Preparing to unpack .../25-dctrl-tools_2.24-3build3_amd64.deb ... 190s Unpacking dctrl-tools (2.24-3build3) ... 190s Selecting previously unselected package libgfortran-14-dev:amd64. 190s Preparing to unpack .../26-libgfortran-14-dev_14.2.0-17ubuntu3_amd64.deb ... 190s Unpacking libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 190s Selecting previously unselected package gfortran-14-x86-64-linux-gnu. 190s Preparing to unpack .../27-gfortran-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 190s Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 190s Selecting previously unselected package gfortran-14. 190s Preparing to unpack .../28-gfortran-14_14.2.0-17ubuntu3_amd64.deb ... 190s Unpacking gfortran-14 (14.2.0-17ubuntu3) ... 190s Selecting previously unselected package gfortran-x86-64-linux-gnu. 190s Preparing to unpack .../29-gfortran-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 190s Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 190s Selecting previously unselected package gfortran. 190s Preparing to unpack .../30-gfortran_4%3a14.2.0-1ubuntu1_amd64.deb ... 190s Unpacking gfortran (4:14.2.0-1ubuntu1) ... 190s Selecting previously unselected package icu-devtools. 190s Preparing to unpack .../31-icu-devtools_76.1-1ubuntu2_amd64.deb ... 190s Unpacking icu-devtools (76.1-1ubuntu2) ... 190s Selecting previously unselected package libblas-dev:amd64. 190s Preparing to unpack .../32-libblas-dev_3.12.1-2_amd64.deb ... 190s Unpacking libblas-dev:amd64 (3.12.1-2) ... 190s Selecting previously unselected package libbz2-dev:amd64. 190s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 190s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 190s Selecting previously unselected package libdeflate-dev:amd64. 190s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 190s Unpacking libdeflate-dev:amd64 (1.23-1) ... 190s Selecting previously unselected package libicu-dev:amd64. 190s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 190s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 190s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 190s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 190s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 190s Selecting previously unselected package libjpeg8-dev:amd64. 190s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 190s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 190s Selecting previously unselected package libjpeg-dev:amd64. 190s Preparing to unpack .../38-libjpeg-dev_8c-2ubuntu11_amd64.deb ... 190s Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... 190s Selecting previously unselected package libjs-jquery. 190s Preparing to unpack .../39-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 190s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 191s Selecting previously unselected package liblapack-dev:amd64. 191s Preparing to unpack .../40-liblapack-dev_3.12.1-2_amd64.deb ... 191s Unpacking liblapack-dev:amd64 (3.12.1-2) ... 191s Selecting previously unselected package libncurses-dev:amd64. 191s Preparing to unpack .../41-libncurses-dev_6.5+20250216-2_amd64.deb ... 191s Unpacking libncurses-dev:amd64 (6.5+20250216-2) ... 191s Selecting previously unselected package libpcre2-16-0:amd64. 191s Preparing to unpack .../42-libpcre2-16-0_10.45-1_amd64.deb ... 191s Unpacking libpcre2-16-0:amd64 (10.45-1) ... 191s Selecting previously unselected package libpcre2-32-0:amd64. 191s Preparing to unpack .../43-libpcre2-32-0_10.45-1_amd64.deb ... 191s Unpacking libpcre2-32-0:amd64 (10.45-1) ... 191s Selecting previously unselected package libpcre2-posix3:amd64. 191s Preparing to unpack .../44-libpcre2-posix3_10.45-1_amd64.deb ... 191s Unpacking libpcre2-posix3:amd64 (10.45-1) ... 191s Selecting previously unselected package libpcre2-dev:amd64. 191s Preparing to unpack .../45-libpcre2-dev_10.45-1_amd64.deb ... 191s Unpacking libpcre2-dev:amd64 (10.45-1) ... 191s Selecting previously unselected package libpkgconf3:amd64. 191s Preparing to unpack .../46-libpkgconf3_1.8.1-4_amd64.deb ... 191s Unpacking libpkgconf3:amd64 (1.8.1-4) ... 191s Selecting previously unselected package zlib1g-dev:amd64. 191s Preparing to unpack .../47-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_amd64.deb ... 191s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 191s Selecting previously unselected package libpng-dev:amd64. 191s Preparing to unpack .../48-libpng-dev_1.6.47-1_amd64.deb ... 191s Unpacking libpng-dev:amd64 (1.6.47-1) ... 191s Selecting previously unselected package libreadline-dev:amd64. 191s Preparing to unpack .../49-libreadline-dev_8.2-6_amd64.deb ... 191s Unpacking libreadline-dev:amd64 (8.2-6) ... 191s Selecting previously unselected package node-html5shiv. 191s Preparing to unpack .../50-node-html5shiv_3.7.3+dfsg-5_all.deb ... 191s Unpacking node-html5shiv (3.7.3+dfsg-5) ... 191s Selecting previously unselected package liblzma-dev:amd64. 191s Preparing to unpack .../51-liblzma-dev_5.6.4-1_amd64.deb ... 191s Unpacking liblzma-dev:amd64 (5.6.4-1) ... 191s Selecting previously unselected package pkgconf-bin. 191s Preparing to unpack .../52-pkgconf-bin_1.8.1-4_amd64.deb ... 191s Unpacking pkgconf-bin (1.8.1-4) ... 191s Selecting previously unselected package pkgconf:amd64. 191s Preparing to unpack .../53-pkgconf_1.8.1-4_amd64.deb ... 191s Unpacking pkgconf:amd64 (1.8.1-4) ... 191s Selecting previously unselected package libtirpc-dev:amd64. 191s Preparing to unpack .../54-libtirpc-dev_1.3.4+ds-1.3_amd64.deb ... 191s Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 191s Selecting previously unselected package r-base-dev. 191s Preparing to unpack .../55-r-base-dev_4.4.3-1_all.deb ... 191s Unpacking r-base-dev (4.4.3-1) ... 191s Selecting previously unselected package pkg-r-autopkgtest. 191s Preparing to unpack .../56-pkg-r-autopkgtest_20231212ubuntu1_all.deb ... 191s Unpacking pkg-r-autopkgtest (20231212ubuntu1) ... 191s Selecting previously unselected package r-cran-expm. 191s Preparing to unpack .../57-r-cran-expm_1.0-0-1_amd64.deb ... 191s Unpacking r-cran-expm (1.0-0-1) ... 191s Selecting previously unselected package r-cran-gee. 191s Preparing to unpack .../58-r-cran-gee_4.13-29-1_amd64.deb ... 191s Unpacking r-cran-gee (4.13-29-1) ... 191s Selecting previously unselected package r-cran-xml2. 191s Preparing to unpack .../59-r-cran-xml2_1.3.7-1_amd64.deb ... 191s Unpacking r-cran-xml2 (1.3.7-1) ... 191s Setting up libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 191s Setting up libncurses-dev:amd64 (6.5+20250216-2) ... 191s Setting up node-html5shiv (3.7.3+dfsg-5) ... 191s Setting up r-cran-expm (1.0-0-1) ... 191s Setting up libreadline-dev:amd64 (8.2-6) ... 191s Setting up libpcre2-16-0:amd64 (10.45-1) ... 191s Setting up libpcre2-32-0:amd64 (10.45-1) ... 191s Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ... 191s Setting up libpkgconf3:amd64 (1.8.1-4) ... 191s Setting up libquadmath0:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libmpc3:amd64 (1.3.1-1build2) ... 191s Setting up icu-devtools (76.1-1ubuntu2) ... 191s Setting up pkgconf-bin (1.8.1-4) ... 191s Setting up liblzma-dev:amd64 (5.6.4-1) ... 191s Setting up libubsan1:amd64 (15-20250222-0ubuntu1) ... 191s Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu1) ... 191s Setting up libpcre2-posix3:amd64 (10.45-1) ... 191s Setting up libhwasan0:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libasan8:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libtsan2:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 191s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 191s Setting up r-cran-gee (4.13-29-1) ... 191s Setting up libisl23:amd64 (0.27-1) ... 191s Setting up libdeflate-dev:amd64 (1.23-1) ... 191s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 191s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ... 191s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libblas-dev:amd64 (3.12.1-2) ... 191s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode 191s Setting up dctrl-tools (2.24-3build3) ... 191s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ... 191s Setting up libbz2-dev:amd64 (1.0.8-6) ... 191s Setting up libpcre2-dev:amd64 (10.45-1) ... 191s Setting up r-cran-xml2 (1.3.7-1) ... 191s Setting up libpng-dev:amd64 (1.6.47-1) ... 191s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 191s Setting up pkgconf:amd64 (1.8.1-4) ... 191s Setting up liblapack-dev:amd64 (3.12.1-2) ... 191s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode 191s Setting up cpp-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 191s Setting up cpp-14 (14.2.0-17ubuntu3) ... 191s Setting up libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 191s Setting up libstdc++-14-dev:amd64 (14.2.0-17ubuntu3) ... 191s Setting up cpp-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 191s Setting up libgfortran-14-dev:amd64 (14.2.0-17ubuntu3) ... 191s Setting up cpp (4:14.2.0-1ubuntu1) ... 191s Setting up gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 191s Setting up gcc-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 191s Setting up gcc-14 (14.2.0-17ubuntu3) ... 191s Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 191s Setting up g++-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 191s Setting up g++-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 191s Setting up g++-14 (14.2.0-17ubuntu3) ... 191s Setting up gfortran-14 (14.2.0-17ubuntu3) ... 191s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 191s Setting up gcc (4:14.2.0-1ubuntu1) ... 192s Setting up g++ (4:14.2.0-1ubuntu1) ... 192s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 192s Setting up build-essential (12.10ubuntu1) ... 192s Setting up gfortran (4:14.2.0-1ubuntu1) ... 192s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 192s update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist 192s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 192s 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 192s Setting up r-base-dev (4.4.3-1) ... 192s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 192s Processing triggers for libc-bin (2.41-1ubuntu2) ... 192s Processing triggers for man-db (2.13.0-1) ... 193s Processing triggers for install-info (7.1.1-1) ... 193s autopkgtest [22:05:45]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 193s autopkgtest [22:05:45]: test pkg-r-autopkgtest: [----------------------- 193s Test: Try to load the R library ape 194s 194s R version 4.4.3 (2025-02-28) -- "Trophy Case" 194s Copyright (C) 2025 The R Foundation for Statistical Computing 194s Platform: x86_64-pc-linux-gnu 194s 194s R is free software and comes with ABSOLUTELY NO WARRANTY. 194s You are welcome to redistribute it under certain conditions. 194s Type 'license()' or 'licence()' for distribution details. 194s 194s R is a collaborative project with many contributors. 194s Type 'contributors()' for more information and 194s 'citation()' on how to cite R or R packages in publications. 194s 194s Type 'demo()' for some demos, 'help()' for on-line help, or 194s 'help.start()' for an HTML browser interface to help. 194s Type 'q()' to quit R. 194s 194s > library('ape') 194s > 194s > 194s Other tests are currently unsupported! 194s They will be progressively added. 194s autopkgtest [22:05:46]: test pkg-r-autopkgtest: -----------------------] 194s autopkgtest [22:05:46]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 194s pkg-r-autopkgtest PASS 195s autopkgtest [22:05:47]: @@@@@@@@@@@@@@@@@@@@ summary 195s run-unit-test PASS 195s pkg-r-autopkgtest PASS 211s nova [W] Skipping flock for amd64 211s Creating nova instance adt-plucky-amd64-r-cran-ape-20250315-220232-juju-7f2275-prod-proposed-migration-environment-2-c4e0bceb-0c8b-4609-9ce6-517bbd795cd0 from image adt/ubuntu-plucky-amd64-server-20250306.img (UUID 60d877d7-b74c-4f24-920d-f4570db0a338)... 211s nova [W] Timed out waiting for b6e69dfb-8448-43d9-afc4-390383504926 to get deleted.