0s autopkgtest [22:39:33]: starting date and time: 2025-03-15 22:39:33+0000 0s autopkgtest [22:39:33]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:39:33]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k8g33tp4/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-vegan --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 builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-22.secgroup --name adt-plucky-amd64-r-cran-vegan-20250315-223933-juju-7f2275-prod-proposed-migration-environment-20-44daef2f-ad81-4693-9c9d-c5f5e1cf7059 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -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/ 47s autopkgtest [22:40:20]: testbed dpkg architecture: amd64 47s autopkgtest [22:40:20]: testbed apt version: 2.9.31ubuntu1 47s autopkgtest [22:40:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [22:40:20]: testbed release detected to be: None 48s autopkgtest [22:40:21]: updating testbed package index (apt update) 49s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 49s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 49s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB] 49s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB] 49s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [44.1 kB] 49s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [67.4 kB] 49s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [85.7 kB] 49s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 c-n-f Metadata [1852 B] 49s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 c-n-f Metadata [116 B] 49s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [342 kB] 49s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [174 kB] 49s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 c-n-f Metadata [15.3 kB] 49s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [16.1 kB] 49s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [8544 B] 49s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 c-n-f Metadata [628 B] 50s Fetched 1265 kB in 1s (1238 kB/s) 51s Reading package lists... 51s Reading package lists... 51s Building dependency tree... 51s 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 53s The following packages will be upgraded: 53s apparmor apt apt-utils binutils binutils-common binutils-x86-64-linux-gnu 53s cloud-init cloud-init-base curl dosfstools exfatprogs fwupd gcc-15-base 53s gir1.2-girepository-2.0 gir1.2-glib-2.0 htop hwdata initramfs-tools 53s initramfs-tools-bin initramfs-tools-core libapparmor1 libapt-pkg7.0 53s libassuan9 libatomic1 libaudit-common libaudit1 libbinutils libbrotli1 53s libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libctf-nobfd0 libctf0 53s libcurl3t64-gnutls libcurl4t64 libestr0 libftdi1-2 libfwupd3 libgcc-s1 53s libgirepository-1.0-1 libglib2.0-0t64 libglib2.0-data libgpgme11t64 53s libgprofng0 libjemalloc2 liblz4-1 liblzma5 libmm-glib0 libncurses6 53s libncursesw6 libnewt0.52 libnl-3-200 libnl-genl-3-200 libnl-route-3-200 53s libnss-systemd libpam-systemd libparted2t64 libpci3 libpython3-stdlib 53s libpython3.13 libpython3.13-minimal libpython3.13-stdlib libseccomp2 53s libselinux1 libsemanage-common libsemanage2 libsframe1 libsqlite3-0 53s libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libxml2 53s linux-firmware linux-generic linux-headers-generic linux-headers-virtual 53s linux-image-generic linux-image-virtual linux-libc-dev linux-tools-common 53s linux-virtual locales media-types ncurses-base ncurses-bin ncurses-term 53s parted pci.ids pciutils pinentry-curses python-apt-common python3 53s python3-apt python3-bcrypt python3-cffi-backend python3-dbus python3-gi 53s python3-jinja2 python3-lazr.uri python3-markupsafe python3-minimal 53s python3-newt python3-rpds-py python3-systemd python3-yaml python3.13 53s python3.13-gdbm python3.13-minimal rsync rsyslog strace systemd 53s systemd-cryptsetup systemd-resolved systemd-sysv systemd-timesyncd 53s ubuntu-kernel-accessories ubuntu-minimal ubuntu-standard udev whiptail 53s xz-utils 53s 126 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 53s Need to get 829 MB of archives. 53s After this operation, 325 MB of additional disk space will be used. 53s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-bin amd64 6.5+20250216-2 [194 kB] 53s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 53s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 54s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 56s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 57s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 57s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-libc-dev amd64 6.14.0-10.10 [1723 kB] 58s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libatomic1 amd64 15-20250222-0ubuntu1 [10.4 kB] 58s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-15-base amd64 15-20250222-0ubuntu1 [53.4 kB] 58s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-s1 amd64 15-20250222-0ubuntu1 [77.8 kB] 58s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++6 amd64 15-20250222-0ubuntu1 [798 kB] 58s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-base all 6.5+20250216-2 [25.9 kB] 58s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 ncurses-term all 6.5+20250216-2 [276 kB] 58s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblz4-1 amd64 1.10.0-4 [66.4 kB] 58s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.4-1 [157 kB] 58s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd0 amd64 257.3-1ubuntu3 [595 kB] 59s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libnss-systemd amd64 257.3-1ubuntu3 [199 kB] 59s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-sysv amd64 257.3-1ubuntu3 [11.9 kB] 59s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-resolved amd64 257.3-1ubuntu3 [345 kB] 59s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-systemd amd64 257.3-1ubuntu3 [302 kB] 59s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libsystemd-shared amd64 257.3-1ubuntu3 [2371 kB] 60s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd amd64 257.3-1ubuntu3 [3052 kB] 61s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-timesyncd amd64 257.3-1ubuntu3 [42.1 kB] 61s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 systemd-cryptsetup amd64 257.3-1ubuntu3 [124 kB] 61s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 udev amd64 257.3-1ubuntu3 [1404 kB] 61s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libudev1 amd64 257.3-1ubuntu3 [215 kB] 61s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu2 [6628 B] 61s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 libcap-ng0 amd64 0.8.5-4build1 [15.6 kB] 61s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu2 [54.0 kB] 61s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libseccomp2 amd64 2.5.5-1ubuntu6 [53.5 kB] 62s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu3 [87.3 kB] 62s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libapparmor1 amd64 4.1.0~beta5-0ubuntu8 [55.0 kB] 62s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.33 [1138 kB] 62s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.33 [1439 kB] 62s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.33 [222 kB] 62s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-minimal amd64 3.13.2-2 [27.7 kB] 62s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 python3 amd64 3.13.2-2 [24.0 kB] 62s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13 amd64 3.13.2-2 [2341 kB] 63s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 media-types all 13.0.0 [29.9 kB] 63s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses6 amd64 6.5+20250216-2 [126 kB] 63s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncursesw6 amd64 6.5+20250216-2 [165 kB] 63s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtinfo6 amd64 6.5+20250216-2 [119 kB] 63s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libsqlite3-0 amd64 3.46.1-2 [715 kB] 63s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.2-2 [735 kB] 63s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.2-2 [2365 kB] 64s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.2-2 [883 kB] 64s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [2066 kB] 65s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.4 kB] 65s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 rsync amd64 3.4.1+ds1-3 [482 kB] 65s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod-common all 0.192-4 [15.4 kB] 65s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2.1build1 [7268 B] 65s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2.1build1 [106 kB] 65s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libassuan9 amd64 3.0.2-2 [43.1 kB] 65s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.83.4-1 [25.3 kB] 65s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.84.0-1 [184 kB] 65s Get:56 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.84.0-1 [1669 kB] 66s Get:57 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.83.4-1 [89.5 kB] 66s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libestr0 amd64 0.1.11-2 [8340 B] 66s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.84.0-1 [53.0 kB] 66s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-newt amd64 0.52.24-4ubuntu2 [21.1 kB] 66s Get:61 http://ftpmaster.internal/ubuntu plucky/main amd64 libnewt0.52 amd64 0.52.24-4ubuntu2 [55.7 kB] 66s Get:62 http://ftpmaster.internal/ubuntu plucky/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2ubuntu5 [772 kB] 66s Get:63 http://ftpmaster.internal/ubuntu plucky/main amd64 python-apt-common all 2.9.9build1 [21.3 kB] 66s Get:64 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-apt amd64 2.9.9build1 [172 kB] 66s Get:65 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-cffi-backend amd64 1.17.1-2build2 [96.6 kB] 66s Get:66 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dbus amd64 1.3.2-5build5 [102 kB] 66s Get:67 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-gi amd64 3.50.0-4build1 [252 kB] 66s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-yaml amd64 6.0.2-1build2 [144 kB] 66s Get:69 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu2 [555 kB] 66s Get:70 http://ftpmaster.internal/ubuntu plucky/main amd64 whiptail amd64 0.52.24-4ubuntu2 [19.1 kB] 66s Get:71 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-minimal amd64 1.549 [11.5 kB] 66s Get:72 http://ftpmaster.internal/ubuntu plucky/main amd64 apparmor amd64 4.1.0~beta5-0ubuntu8 [701 kB] 66s Get:73 http://ftpmaster.internal/ubuntu plucky/main amd64 dosfstools amd64 4.2-1.2 [95.0 kB] 66s Get:74 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-genl-3-200 amd64 3.7.0-1 [12.2 kB] 66s Get:75 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-route-3-200 amd64 3.7.0-1 [191 kB] 66s Get:76 http://ftpmaster.internal/ubuntu plucky/main amd64 libnl-3-200 amd64 3.7.0-1 [64.9 kB] 66s Get:77 http://ftpmaster.internal/ubuntu plucky/main amd64 parted amd64 3.6-5 [53.9 kB] 66s Get:78 http://ftpmaster.internal/ubuntu plucky/main amd64 libparted2t64 amd64 3.6-5 [158 kB] 66s Get:79 http://ftpmaster.internal/ubuntu plucky/main amd64 pci.ids all 0.0~2025.03.09-1 [285 kB] 66s Get:80 http://ftpmaster.internal/ubuntu plucky/main amd64 pciutils amd64 1:3.13.0-2 [110 kB] 66s Get:81 http://ftpmaster.internal/ubuntu plucky/main amd64 libpci3 amd64 1:3.13.0-2 [39.8 kB] 66s Get:82 http://ftpmaster.internal/ubuntu plucky/main amd64 strace amd64 6.13+ds-1ubuntu1 [622 kB] 66s Get:83 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.4-1 [278 kB] 67s Get:84 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-standard amd64 1.549 [11.5 kB] 67s Get:85 http://ftpmaster.internal/ubuntu plucky/main amd64 libgprofng0 amd64 2.44-3ubuntu1 [886 kB] 67s Get:86 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf0 amd64 2.44-3ubuntu1 [96.5 kB] 67s Get:87 http://ftpmaster.internal/ubuntu plucky/main amd64 libctf-nobfd0 amd64 2.44-3ubuntu1 [98.9 kB] 67s Get:88 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-x86-64-linux-gnu amd64 2.44-3ubuntu1 [1108 kB] 67s Get:89 http://ftpmaster.internal/ubuntu plucky/main amd64 libbinutils amd64 2.44-3ubuntu1 [585 kB] 67s Get:90 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils amd64 2.44-3ubuntu1 [208 kB] 67s Get:91 http://ftpmaster.internal/ubuntu plucky/main amd64 binutils-common amd64 2.44-3ubuntu1 [215 kB] 67s Get:92 http://ftpmaster.internal/ubuntu plucky/main amd64 libsframe1 amd64 2.44-3ubuntu1 [14.8 kB] 67s Get:93 http://ftpmaster.internal/ubuntu plucky/main amd64 hwdata all 0.393-3 [1562 B] 67s Get:94 http://ftpmaster.internal/ubuntu plucky/main amd64 pnp.ids all 0.393-3 [29.5 kB] 67s Get:95 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-common all 6.14.0-10.10 [295 kB] 67s Get:96 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftool amd64 7.6.0+6.14.0-10.10 [1147 kB] 67s Get:97 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-markupsafe amd64 2.1.5-1build4 [13.4 kB] 67s Get:98 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 67s Get:99 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init-base all 25.1-0ubuntu3 [616 kB] 67s Get:100 http://ftpmaster.internal/ubuntu plucky/main amd64 libbrotli1 amd64 1.1.0-2build4 [365 kB] 67s Get:101 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.12.1-3ubuntu1 [258 kB] 68s Get:102 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.12.1-3ubuntu1 [437 kB] 68s Get:103 http://ftpmaster.internal/ubuntu plucky/main amd64 exfatprogs amd64 1.2.8-1 [76.3 kB] 68s Get:104 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.12.1-3ubuntu1 [432 kB] 68s Get:105 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd amd64 2.0.6-4 [5408 kB] 69s Get:106 http://ftpmaster.internal/ubuntu plucky/main amd64 libfwupd3 amd64 2.0.6-4 [136 kB] 69s Get:107 http://ftpmaster.internal/ubuntu plucky/main amd64 libmm-glib0 amd64 1.23.4-0ubuntu3 [251 kB] 70s Get:108 http://ftpmaster.internal/ubuntu plucky/main amd64 htop amd64 3.4.0-2 [195 kB] 70s Get:109 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-firmware amd64 20250310.git9e1370d3-0ubuntu1 [571 MB] 94s Get:110 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools all 0.146ubuntu1 [7920 B] 94s Get:111 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-core all 0.146ubuntu1 [51.9 kB] 94s Get:112 http://ftpmaster.internal/ubuntu plucky/main amd64 initramfs-tools-bin amd64 0.146ubuntu1 [26.2 kB] 94s Get:113 http://ftpmaster.internal/ubuntu plucky/main amd64 libdebuginfod1t64 amd64 0.192-4 [21.0 kB] 94s Get:114 http://ftpmaster.internal/ubuntu plucky/main amd64 libftdi1-2 amd64 1.5-8build1 [30.2 kB] 94s Get:115 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu2 [155 kB] 94s Get:116 http://ftpmaster.internal/ubuntu plucky/main amd64 libjemalloc2 amd64 5.3.0-3 [277 kB] 94s Get:117 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-6.14.0-10-generic amd64 6.14.0-10.10 [41.2 MB] 94s Get:118 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-6.14.0-10-generic amd64 6.14.0-10.10 [15.3 MB] 95s Get:119 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-modules-extra-6.14.0-10-generic amd64 6.14.0-10.10 [120 MB] 98s Get:120 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-generic amd64 6.14.0-10.10 [1730 B] 98s Get:121 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-generic amd64 6.14.0-10.10 [11.1 kB] 98s Get:122 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-virtual amd64 6.14.0-10.10 [1722 B] 98s Get:123 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-image-virtual amd64 6.14.0-10.10 [11.1 kB] 98s Get:124 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-virtual amd64 6.14.0-10.10 [1642 B] 98s Get:125 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10 all 6.14.0-10.10 [14.2 MB] 98s Get:126 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-6.14.0-10-generic amd64 6.14.0-10.10 [3915 kB] 99s Get:127 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-headers-generic amd64 6.14.0-10.10 [11.0 kB] 99s Get:128 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-perf amd64 6.14.0-10.10 [4122 kB] 99s Get:129 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10 amd64 6.14.0-10.10 [1394 kB] 99s Get:130 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-tools-6.14.0-10-generic amd64 6.14.0-10.10 [830 B] 99s Get:131 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-2ubuntu3 [42.3 kB] 99s Get:132 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-lazr.uri all 1.0.6-6 [13.7 kB] 99s Get:133 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu2 [278 kB] 99s Get:134 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-systemd amd64 235-1build6 [43.9 kB] 99s Get:135 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.2-2 [31.9 kB] 99s Get:136 http://ftpmaster.internal/ubuntu plucky/main amd64 ubuntu-kernel-accessories amd64 1.549 [11.2 kB] 99s Get:137 http://ftpmaster.internal/ubuntu plucky/main amd64 cloud-init all 25.1-0ubuntu3 [2100 B] 99s Get:138 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-bcrypt amd64 4.2.0-2.1build1 [221 kB] 99s Preconfiguring packages ... 100s Fetched 829 MB in 46s (17.9 MB/s) 100s (Reading database ... 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(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 ... 109140 files and directories currently installed.) 100s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 100s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 100s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 100s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 100s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 100s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 101s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 101s Checking for services that may need to be restarted... 101s Checking init scripts... 101s Checking for services that may need to be restarted... 101s Checking init scripts... 101s Stopping some services possibly affected by the upgrade (will be restarted later): 101s cron: stopping...done. 101s 101s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 101s Setting up libc6:amd64 (2.41-1ubuntu1) ... 101s Checking for services that may need to be restarted... 101s Checking init scripts... 101s Restarting services possibly affected by the upgrade: 101s cron: restarting...done. 101s 101s Services restarted successfully. 102s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 105s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu2_amd64.deb ... 105s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu2) over (1:4.0.2-2ubuntu1) ... 105s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu2) ... 105s (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 ... 109146 files and directories currently installed.) 105s Preparing to unpack .../libseccomp2_2.5.5-1ubuntu6_amd64.deb ... 105s Unpacking libseccomp2:amd64 (2.5.5-1ubuntu6) over (2.5.5-1ubuntu5) ... 105s Setting up libseccomp2:amd64 (2.5.5-1ubuntu6) ... 105s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 105s Preparing to unpack .../libapparmor1_4.1.0~beta5-0ubuntu8_amd64.deb ... 105s Unpacking libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) over (4.1.0~beta5-0ubuntu5) ... 105s Preparing to unpack .../libapt-pkg7.0_2.9.33_amd64.deb ... 105s Unpacking libapt-pkg7.0:amd64 (2.9.33) over (2.9.31ubuntu1) ... 106s Setting up libapt-pkg7.0:amd64 (2.9.33) ... 106s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 107s Preparing to unpack .../apt-utils_2.9.33_amd64.deb ... 107s Unpacking apt-utils (2.9.33) over (2.9.31ubuntu1) ... 107s Preparing to unpack .../python3-minimal_3.13.2-2_amd64.deb ... 107s Unpacking python3-minimal (3.13.2-2) over (3.13.2-1) ... 107s Setting up python3-minimal (3.13.2-2) ... 107s (Reading database ... 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(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 ... 109146 files and directories currently installed.) 107s Preparing to unpack .../0-libsqlite3-0_3.46.1-2_amd64.deb ... 107s Unpacking libsqlite3-0:amd64 (3.46.1-2) over (3.46.1-1) ... 107s Preparing to unpack .../1-python3.13_3.13.2-2_amd64.deb ... 107s Unpacking python3.13 (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../2-python3.13-minimal_3.13.2-2_amd64.deb ... 108s Unpacking python3.13-minimal (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../3-libpython3.13-minimal_3.13.2-2_amd64.deb ... 108s Unpacking libpython3.13-minimal:amd64 (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../4-libpython3.13-stdlib_3.13.2-2_amd64.deb ... 108s Unpacking libpython3.13-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../5-libpython3-stdlib_3.13.2-2_amd64.deb ... 108s Unpacking libpython3-stdlib:amd64 (3.13.2-2) over (3.13.2-1) ... 108s Preparing to unpack .../6-rsync_3.4.1+ds1-3_amd64.deb ... 108s Unpacking rsync (3.4.1+ds1-3) over (3.4.1-0syncable1) ... 108s Selecting previously unselected package libdebuginfod-common. 108s Preparing to unpack .../7-libdebuginfod-common_0.192-4_all.deb ... 108s Unpacking libdebuginfod-common (0.192-4) ... 108s Preparing to unpack .../8-libsemanage-common_3.7-2.1build1_all.deb ... 108s Unpacking libsemanage-common (3.7-2.1build1) over (3.7-2.1) ... 108s Setting up libsemanage-common (3.7-2.1build1) ... 108s (Reading database ... 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(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 ... 109155 files and directories currently installed.) 108s Preparing to unpack .../libassuan9_3.0.2-2_amd64.deb ... 108s Unpacking libassuan9:amd64 (3.0.2-2) over (3.0.1-2) ... 108s Setting up libassuan9:amd64 (3.0.2-2) ... 109s (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 ... 109155 files and directories currently installed.) 109s Preparing to unpack .../00-gir1.2-girepository-2.0_1.83.4-1_amd64.deb ... 109s Unpacking gir1.2-girepository-2.0:amd64 (1.83.4-1) over (1.82.0-4) ... 109s Preparing to unpack .../01-gir1.2-glib-2.0_2.84.0-1_amd64.deb ... 109s Unpacking gir1.2-glib-2.0:amd64 (2.84.0-1) over (2.83.5-1) ... 109s Preparing to unpack .../02-libglib2.0-0t64_2.84.0-1_amd64.deb ... 109s Unpacking libglib2.0-0t64:amd64 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.../23-parted_3.6-5_amd64.deb ... 111s Unpacking parted (3.6-5) over (3.6-4build1) ... 111s Preparing to unpack .../24-libparted2t64_3.6-5_amd64.deb ... 111s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 111s Adding 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 111s Unpacking libparted2t64:amd64 (3.6-5) over (3.6-4build1) ... 111s Preparing to unpack .../25-pci.ids_0.0~2025.03.09-1_all.deb ... 111s Unpacking pci.ids (0.0~2025.03.09-1) over (0.0~2025.02.12-1) ... 112s Preparing to unpack .../26-pciutils_1%3a3.13.0-2_amd64.deb ... 112s Unpacking pciutils (1:3.13.0-2) over (1:3.13.0-1) ... 112s Preparing to unpack .../27-libpci3_1%3a3.13.0-2_amd64.deb ... 112s Unpacking libpci3:amd64 (1:3.13.0-2) over (1:3.13.0-1) ... 112s Preparing to unpack .../28-strace_6.13+ds-1ubuntu1_amd64.deb ... 112s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 112s Preparing to unpack .../29-xz-utils_5.6.4-1_amd64.deb ... 112s Unpacking xz-utils (5.6.4-1) over (5.6.3-1) ... 112s Preparing to unpack .../30-ubuntu-standard_1.549_amd64.deb ... 112s Unpacking ubuntu-standard (1.549) over (1.548) ... 112s Preparing to unpack .../31-libgprofng0_2.44-3ubuntu1_amd64.deb ... 112s Unpacking libgprofng0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../32-libctf0_2.44-3ubuntu1_amd64.deb ... 112s Unpacking libctf0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../33-libctf-nobfd0_2.44-3ubuntu1_amd64.deb ... 112s Unpacking libctf-nobfd0:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../34-binutils-x86-64-linux-gnu_2.44-3ubuntu1_amd64.deb ... 112s Unpacking binutils-x86-64-linux-gnu (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../35-libbinutils_2.44-3ubuntu1_amd64.deb ... 112s Unpacking libbinutils:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../36-binutils_2.44-3ubuntu1_amd64.deb ... 112s Unpacking binutils (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../37-binutils-common_2.44-3ubuntu1_amd64.deb ... 112s Unpacking binutils-common:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../38-libsframe1_2.44-3ubuntu1_amd64.deb ... 112s Unpacking libsframe1:amd64 (2.44-3ubuntu1) over (2.44-2ubuntu1) ... 112s Preparing to unpack .../39-hwdata_0.393-3_all.deb ... 112s Unpacking hwdata (0.393-3) over (0.392-1) ... 112s Selecting previously unselected package pnp.ids. 112s Preparing to unpack .../40-pnp.ids_0.393-3_all.deb ... 112s Unpacking pnp.ids (0.393-3) ... 112s Preparing to unpack .../41-linux-tools-common_6.14.0-10.10_all.deb ... 112s Unpacking linux-tools-common (6.14.0-10.10) over (6.12.0-16.16) ... 112s Selecting previously unselected package bpftool. 112s Preparing to unpack .../42-bpftool_7.6.0+6.14.0-10.10_amd64.deb ... 112s Unpacking bpftool (7.6.0+6.14.0-10.10) ... 112s Preparing to unpack .../43-python3-markupsafe_2.1.5-1build4_amd64.deb ... 112s Unpacking python3-markupsafe (2.1.5-1build4) over (2.1.5-1build3) ... 113s Preparing to unpack .../44-python3-jinja2_3.1.5-2ubuntu1_all.deb ... 113s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 113s Preparing to unpack .../45-cloud-init-base_25.1-0ubuntu3_all.deb ... 113s Unpacking cloud-init-base (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 113s Preparing to unpack .../46-libbrotli1_1.1.0-2build4_amd64.deb ... 113s Unpacking libbrotli1:amd64 (1.1.0-2build4) over (1.1.0-2build3) ... 113s Preparing to unpack .../47-curl_8.12.1-3ubuntu1_amd64.deb ... 113s Unpacking curl (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 113s Preparing to unpack .../48-libcurl4t64_8.12.1-3ubuntu1_amd64.deb ... 113s Unpacking libcurl4t64:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 113s Preparing to unpack .../49-exfatprogs_1.2.8-1_amd64.deb ... 113s Unpacking exfatprogs (1.2.8-1) over (1.2.7-3) ... 113s Preparing to unpack .../50-libcurl3t64-gnutls_8.12.1-3ubuntu1_amd64.deb ... 113s Unpacking libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) over (8.12.1-2ubuntu1) ... 113s Preparing to unpack .../51-fwupd_2.0.6-4_amd64.deb ... 114s Unpacking fwupd (2.0.6-4) over (2.0.6-3) ... 114s Preparing to unpack .../52-libfwupd3_2.0.6-4_amd64.deb ... 114s Unpacking libfwupd3:amd64 (2.0.6-4) over (2.0.6-3) ... 114s Preparing to unpack .../53-libmm-glib0_1.23.4-0ubuntu3_amd64.deb ... 114s Unpacking libmm-glib0:amd64 (1.23.4-0ubuntu3) over (1.23.4-0ubuntu2) ... 114s Preparing to unpack .../54-htop_3.4.0-2_amd64.deb ... 114s Unpacking htop (3.4.0-2) over (3.3.0-5) ... 114s Preparing to unpack .../55-linux-firmware_20250310.git9e1370d3-0ubuntu1_amd64.deb ... 114s Unpacking linux-firmware (20250310.git9e1370d3-0ubuntu1) over (20250204.git0fd450ee-0ubuntu1) ... 117s Preparing to unpack .../56-initramfs-tools_0.146ubuntu1_all.deb ... 117s Unpacking initramfs-tools (0.146ubuntu1) over (0.145ubuntu3) ... 117s Preparing to unpack .../57-initramfs-tools-core_0.146ubuntu1_all.deb ... 117s Unpacking initramfs-tools-core (0.146ubuntu1) over (0.145ubuntu3) ... 117s Preparing to unpack .../58-initramfs-tools-bin_0.146ubuntu1_amd64.deb ... 117s Unpacking initramfs-tools-bin (0.146ubuntu1) over (0.145ubuntu3) ... 117s Selecting previously unselected package libdebuginfod1t64:amd64. 117s Preparing to unpack .../59-libdebuginfod1t64_0.192-4_amd64.deb ... 117s Unpacking libdebuginfod1t64:amd64 (0.192-4) ... 118s Preparing to unpack .../60-libftdi1-2_1.5-8build1_amd64.deb ... 118s Unpacking libftdi1-2:amd64 (1.5-8build1) over (1.5-8) ... 118s Preparing to unpack .../61-libgpgme11t64_1.24.2-1ubuntu2_amd64.deb ... 118s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu2) over (1.24.2-1ubuntu1) ... 118s Preparing to unpack .../62-libjemalloc2_5.3.0-3_amd64.deb ... 118s Unpacking libjemalloc2:amd64 (5.3.0-3) over (5.3.0-2build1) ... 118s Selecting previously unselected package linux-modules-6.14.0-10-generic. 118s Preparing to unpack .../63-linux-modules-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 118s Unpacking linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 118s Selecting previously unselected package linux-image-6.14.0-10-generic. 118s Preparing to unpack .../64-linux-image-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 118s Unpacking linux-image-6.14.0-10-generic (6.14.0-10.10) ... 118s Selecting previously unselected package linux-modules-extra-6.14.0-10-generic. 118s Preparing to unpack .../65-linux-modules-extra-6.14.0-10-generic_6.14.0-10.10_amd64.deb ... 118s Unpacking linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 120s Preparing to unpack .../66-linux-generic_6.14.0-10.10_amd64.deb ... 120s Unpacking linux-generic (6.14.0-10.10) over (6.12.0-16.16+2) ... 120s Preparing to unpack .../67-linux-image-generic_6.14.0-10.10_amd64.deb ... 120s 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(1.0.6-6) over (1.0.6-5) ... 125s Preparing to unpack .../79-python3-rpds-py_0.21.0-2ubuntu2_amd64.deb ... 125s Unpacking python3-rpds-py (0.21.0-2ubuntu2) over (0.21.0-2ubuntu1) ... 125s Preparing to unpack .../80-python3-systemd_235-1build6_amd64.deb ... 125s Unpacking python3-systemd (235-1build6) over (235-1build5) ... 125s Preparing to unpack .../81-python3.13-gdbm_3.13.2-2_amd64.deb ... 125s Unpacking python3.13-gdbm (3.13.2-2) over (3.13.2-1) ... 125s Preparing to unpack .../82-ubuntu-kernel-accessories_1.549_amd64.deb ... 125s Unpacking ubuntu-kernel-accessories (1.549) over (1.548) ... 126s Preparing to unpack .../83-cloud-init_25.1-0ubuntu3_all.deb ... 126s Unpacking cloud-init (25.1-0ubuntu3) over (25.1-0ubuntu2) ... 126s Preparing to unpack .../84-python3-bcrypt_4.2.0-2.1build1_amd64.deb ... 126s Unpacking python3-bcrypt (4.2.0-2.1build1) over (4.2.0-2.1) ... 126s Setting up linux-headers-6.14.0-10 (6.14.0-10.10) ... 126s Setting up media-types (13.0.0) ... 126s Installing new version of config file /etc/mime.types ... 126s Setting up linux-headers-6.14.0-10-generic (6.14.0-10.10) ... 126s Setting up ubuntu-kernel-accessories (1.549) ... 126s Setting up libapparmor1:amd64 (4.1.0~beta5-0ubuntu8) ... 126s Setting up pci.ids (0.0~2025.03.09-1) ... 126s Setting up libnewt0.52:amd64 (0.52.24-4ubuntu2) ... 126s Setting up apt-utils (2.9.33) ... 126s Setting up libdebuginfod-common (0.192-4) ... 126s Setting up exfatprogs (1.2.8-1) ... 126s Setting up linux-firmware (20250310.git9e1370d3-0ubuntu1) ... 126s Setting up bpftool (7.6.0+6.14.0-10.10) ... 126s Setting up libestr0:amd64 (0.1.11-2) ... 126s Setting up libbrotli1:amd64 (1.1.0-2build4) ... 126s Setting up libsqlite3-0:amd64 (3.46.1-2) ... 126s Setting up dosfstools (4.2-1.2) ... 126s Setting up rsyslog (8.2412.0-2ubuntu2) ... 126s info: The user `syslog' is already a member of `adm'. 127s Setting up binutils-common:amd64 (2.44-3ubuntu1) ... 127s Setting up libcurl3t64-gnutls:amd64 (8.12.1-3ubuntu1) ... 127s Setting up linux-libc-dev:amd64 (6.14.0-10.10) ... 127s Setting up libctf-nobfd0:amd64 (2.44-3ubuntu1) ... 127s Setting up systemd (257.3-1ubuntu3) ... 127s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 127s Created symlink '/run/systemd/system/tmp.mount' → '/dev/null'. 128s /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. 128s Setting up libparted2t64:amd64 (3.6-5) ... 128s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2 to /lib/x86_64-linux-gnu/libparted.so.2.usr-is-merged by libparted2t64' 128s Removing 'diversion of /lib/x86_64-linux-gnu/libparted.so.2.0.5 to /lib/x86_64-linux-gnu/libparted.so.2.0.5.usr-is-merged by libparted2t64' 128s Setting up linux-headers-generic (6.14.0-10.10) ... 128s Setting up libjemalloc2:amd64 (5.3.0-3) ... 128s Setting up locales (2.41-1ubuntu1) ... 128s Installing new version of config file /etc/locale.alias ... 129s Generating locales (this might take a while)... 131s en_US.UTF-8... done 131s Generation complete. 131s Setting up libsframe1:amd64 (2.44-3ubuntu1) ... 131s Setting up libpython3.13-minimal:amd64 (3.13.2-2) ... 131s Setting up apparmor (4.1.0~beta5-0ubuntu8) ... 131s Installing new version of config file /etc/apparmor.d/fusermount3 ... 131s Installing new version of config file /etc/apparmor.d/lsusb ... 131s Installing new version of config file /etc/apparmor.d/openvpn ... 132s Reloading AppArmor profiles 134s Setting up libftdi1-2:amd64 (1.5-8build1) ... 134s Setting up libglib2.0-data (2.84.0-1) ... 134s Setting up systemd-cryptsetup (257.3-1ubuntu3) ... 134s Setting up libncurses6:amd64 (6.5+20250216-2) ... 134s Setting up strace (6.13+ds-1ubuntu1) ... 134s Setting up xz-utils (5.6.4-1) ... 134s Setting up systemd-timesyncd (257.3-1ubuntu3) ... 134s systemd-time-wait-sync.service is a disabled or a static unit not running, not starting it. 134s Setting up libatomic1:amd64 (15-20250222-0ubuntu1) ... 134s Setting up udev (257.3-1ubuntu3) ... 136s Setting up linux-modules-6.14.0-10-generic (6.14.0-10.10) ... 138s Setting up libncursesw6:amd64 (6.5+20250216-2) ... 138s Setting up libpci3:amd64 (1:3.13.0-2) ... 138s Setting up whiptail (0.52.24-4ubuntu2) ... 138s Setting up python-apt-common (2.9.9build1) ... 138s Setting up pnp.ids (0.393-3) ... 138s Setting up libnl-3-200:amd64 (3.7.0-1) ... 138s Setting up python3.13-minimal (3.13.2-2) ... 139s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu2) ... 139s Setting up libbinutils:amd64 (2.44-3ubuntu1) ... 139s Setting up libc-dev-bin (2.41-1ubuntu1) ... 139s Setting up libpython3.13-stdlib:amd64 (3.13.2-2) ... 139s Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2ubuntu5) ... 139s Setting up rsync (3.4.1+ds1-3) ... 140s rsync.service is a disabled or a static unit not running, not starting it. 140s Setting up python3.13-gdbm (3.13.2-2) ... 140s Setting up libpython3-stdlib:amd64 (3.13.2-2) ... 140s Setting up systemd-resolved (257.3-1ubuntu3) ... 140s Setting up initramfs-tools-bin (0.146ubuntu1) ... 140s Setting up ncurses-term (6.5+20250216-2) ... 140s Setting up libctf0:amd64 (2.44-3ubuntu1) ... 140s Setting up libpython3.13:amd64 (3.13.2-2) ... 140s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 140s Setting up libdebuginfod1t64:amd64 (0.192-4) ... 140s Setting up systemd-sysv (257.3-1ubuntu3) ... 140s Setting up linux-headers-virtual (6.14.0-10.10) ... 140s Setting up libcurl4t64:amd64 (8.12.1-3ubuntu1) ... 140s Setting up python3.13 (3.13.2-2) ... 141s Setting up htop (3.4.0-2) ... 141s Setting up linux-image-6.14.0-10-generic (6.14.0-10.10) ... 144s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.12.0-16-generic 144s I: /boot/initrd.img.old is now a symlink to initrd.img-6.12.0-16-generic 144s I: /boot/vmlinuz is now a symlink to vmlinuz-6.14.0-10-generic 144s I: /boot/initrd.img is now a symlink to initrd.img-6.14.0-10-generic 144s Setting up parted (3.6-5) ... 144s Setting up libnss-systemd:amd64 (257.3-1ubuntu3) ... 144s Setting up python3 (3.13.2-2) ... 144s Setting up python3-newt:amd64 (0.52.24-4ubuntu2) ... 144s Setting up python3-markupsafe (2.1.5-1build4) ... 144s Setting up linux-modules-extra-6.14.0-10-generic (6.14.0-10.10) ... 146s Setting up libnl-route-3-200:amd64 (3.7.0-1) ... 146s Setting up hwdata (0.393-3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up libglib2.0-0t64:amd64 (2.84.0-1) ... 146s No schema files found: doing nothing. 146s Setting up libgprofng0:amd64 (2.44-3ubuntu1) ... 146s Setting up linux-perf (6.14.0-10.10) ... 146s Setting up gir1.2-glib-2.0:amd64 (2.84.0-1) ... 146s Setting up pciutils (1:3.13.0-2) ... 146s Setting up python3-rpds-py (0.21.0-2ubuntu2) ... 146s Setting up libmm-glib0:amd64 (1.23.4-0ubuntu3) ... 146s Setting up libnl-genl-3-200:amd64 (3.7.0-1) ... 146s Setting up libpam-systemd:amd64 (257.3-1ubuntu3) ... 147s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 147s Setting up libgirepository-1.0-1:amd64 (1.83.4-1) ... 147s Setting up curl (8.12.1-3ubuntu1) ... 147s Setting up linux-image-virtual (6.14.0-10.10) ... 147s Setting up initramfs-tools-core (0.146ubuntu1) ... 147s Setting up linux-tools-common (6.14.0-10.10) ... 147s Setting up python3-systemd (235-1build6) ... 147s Setting up python3-cffi-backend:amd64 (1.17.1-2build2) ... 147s Setting up binutils-x86-64-linux-gnu (2.44-3ubuntu1) ... 147s Setting up linux-image-generic (6.14.0-10.10) ... 147s Setting up python3-dbus (1.3.2-5build5) ... 147s Setting up linux-tools-6.14.0-10 (6.14.0-10.10) ... 147s Setting up initramfs-tools (0.146ubuntu1) ... 147s Installing new version of config file /etc/kernel/postinst.d/initramfs-tools ... 147s Installing new version of config file /etc/kernel/postrm.d/initramfs-tools ... 147s update-initramfs: deferring update (trigger activated) 147s Setting up linux-generic (6.14.0-10.10) ... 147s Setting up ubuntu-minimal (1.549) ... 147s Setting up python3-apt (2.9.9build1) ... 147s Setting up python3-bcrypt (4.2.0-2.1build1) ... 147s Setting up python3-yaml (6.0.2-1build2) ... 147s Setting up libfwupd3:amd64 (2.0.6-4) ... 147s Setting up python3-lazr.uri (1.0.6-6) ... 148s Setting up binutils (2.44-3ubuntu1) ... 148s Setting up ubuntu-standard (1.549) ... 148s Setting up cloud-init-base (25.1-0ubuntu3) ... 149s Setting up linux-virtual (6.14.0-10.10) ... 149s Setting up gir1.2-girepository-2.0:amd64 (1.83.4-1) ... 149s Setting up python3-gi (3.50.0-4build1) ... 150s Setting up linux-tools-6.14.0-10-generic (6.14.0-10.10) ... 150s Setting up fwupd (2.0.6-4) ... 150s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 150s fwupd.service is a disabled or a static unit not running, not starting it. 150s Setting up cloud-init (25.1-0ubuntu3) ... 150s Processing triggers for man-db (2.13.0-1) ... 152s Processing triggers for dbus (1.16.2-1ubuntu1) ... 152s Processing triggers for shared-mime-info (2.4-5) ... 152s Warning: program compiled against libxml 212 using older 209 153s Processing triggers for libc-bin (2.41-1ubuntu1) ... 153s Processing triggers for linux-image-6.14.0-10-generic (6.14.0-10.10) ... 153s /etc/kernel/postinst.d/initramfs-tools: 153s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 153s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 165s /etc/kernel/postinst.d/zz-update-grub: 165s Sourcing file `/etc/default/grub' 165s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 165s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 165s Generating grub configuration file ... 165s Found linux image: /boot/vmlinuz-6.14.0-10-generic 165s Found initrd image: /boot/initrd.img-6.14.0-10-generic 165s Found linux image: /boot/vmlinuz-6.12.0-16-generic 165s Found initrd image: /boot/initrd.img-6.12.0-16-generic 165s Found linux image: /boot/vmlinuz-6.11.0-8-generic 165s Found initrd image: /boot/initrd.img-6.11.0-8-generic 165s Warning: os-prober will not be executed to detect other bootable partitions. 165s Systems on them will not be added to the GRUB boot configuration. 165s Check GRUB_DISABLE_OS_PROBER documentation entry. 165s Adding boot menu entry for UEFI Firmware Settings ... 165s done 165s Processing triggers for initramfs-tools (0.146ubuntu1) ... 165s update-initramfs: Generating /boot/initrd.img-6.14.0-10-generic 165s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 178s Reading package lists... 178s Building dependency tree... 178s Reading state information... 178s Solving dependencies... 178s The following packages will be REMOVED: 178s libnl-genl-3-200* libnsl2* libpython3.12-minimal* libpython3.12-stdlib* 178s libpython3.12t64* linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 178s linux-headers-6.12.0-16* linux-headers-6.12.0-16-generic* 178s linux-image-6.11.0-8-generic* linux-image-6.12.0-16-generic* 178s linux-modules-6.11.0-8-generic* linux-modules-6.12.0-16-generic* 178s linux-modules-extra-6.12.0-16-generic* linux-tools-6.11.0-8* 178s linux-tools-6.11.0-8-generic* linux-tools-6.12.0-16* 178s linux-tools-6.12.0-16-generic* 179s 0 upgraded, 0 newly installed, 18 to remove and 5 not upgraded. 179s After this operation, 545 MB disk space will be freed. 179s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 148643 files and directories currently installed.) 179s Removing libnl-genl-3-200:amd64 (3.7.0-1) ... 179s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 179s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 179s Removing libpython3.12t64:amd64 (3.12.9-1) ... 179s Removing libpython3.12-stdlib:amd64 (3.12.9-1) ... 179s Removing libnsl2:amd64 (1.3.0-3build3) ... 179s Removing libpython3.12-minimal:amd64 (3.12.9-1) ... 179s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 180s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 182s Removing linux-headers-6.12.0-16-generic (6.12.0-16.16) ... 183s Removing linux-headers-6.12.0-16 (6.12.0-16.16) ... 185s Removing linux-image-6.11.0-8-generic (6.11.0-8.8) ... 185s /etc/kernel/postrm.d/initramfs-tools: 185s update-initramfs: Deleting /boot/initrd.img-6.11.0-8-generic 185s /etc/kernel/postrm.d/zz-update-grub: 185s Sourcing file `/etc/default/grub' 185s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 185s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 185s Generating grub configuration file ... 185s Found linux image: /boot/vmlinuz-6.14.0-10-generic 185s Found initrd image: /boot/initrd.img-6.14.0-10-generic 186s Found linux image: /boot/vmlinuz-6.12.0-16-generic 186s Found initrd image: /boot/initrd.img-6.12.0-16-generic 186s Warning: os-prober will not be executed to detect other bootable partitions. 186s Systems on them will not be added to the GRUB boot configuration. 186s Check GRUB_DISABLE_OS_PROBER documentation entry. 186s Adding boot menu entry for UEFI Firmware Settings ... 186s done 186s Removing linux-image-6.12.0-16-generic (6.12.0-16.16) ... 186s W: Removing the running kernel 186s I: /boot/vmlinuz.old is now a symlink to vmlinuz-6.14.0-10-generic 186s I: /boot/initrd.img.old is now a symlink to initrd.img-6.14.0-10-generic 186s /etc/kernel/postrm.d/initramfs-tools: 186s update-initramfs: Deleting /boot/initrd.img-6.12.0-16-generic 186s /etc/kernel/postrm.d/zz-update-grub: 186s Sourcing file `/etc/default/grub' 186s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 186s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 186s Generating grub configuration file ... 186s Found linux image: /boot/vmlinuz-6.14.0-10-generic 186s Found initrd image: /boot/initrd.img-6.14.0-10-generic 187s Warning: os-prober will not be executed to detect other bootable partitions. 187s Systems on them will not be added to the GRUB boot configuration. 187s Check GRUB_DISABLE_OS_PROBER documentation entry. 187s Adding boot menu entry for UEFI Firmware Settings ... 187s done 187s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 187s Removing linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 189s Removing linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 189s Removing linux-tools-6.12.0-16-generic (6.12.0-16.16) ... 189s Removing linux-tools-6.12.0-16 (6.12.0-16.16) ... 189s Processing triggers for libc-bin (2.41-1ubuntu1) ... 189s (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.) 189s Purging configuration files for linux-image-6.11.0-8-generic (6.11.0-8.8) ... 189s Purging configuration files for libpython3.12-minimal:amd64 (3.12.9-1) ... 189s Purging configuration files for linux-modules-extra-6.12.0-16-generic (6.12.0-16.16) ... 189s Purging configuration files for linux-modules-6.12.0-16-generic (6.12.0-16.16) ... 189s dpkg: warning: while removing linux-modules-6.12.0-16-generic, directory '/lib/modules/6.12.0-16-generic' not empty so not removed 189s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 189s Purging configuration files for linux-image-6.12.0-16-generic (6.12.0-16.16) ... 189s rmdir: failed to remove '/lib/modules/6.12.0-16-generic': Directory not empty 190s autopkgtest [22:42:43]: upgrading testbed (apt dist-upgrade and autopurge) 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 191s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 191s Starting 2 pkgProblemResolver with broken count: 0 191s Done 191s Entering ResolveByKeep 191s 192s Calculating upgrade... 192s The following packages will be upgraded: 192s libc-bin libc-dev-bin libc6 libc6-dev locales 192s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 192s Need to get 10.5 MB of archives. 192s After this operation, 1024 B of additional disk space will be used. 192s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu2 [2183 kB] 193s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu2 [24.7 kB] 193s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu2 [3327 kB] 193s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu2 [700 kB] 193s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu2 [4246 kB] 193s Preconfiguring packages ... 193s Fetched 10.5 MB in 1s (10.1 MB/s) 193s (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.) 193s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_amd64.deb ... 193s Unpacking libc6-dev:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_amd64.deb ... 194s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Preparing to unpack .../libc6_2.41-1ubuntu2_amd64.deb ... 194s Unpacking libc6:amd64 (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Setting up libc6:amd64 (2.41-1ubuntu2) ... 194s (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.) 194s Preparing to unpack .../libc-bin_2.41-1ubuntu2_amd64.deb ... 194s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 194s Setting up libc-bin (2.41-1ubuntu2) ... 194s (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.) 194s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 194s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 195s Setting up locales (2.41-1ubuntu2) ... 195s Generating locales (this might take a while)... 197s en_US.UTF-8... done 197s Generation complete. 197s Setting up libc-dev-bin (2.41-1ubuntu2) ... 197s Setting up libc6-dev:amd64 (2.41-1ubuntu2) ... 197s Processing triggers for man-db (2.13.0-1) ... 198s Processing triggers for systemd (257.3-1ubuntu3) ... 199s Reading package lists... 199s Building dependency tree... 199s Reading state information... 199s Starting pkgProblemResolver with broken count: 0 200s Starting 2 pkgProblemResolver with broken count: 0 200s Done 200s Solving dependencies... 200s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 201s autopkgtest [22:42:54]: rebooting testbed after setup commands that affected boot 224s autopkgtest [22:43:17]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP PREEMPT_DYNAMIC Wed Mar 12 16:07:00 UTC 2025 227s autopkgtest [22:43:20]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 229s Get:1 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (dsc) [2293 B] 229s Get:2 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (tar) [1207 kB] 229s Get:3 http://ftpmaster.internal/ubuntu plucky/universe r-cran-vegan 2.6-10+dfsg-1ubuntu2 (diff) [6736 B] 230s gpgv: Signature made Sun Mar 9 19:53:35 2025 UTC 230s gpgv: using RSA key 5C7ABEA20F8630459CC8C8B5E27F2CF8458C2FA4 230s gpgv: Can't check signature: No public key 230s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-1ubuntu2.dsc: no acceptable signature found 230s autopkgtest [22:43:23]: testing package r-cran-vegan version 2.6-10+dfsg-1ubuntu2 230s autopkgtest [22:43:23]: build not needed 235s autopkgtest [22:43:28]: test run-unit-test: preparing testbed 235s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s Starting pkgProblemResolver with broken count: 0 236s Starting 2 pkgProblemResolver with broken count: 0 236s Done 237s The following NEW packages will be installed: 237s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 237s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 237s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 237s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 237s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 237s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 237s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 237s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 237s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 237s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 237s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 237s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 237s x11-common xdg-utils zip 237s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 237s Need to get 68.6 MB of archives. 237s After this operation, 165 MB of additional disk space will be used. 237s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 237s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 237s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig-config amd64 2.15.0-2ubuntu1 [37.4 kB] 237s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libfontconfig1 amd64 2.15.0-2ubuntu1 [164 kB] 237s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 fontconfig amd64 2.15.0-2ubuntu1 [180 kB] 237s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [118 kB] 237s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 238s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 238s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libpixman-1-0 amd64 0.44.0-3 [427 kB] 238s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-render0 amd64 1.17.0-2 [16.2 kB] 238s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libxcb-shm0 amd64 1.17.0-2 [5758 B] 238s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 238s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libcairo2 amd64 1.18.2-2 [569 kB] 238s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB] 238s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate0 amd64 1.23-1 [64.1 kB] 238s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250222-0ubuntu1 [919 kB] 238s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 15-20250222-0ubuntu1 [148 kB] 238s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libgraphite2-3 amd64 1.3.14-2ubuntu1 [73.1 kB] 238s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libharfbuzz0b amd64 10.2.0-1 [543 kB] 238s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 238s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 libice6 amd64 2:1.1.1-1 [44.1 kB] 238s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8 amd64 2.1.5-3ubuntu2 [179 kB] 238s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 238s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-bootstrap all 3.4.1+dfsg-3 [129 kB] 238s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-highlight.js all 9.18.5+dfsg1-2 [385 kB] 238s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 238s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2 [146 kB] 238s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 238s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu1 [271 kB] 238s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai-data all 0.1.29-2build1 [158 kB] 238s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB] 238s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 libpango-1.0-0 amd64 1.56.2-1 [255 kB] 238s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangoft2-1.0-0 amd64 1.56.2-1 [52.6 kB] 238s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libpangocairo-1.0-0 amd64 1.56.2-1 [29.1 kB] 238s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper2 amd64 2.2.5-0.3 [17.4 kB] 238s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libpaper-utils amd64 2.2.5-0.3 [15.5 kB] 238s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [25.9 kB] 238s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libsm6 amd64 2:1.2.4-1 [17.4 kB] 238s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1086 kB] 238s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB] 238s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libwebp7 amd64 1.5.0-0.1 [378 kB] 238s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu4 [200 kB] 238s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 238s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 238s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libtk8.6 amd64 8.6.16-1 [868 kB] 238s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] 238s Get:47 http://ftpmaster.internal/ubuntu plucky/universe amd64 node-normalize.css all 8.0.1-5 [10.8 kB] 238s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 zip amd64 3.0-14ubuntu2 [185 kB] 238s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 unzip amd64 6.0-28ubuntu6 [181 kB] 238s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 xdg-utils all 1.2.1-2ubuntu1 [66.0 kB] 238s Get:51 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-core amd64 4.4.3-1 [28.9 MB] 240s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-cluster amd64 2.1.8.1-1 [579 kB] 240s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-commonmark amd64 1.9.2-2 [137 kB] 240s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-evaluate all 1.0.3-1 [114 kB] 240s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-xfun amd64 0.51+dfsg-1 [574 kB] 240s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 240s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 240s Get:58 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 240s Get:59 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-knitr all 1.49+dfsg-1 [859 kB] 240s Get:60 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-lattice amd64 0.22-6-1 [1340 kB] 240s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-markdown all 1.13-1 [162 kB] 240s Get:62 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mass amd64 7.3-64-1 [1114 kB] 240s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-matrix amd64 1.7-3-1 [4349 kB] 240s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-nlme amd64 3.1.167-1 [2320 kB] 240s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 241s Get:66 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-permute all 0.9-7-1 [228 kB] 241s Get:67 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-cran-vegan amd64 2.6-10+dfsg-1ubuntu2 [3145 kB] 241s Preconfiguring packages ... 241s Fetched 68.6 MB in 4s (17.5 MB/s) 241s Selecting previously unselected package fonts-dejavu-mono. 241s (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.) 241s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8_all.deb ... 241s Unpacking fonts-dejavu-mono (2.37-8) ... 241s Selecting previously unselected package fonts-dejavu-core. 241s Preparing to unpack .../01-fonts-dejavu-core_2.37-8_all.deb ... 241s Unpacking fonts-dejavu-core (2.37-8) ... 242s Selecting previously unselected package fontconfig-config. 242s Preparing to unpack .../02-fontconfig-config_2.15.0-2ubuntu1_amd64.deb ... 242s Unpacking fontconfig-config (2.15.0-2ubuntu1) ... 242s Selecting previously unselected package libfontconfig1:amd64. 242s Preparing to unpack .../03-libfontconfig1_2.15.0-2ubuntu1_amd64.deb ... 242s Unpacking libfontconfig1:amd64 (2.15.0-2ubuntu1) ... 242s Selecting previously unselected package fontconfig. 242s Preparing to unpack .../04-fontconfig_2.15.0-2ubuntu1_amd64.deb ... 242s Unpacking fontconfig (2.15.0-2ubuntu1) ... 242s Selecting previously unselected package fonts-glyphicons-halflings. 242s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-3_all.deb ... 242s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-3) ... 242s Selecting previously unselected package fonts-mathjax. 242s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 242s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 242s Selecting previously unselected package libblas3:amd64. 242s Preparing to unpack .../07-libblas3_3.12.1-2_amd64.deb ... 242s Unpacking libblas3:amd64 (3.12.1-2) ... 242s Selecting previously unselected package libpixman-1-0:amd64. 242s Preparing to unpack .../08-libpixman-1-0_0.44.0-3_amd64.deb ... 242s Unpacking libpixman-1-0:amd64 (0.44.0-3) ... 242s Selecting previously unselected package libxcb-render0:amd64. 242s Preparing to unpack .../09-libxcb-render0_1.17.0-2_amd64.deb ... 242s Unpacking libxcb-render0:amd64 (1.17.0-2) ... 242s Selecting previously unselected package libxcb-shm0:amd64. 242s Preparing to unpack .../10-libxcb-shm0_1.17.0-2_amd64.deb ... 242s Unpacking libxcb-shm0:amd64 (1.17.0-2) ... 242s Selecting previously unselected package libxrender1:amd64. 242s Preparing to unpack .../11-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 242s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 242s Selecting previously unselected package libcairo2:amd64. 242s Preparing to unpack .../12-libcairo2_1.18.2-2_amd64.deb ... 242s Unpacking libcairo2:amd64 (1.18.2-2) ... 242s Selecting previously unselected package libdatrie1:amd64. 242s Preparing to unpack .../13-libdatrie1_0.2.13-3build1_amd64.deb ... 242s Unpacking libdatrie1:amd64 (0.2.13-3build1) ... 242s Selecting previously unselected package libdeflate0:amd64. 242s Preparing to unpack .../14-libdeflate0_1.23-1_amd64.deb ... 242s Unpacking libdeflate0:amd64 (1.23-1) ... 242s Selecting previously unselected package libgfortran5:amd64. 242s Preparing to unpack .../15-libgfortran5_15-20250222-0ubuntu1_amd64.deb ... 242s Unpacking libgfortran5:amd64 (15-20250222-0ubuntu1) ... 242s Selecting previously unselected package libgomp1:amd64. 242s Preparing to unpack .../16-libgomp1_15-20250222-0ubuntu1_amd64.deb ... 242s Unpacking libgomp1:amd64 (15-20250222-0ubuntu1) ... 242s Selecting previously unselected package libgraphite2-3:amd64. 242s Preparing to unpack .../17-libgraphite2-3_1.3.14-2ubuntu1_amd64.deb ... 242s Unpacking libgraphite2-3:amd64 (1.3.14-2ubuntu1) ... 242s Selecting previously unselected package libharfbuzz0b:amd64. 242s Preparing to unpack .../18-libharfbuzz0b_10.2.0-1_amd64.deb ... 242s Unpacking libharfbuzz0b:amd64 (10.2.0-1) ... 242s Selecting previously unselected package x11-common. 242s Preparing to unpack .../19-x11-common_1%3a7.7+23ubuntu3_all.deb ... 242s Unpacking x11-common (1:7.7+23ubuntu3) ... 243s Selecting previously unselected package libice6:amd64. 243s Preparing to unpack .../20-libice6_2%3a1.1.1-1_amd64.deb ... 243s Unpacking libice6:amd64 (2:1.1.1-1) ... 243s Selecting previously unselected package libjpeg-turbo8:amd64. 243s Preparing to unpack .../21-libjpeg-turbo8_2.1.5-3ubuntu2_amd64.deb ... 243s Unpacking libjpeg-turbo8:amd64 (2.1.5-3ubuntu2) ... 243s Selecting previously unselected package libjpeg8:amd64. 243s Preparing to unpack .../22-libjpeg8_8c-2ubuntu11_amd64.deb ... 243s Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... 243s Selecting previously unselected package libjs-bootstrap. 243s Preparing to unpack .../23-libjs-bootstrap_3.4.1+dfsg-3_all.deb ... 243s Unpacking libjs-bootstrap (3.4.1+dfsg-3) ... 243s Selecting previously unselected package libjs-highlight.js. 243s Preparing to unpack .../24-libjs-highlight.js_9.18.5+dfsg1-2_all.deb ... 243s Unpacking libjs-highlight.js (9.18.5+dfsg1-2) ... 243s Selecting previously unselected package libjs-jquery. 243s Preparing to unpack .../25-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 243s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 243s Selecting previously unselected package libjs-jquery-datatables. 243s Preparing to unpack .../26-libjs-jquery-datatables_1.11.5+dfsg-2_all.deb ... 243s Unpacking libjs-jquery-datatables (1.11.5+dfsg-2) ... 243s Selecting previously unselected package liblapack3:amd64. 243s Preparing to unpack .../27-liblapack3_3.12.1-2_amd64.deb ... 243s Unpacking liblapack3:amd64 (3.12.1-2) ... 243s Selecting previously unselected package liblerc4:amd64. 243s Preparing to unpack .../28-liblerc4_4.0.0+ds-5ubuntu1_amd64.deb ... 243s Unpacking liblerc4:amd64 (4.0.0+ds-5ubuntu1) ... 243s Selecting previously unselected package libthai-data. 243s Preparing to unpack .../29-libthai-data_0.1.29-2build1_all.deb ... 243s Unpacking libthai-data (0.1.29-2build1) ... 243s Selecting previously unselected package libthai0:amd64. 243s Preparing to unpack .../30-libthai0_0.1.29-2build1_amd64.deb ... 243s Unpacking libthai0:amd64 (0.1.29-2build1) ... 243s Selecting previously unselected package libpango-1.0-0:amd64. 243s Preparing to unpack .../31-libpango-1.0-0_1.56.2-1_amd64.deb ... 243s Unpacking libpango-1.0-0:amd64 (1.56.2-1) ... 243s Selecting previously unselected package libpangoft2-1.0-0:amd64. 243s Preparing to unpack .../32-libpangoft2-1.0-0_1.56.2-1_amd64.deb ... 243s Unpacking libpangoft2-1.0-0:amd64 (1.56.2-1) ... 243s Selecting previously unselected package libpangocairo-1.0-0:amd64. 243s Preparing to unpack .../33-libpangocairo-1.0-0_1.56.2-1_amd64.deb ... 243s Unpacking libpangocairo-1.0-0:amd64 (1.56.2-1) ... 243s Selecting previously unselected package libpaper2:amd64. 243s Preparing to unpack .../34-libpaper2_2.2.5-0.3_amd64.deb ... 243s Unpacking libpaper2:amd64 (2.2.5-0.3) ... 243s Selecting previously unselected package libpaper-utils. 243s Preparing to unpack .../35-libpaper-utils_2.2.5-0.3_amd64.deb ... 243s Unpacking libpaper-utils (2.2.5-0.3) ... 243s Selecting previously unselected package libsharpyuv0:amd64. 243s Preparing to unpack .../36-libsharpyuv0_1.5.0-0.1_amd64.deb ... 243s Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ... 243s Selecting previously unselected package libsm6:amd64. 243s Preparing to unpack .../37-libsm6_2%3a1.2.4-1_amd64.deb ... 243s Unpacking libsm6:amd64 (2:1.2.4-1) ... 243s Selecting previously unselected package libtcl8.6:amd64. 243s Preparing to unpack .../38-libtcl8.6_8.6.16+dfsg-1_amd64.deb ... 243s Unpacking libtcl8.6:amd64 (8.6.16+dfsg-1) ... 243s Selecting previously unselected package libjbig0:amd64. 243s Preparing to unpack .../39-libjbig0_2.1-6.1ubuntu2_amd64.deb ... 243s Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ... 243s Selecting previously unselected package libwebp7:amd64. 243s Preparing to unpack .../40-libwebp7_1.5.0-0.1_amd64.deb ... 243s Unpacking libwebp7:amd64 (1.5.0-0.1) ... 243s Selecting previously unselected package libtiff6:amd64. 243s Preparing to unpack .../41-libtiff6_4.5.1+git230720-4ubuntu4_amd64.deb ... 243s Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu4) ... 243s Selecting previously unselected package libxft2:amd64. 243s Preparing to unpack .../42-libxft2_2.3.6-1build1_amd64.deb ... 243s Unpacking libxft2:amd64 (2.3.6-1build1) ... 243s Selecting previously unselected package libxss1:amd64. 243s Preparing to unpack .../43-libxss1_1%3a1.2.3-1build3_amd64.deb ... 243s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 244s Selecting previously unselected package libtk8.6:amd64. 244s Preparing to unpack .../44-libtk8.6_8.6.16-1_amd64.deb ... 244s Unpacking libtk8.6:amd64 (8.6.16-1) ... 244s Selecting previously unselected package libxt6t64:amd64. 244s Preparing to unpack .../45-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ... 244s Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ... 244s Selecting previously unselected package node-normalize.css. 244s Preparing to unpack .../46-node-normalize.css_8.0.1-5_all.deb ... 244s Unpacking node-normalize.css (8.0.1-5) ... 244s Selecting previously unselected package zip. 244s Preparing to unpack .../47-zip_3.0-14ubuntu2_amd64.deb ... 244s Unpacking zip (3.0-14ubuntu2) ... 244s Selecting previously unselected package unzip. 244s Preparing to unpack .../48-unzip_6.0-28ubuntu6_amd64.deb ... 244s Unpacking unzip (6.0-28ubuntu6) ... 244s Selecting previously unselected package xdg-utils. 244s Preparing to unpack .../49-xdg-utils_1.2.1-2ubuntu1_all.deb ... 244s Unpacking xdg-utils (1.2.1-2ubuntu1) ... 244s Selecting previously unselected package r-base-core. 244s Preparing to unpack .../50-r-base-core_4.4.3-1_amd64.deb ... 244s Unpacking r-base-core (4.4.3-1) ... 244s Selecting previously unselected package r-cran-cluster. 244s Preparing to unpack .../51-r-cran-cluster_2.1.8.1-1_amd64.deb ... 244s Unpacking r-cran-cluster (2.1.8.1-1) ... 244s Selecting previously unselected package r-cran-commonmark. 244s Preparing to unpack .../52-r-cran-commonmark_1.9.2-2_amd64.deb ... 244s Unpacking r-cran-commonmark (1.9.2-2) ... 244s Selecting previously unselected package r-cran-evaluate. 244s Preparing to unpack .../53-r-cran-evaluate_1.0.3-1_all.deb ... 244s Unpacking r-cran-evaluate (1.0.3-1) ... 244s Selecting previously unselected package r-cran-xfun. 244s Preparing to unpack .../54-r-cran-xfun_0.51+dfsg-1_amd64.deb ... 244s Unpacking r-cran-xfun (0.51+dfsg-1) ... 244s Selecting previously unselected package r-cran-highr. 244s Preparing to unpack .../55-r-cran-highr_0.11+dfsg-1_all.deb ... 244s Unpacking r-cran-highr (0.11+dfsg-1) ... 244s Selecting previously unselected package r-cran-yaml. 244s Preparing to unpack .../56-r-cran-yaml_2.3.10-1_amd64.deb ... 244s Unpacking r-cran-yaml (2.3.10-1) ... 244s Selecting previously unselected package libjs-mathjax. 244s Preparing to unpack .../57-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 244s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 245s Selecting previously unselected package r-cran-knitr. 245s Preparing to unpack .../58-r-cran-knitr_1.49+dfsg-1_all.deb ... 245s Unpacking r-cran-knitr (1.49+dfsg-1) ... 245s Selecting previously unselected package r-cran-lattice. 245s Preparing to unpack .../59-r-cran-lattice_0.22-6-1_amd64.deb ... 245s Unpacking r-cran-lattice (0.22-6-1) ... 245s Selecting previously unselected package r-cran-markdown. 245s Preparing to unpack .../60-r-cran-markdown_1.13-1_all.deb ... 245s Unpacking r-cran-markdown (1.13-1) ... 245s Selecting previously unselected package r-cran-mass. 245s Preparing to unpack .../61-r-cran-mass_7.3-64-1_amd64.deb ... 245s Unpacking r-cran-mass 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test run-unit-test: [----------------------- 252s 252s R version 4.4.3 (2025-02-28) -- "Trophy Case" 252s Copyright (C) 2025 The R Foundation for Statistical Computing 252s Platform: x86_64-pc-linux-gnu 252s 252s R is free software and comes with ABSOLUTELY NO WARRANTY. 252s You are welcome to redistribute it under certain conditions. 252s Type 'license()' or 'licence()' for distribution details. 252s 252s R is a collaborative project with many contributors. 252s Type 'contributors()' for more information and 252s 'citation()' on how to cite R or R packages in publications. 252s 252s Type 'demo()' for some demos, 'help()' for on-line help, or 252s 'help.start()' for an HTML browser interface to help. 252s Type 'q()' to quit R. 252s 252s > Stangle("decision-vegan.Rnw") 252s Writing to file decision-vegan.R 252s > source("decision-vegan.R", echo=TRUE) 252s 252s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 252s 252s > options(SweaveHooks = list(fig = figset)) 252s 252s > options(prompt = "> ", continue = " ") 252s 252s > options(width = 55) 252s 252s > require(vegan) 252s Loading required package: vegan 252s Loading required package: permute 252s Loading required package: lattice 253s 253s > data(sipoo) 253s 253s > mod <- nestedtemp(sipoo) 254s 254s > plot(mod, "i") 254s 254s > x <- mod$c["Falcsubb"] 254s 254s > y <- 1 - mod$r["Svartholm"] 254s 254s > points(x, y, pch = 16, cex = 1.5) 254s 254s > abline(x + y, -1, lty = 2) 254s 254s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 254s 254s > cross <- function(x, a, p) f(x, p) - a + x 254s 254s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 254s 254s > arrows(x, y, r, f(r, mod$p), lwd = 4) 254s 254s > library(vegan) 254s 254s > data(varespec) 254s 254s > data(varechem) 254s 254s > orig <- cca(varespec ~ Al + K, varechem) 254s 254s > plot(orig, dis = c("lc", "bp")) 254s 254s > plot(orig, dis = c("lc", "bp")) 254s 254s > i <- sample(nrow(varespec)) 254s 254s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 254s 254s > plot(shuff, dis = c("lc", "bp")) 254s 254s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 254s + dis = "lc"))) 254s 254s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 254s + dis = "lc"))) 254s 254s > tmp1 <- rda(varespec ~ Al + K, varechem) 254s 254s > i <- sample(nrow(varespec)) 254s 254s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 254s 254s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 254s + dis = "lc"))) 254s 254s > orig 254s Call: cca(formula = varespec ~ Al + K, data = 254s varechem) 254s 254s -- Model Summary -- 254s 254s Inertia Proportion Rank 254s Total 2.0832 1.0000 254s Constrained 0.4760 0.2285 2 254s Unconstrained 1.6072 0.7715 21 254s 254s Inertia is scaled Chi-square 254s 254s -- Eigenvalues -- 254s 254s Eigenvalues for constrained axes: 254s CCA1 CCA2 254s 0.3608 0.1152 254s 254s Eigenvalues for unconstrained axes: 254s CA1 CA2 CA3 CA4 CA5 CA6 CA7 254s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 254s CA8 254s 0.0757 254s (Showing 8 of 21 unconstrained eigenvalues) 254s 254s 254s > shuff 254s Call: cca(formula = varespec[i, ] ~ Al + K, data = 254s varechem) 254s 254s -- Model Summary -- 254s 254s Inertia Proportion Rank 254s Total 2.08320 1.00000 254s Constrained 0.15151 0.07273 2 254s Unconstrained 1.93169 0.92727 21 254s 254s Inertia is scaled Chi-square 254s 254s -- Eigenvalues -- 254s 254s Eigenvalues for constrained axes: 254s CCA1 CCA2 254s 0.09129 0.06022 254s 254s Eigenvalues for unconstrained axes: 254s CA1 CA2 CA3 CA4 CA5 CA6 CA7 254s 0.5241 0.3056 0.2313 0.1868 0.1703 0.1039 0.0954 254s CA8 254s 0.0803 254s (Showing 8 of 21 unconstrained eigenvalues) 254s 254s 254s > plot(procrustes(orig, shuff)) 254s 254s > tmp1 <- rda(varespec ~ ., varechem) 254s 254s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 254s 254s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 254s + scores(tmp2, dis = "lc", choi = 1:14)) 254s 254s > max(residuals(proc)) 254s [1] 3.473561e-14 254s 254s > data(dune) 254s 254s > data(dune.env) 254s 254s > orig <- cca(dune ~ Moisture, dune.env) 254s 254s > plot(orig, dis = "lc") 254s 254s > plot(orig, display = "wa", type = "points") 254s 254s > ordispider(orig, col = "red") 254s 254s > text(orig, dis = "cn", col = "blue") 254s 254s > plot(orig, display = "wa", type = "points") 254s 254s > ordispider(orig, col = "red") 254s 254s > text(orig, dis = "cn", col = "blue") 254s > 254s 254s R version 4.4.3 (2025-02-28) -- "Trophy Case" 254s Copyright (C) 2025 The R Foundation for Statistical Computing 254s Platform: x86_64-pc-linux-gnu 254s 254s R is free software and comes with ABSOLUTELY NO WARRANTY. 254s You are welcome to redistribute it under certain conditions. 254s Type 'license()' or 'licence()' for distribution details. 254s 254s R is a collaborative project with many contributors. 254s Type 'contributors()' for more information and 254s 'citation()' on how to cite R or R packages in publications. 254s 254s Type 'demo()' for some demos, 'help()' for on-line help, or 254s 'help.start()' for an HTML browser interface to help. 254s Type 'q()' to quit R. 254s 254s > Stangle("diversity-vegan.Rnw") 254s Writing to file diversity-vegan.R 254s > source("diversity-vegan.R", echo=TRUE) 254s 254s > par(mfrow = c(1, 1)) 254s 254s > options(width = 55) 254s 254s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 254s 254s > options(SweaveHooks = list(fig = figset)) 254s 254s > options(prompt = "> ", continue = " ") 254s 254s > library(vegan) 254s Loading required package: permute 254s Loading required package: lattice 255s 255s > data(BCI) 255s 255s > H <- diversity(BCI) 255s 255s > J <- H/log(specnumber(BCI)) 255s 255s > k <- sample(nrow(BCI), 6) 255s 255s > R <- renyi(BCI[k, ]) 255s 255s > print(plot(R)) 255s 255s > alpha <- fisher.alpha(BCI) 255s 255s > quantile(rowSums(BCI)) 255s 0% 25% 50% 75% 100% 255s 340.0 409.0 428.0 443.5 601.0 255s 255s > Srar <- rarefy(BCI, min(rowSums(BCI))) 255s 255s > S2 <- rarefy(BCI, 2) 255s 255s > all(rank(Srar) == rank(S2)) 255s [1] FALSE 255s 255s > range(diversity(BCI, "simp") - (S2 - 1)) 255s [1] -0.002868298 -0.001330663 255s 255s > data(dune) 255s 255s > data(dune.taxon) 255s 255s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 255s 255s > mod <- taxondive(dune, taxdis) 255s 255s > plot(mod) 255s 255s > tr <- hclust(taxdis, "aver") 255s 255s > mod <- treedive(dune, tr) 255s 255s > k <- sample(nrow(BCI), 1) 255s 255s > fish <- fisherfit(BCI[k, ]) 255s 255s > fish 255s 255s Fisher log series model 255s No. of species: 99 255s Fisher alpha: 46.92764 255s 255s 255s > plot(fish) 255s 255s > prestondistr(BCI[k, ]) 255s forced matching of 'tree' labels and 'comm' names 255s 255s Preston lognormal model 255s Method: maximized likelihood to log2 abundances 255s No. of species: 99 255s 255s mode width S0 255s 0.7284236 1.5341408 29.5892910 255s 255s Frequencies by Octave 255s 0 1 2 3 4 255s Observed 22.00000 33.00000 18.50000 16.500000 5.000000 255s Fitted 26.43505 29.12929 20.98723 9.886808 3.045317 255s 5 255s Observed 4.0000000 255s Fitted 0.6133164 255s 255s 255s > rad <- radfit(BCI[k, ]) 255s 255s > rad 255s 255s RAD models, family poisson 255s No. of species 99, total abundance 340 255s 255s par1 par2 par3 Deviance 255s Null 55.4639 255s Preemption 0.038291 53.4573 255s Lognormal 0.7158 1.0327 21.9550 255s Zipf 0.11689 -0.77842 20.0961 255s Mandelbrot 0.50968 -1.1574 3.9378 7.4609 255s AIC BIC 255s Null 322.9662 322.9662 255s Preemption 322.9597 325.5548 255s Lognormal 293.4574 298.6476 255s Zipf 291.5984 296.7887 255s Mandelbrot 280.9632 288.7486 255s 255s > print(radlattice(rad)) 255s 255s > sac <- specaccum(BCI) 255s 255s > plot(sac, ci.type = "polygon", ci.col = "yellow") 255s 255s > sac <- specaccum(BCI) 255s 255s > plot(sac, ci.type = "polygon", ci.col = "yellow") 255s 255s > ncol(BCI)/mean(specnumber(BCI)) - 1 255s [1] 1.478519 255s 255s > beta <- vegdist(BCI, binary = TRUE) 255s 255s > mean(beta) 255s [1] 0.3399075 255s 255s > betadiver(help = TRUE) 255s 1 "w" = (b+c)/(2*a+b+c) 255s 2 "-1" = (b+c)/(2*a+b+c) 255s 3 "c" = (b+c)/2 255s 4 "wb" = b+c 255s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 255s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 255s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 255s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 255s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 255s (2*a+b+c))-1 255s 8 "t" = (b+c)/(2*a+b+c) 255s 9 "me" = (b+c)/(2*a+b+c) 255s 10 "j" = a/(a+b+c) 255s 11 "sor" = 2*a/(2*a+b+c) 255s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 255s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 255s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 255s 15 "cc" = (b+c)/(a+b+c) 255s 16 "g" = (b+c)/(a+b+c) 255s 17 "-3" = pmin.int(b,c)/(a+b+c) 255s 18 "l" = (b+c)/2 255s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 255s 20 "hk" = (b+c)/(2*a+b+c) 255s 21 "rlb" = a/(a+c) 255s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 255s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 255s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 255s 255s > z <- betadiver(BCI, "z") 255s 255s > quantile(z) 255s 0% 25% 50% 75% 100% 255s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 255s 255s > data(dune) 255s 255s > data(dune.env) 255s 255s > z <- betadiver(dune, "z") 255s 255s > mod <- with(dune.env, betadisper(z, Management)) 255s 255s > mod 255s 255s Homogeneity of multivariate dispersions 255s 255s Call: betadisper(d = z, group = Management) 255s 255s No. of Positive Eigenvalues: 12 255s No. of Negative Eigenvalues: 7 255s 255s Average distance to median: 255s BF HF NM SF 255s 0.2532 0.2512 0.4406 0.3635 255s 255s Eigenvalues for PCoA axes: 255s (Showing 8 of 19 eigenvalues) 255s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 255s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 255s PCoA7 PCoA8 255s 0.16128 0.08099 255s 255s > boxplot(mod) 255s 255s > specpool(BCI) 255s Species chao chao.se jack1 jack1.se jack2 255s All 225 236.3732 6.54361 245.58 5.650522 247.8722 255s boot boot.se n 255s All 235.6862 3.468888 50 255s 255s > s <- sample(nrow(BCI), 25) 255s 255s > specpool(BCI[s, ]) 255s Species chao chao.se jack1 jack1.se jack2 255s All 212 230.816 9.332497 238.88 7.64492 247.0067 255s boot boot.se n 255s All 225.1888 4.428898 25 255s 255s > estimateR(BCI[k, ]) 255s 23 255s S.obs 99.000000 255s S.chao1 140.130435 255s se.chao1 16.395758 255s S.ACE 155.213269 255s se.ACE 7.091696 255s 255s > veiledspec(prestondistr(BCI[k, ])) 255s Extrapolated Observed Veiled 255s 113.78623 99.00000 14.78623 255s 255s > veiledspec(BCI[k, ]) 255s Extrapolated Observed Veiled 255s 131.19898 99.00000 32.19898 255s 255s > smo <- beals(BCI) 255s 255s > j <- which(colnames(BCI) == "Ceiba.pentandra") 255s 255s > plot(beals(BCI, species = j, include = FALSE), BCI[, 255s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 255s 255s > j <- which(colnames(BCI) == "Ceiba.pentandra") 255s 255s > plot(beals(BCI, species = j, include = FALSE), BCI[, 255s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 255s Warning messages: 255s 1: In cor(x > 0) : the standard deviation is zero 255s 2: In cor(x > 0) :> 255s the standard deviation is zero 255s 3: In betadisper(z, Management) : 255s some squared distances are negative and changed to zero 256s 256s R version 4.4.3 (2025-02-28) -- "Trophy Case" 256s Copyright (C) 2025 The R Foundation for Statistical Computing 256s Platform: x86_64-pc-linux-gnu 256s 256s R is free software and comes with ABSOLUTELY NO WARRANTY. 256s You are welcome to redistribute it under certain conditions. 256s Type 'license()' or 'licence()' for distribution details. 256s 256s R is a collaborative project with many contributors. 256s Type 'contributors()' for more information and 256s 'citation()' on how to cite R or R packages in publications. 256s 256s Type 'demo()' for some demos, 'help()' for on-line help, or 256s 'help.start()' for an HTML browser interface to help. 256s Type 'q()' to quit R. 256s 256s > Stangle("intro-vegan.Rnw") 256s Writing to file intro-vegan.R 256s > source("intro-vegan.R", echo=TRUE) 256s 256s > par(mfrow = c(1, 1)) 256s 256s > options(width = 72) 256s 256s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 256s 256s > options(SweaveHooks = list(fig = figset)) 256s 256s > options(prompt = "> ", continue = " ") 256s 256s > library(vegan) 256s Loading required package: permute 256s Loading required package: lattice 257s 257s > data(dune) 257s 257s > ord <- decorana(dune) 257s 257s > ord 257s 257s Call: 257s decorana(veg = dune) 257s 257s Detrended correspondence analysis with 26 segments. 257s Rescaling of axes with 4 iterations. 257s Total inertia (scaled Chi-square): 2.1153 257s 257s DCA1 DCA2 DCA3 DCA4 257s Eigenvalues 0.5117 0.3036 0.12125 0.14267 257s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 257s Decorana values 0.5360 0.2869 0.08136 0.04814 257s Axis lengths 3.7004 3.1166 1.30055 1.47888 257s 257s 257s > ord <- metaMDS(dune, trace = FALSE) 257s 257s > ord 257s 257s Call: 257s metaMDS(comm = dune, trace = FALSE) 257s 257s global Multidimensional Scaling using monoMDS 257s 257s Data: dune 257s Distance: bray 257s 257s Dimensions: 2 257s Stress: 0.1183186 257s Stress type 1, weak ties 257s Best solution was repeated 7 times in 20 tries 257s The best solution was from try 3 (random start) 257s Scaling: centring, PC rotation, halfchange scaling 257s Species: expanded scores based on ‘dune’ 257s 257s 257s > plot(ord) 257s 257s > plot(ord) 257s 257s > plot(ord, type = "n") 257s 257s > points(ord, display = "sites", cex = 0.8, pch = 21, 257s + col = "red", bg = "yellow") 257s 257s > text(ord, display = "species", cex = 0.7, col = "blue") 257s 257s > plot(ord, type = "n") 257s 257s > points(ord, display = "sites", cex = 0.8, pch = 21, 257s + col = "red", bg = "yellow") 257s 257s > text(ord, display = "species", cex = 0.7, col = "blue") 257s 257s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 257s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 257s + col = "blue") 257s 257s > data(dune.env) 257s 257s > attach(dune.env) 257s 257s > plot(ord, disp = "sites", type = "n") 257s 257s > ordihull(ord, Management, col = 1:4, lwd = 3) 257s 257s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 257s + lwd = 3) 257s 257s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 257s 257s > ordispider(ord, Management, col = 1:4, label = TRUE) 257s 257s > points(ord, disp = "sites", pch = 21, col = "red", 257s + bg = "yellow", cex = 1.3) 257s 257s > plot(ord, disp = "sites", type = "n") 257s 257s > ordihull(ord, Management, col = 1:4, lwd = 3) 257s 257s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 257s + lwd = 3) 257s 257s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 257s 257s > ordispider(ord, Management, col = 1:4, label = TRUE) 257s 257s > points(ord, disp = "sites", pch = 21, col = "red", 257s + bg = "yellow", cex = 1.3) 257s 257s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 257s + perm = 999) 257s 257s > ord.fit 257s 257s ***VECTORS 257s 257s NMDS1 NMDS2 r2 Pr(>r) 257s A1 0.96474 0.26322 0.3649 0.016 * 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s Permutation: free 257s Number of permutations: 999 257s 257s ***FACTORS: 257s 257s Centroids: 257s NMDS1 NMDS2 257s ManagementBF -0.4534 -0.0102 257s ManagementHF -0.2636 -0.1282 257s ManagementNM 0.2958 0.5790 257s ManagementSF 0.1506 -0.4670 257s 257s Goodness of fit: 257s r2 Pr(>r) 257s Management 0.4134 0.005 ** 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s Permutation: free 257s Number of permutations: 999 257s 257s 257s 257s > plot(ord, dis = "site") 257s 257s > plot(ord.fit) 257s 257s > ordisurf(ord, A1, add = TRUE) 257s 257s Family: gaussian 257s Link function: identity 257s 257s Formula: 257s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 257s 257s Estimated degrees of freedom: 257s 1.59 total = 2.59 257s 257s REML score: 41.58728 257s 257s > plot(ord, dis = "site") 257s 257s > plot(ord.fit) 257s 257s > ordisurf(ord, A1, add = TRUE) 257s 257s Family: gaussian 257s Link function: identity 257s 257s Formula: 257s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 257s 257s Estimated degrees of freedom: 257s 1.59 total = 2.59 257s 257s REML score: 41.58728 257s 257s > ord <- cca(dune ~ A1 + Management, data = dune.env) 257s 257s > ord 257s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 257s 257s -- Model Summary -- 257s 257s Inertia Proportion Rank 257s Total 2.1153 1.0000 257s Constrained 0.7798 0.3686 4 257s Unconstrained 1.3355 0.6314 15 257s 257s Inertia is scaled Chi-square 257s 257s -- Eigenvalues -- 257s 257s Eigenvalues for constrained axes: 257s CCA1 CCA2 CCA3 CCA4 257s 0.3187 0.2372 0.1322 0.0917 257s 257s Eigenvalues for unconstrained axes: 257s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 257s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 257s CA11 CA12 CA13 CA14 CA15 257s 0.0317 0.0178 0.0116 0.0087 0.0047 257s 257s 257s > plot(ord) 257s 257s > plot(ord) 257s 257s > cca(dune ~ ., data = dune.env) 257s 257s Some constraints or conditions were aliased because they were 257s redundant. This can happen if terms are linearly dependent (collinear): 257s ‘Manure^4’ 257s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 257s Manure, data = dune.env) 257s 257s -- Model Summary -- 257s 257s Inertia Proportion Rank 257s Total 2.1153 1.0000 257s Constrained 1.5032 0.7106 12 257s Unconstrained 0.6121 0.2894 7 257s 257s Inertia is scaled Chi-square 257s 257s -- Note -- 257s 257s Some constraints or conditions were aliased because they were 257s redundant. This can happen if terms are linearly dependent 257s (collinear): ‘Manure^4’ 257s 257s -- Eigenvalues -- 257s 257s Eigenvalues for constrained axes: 257s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 257s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 257s CCA11 CCA12 257s 0.0228 0.0108 257s 257s Eigenvalues for unconstrained axes: 257s CA1 CA2 CA3 CA4 CA5 CA6 CA7 257s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 257s 257s 257s > anova(ord) 257s Permutation test for cca under reduced model 257s Permutation: free 257s Number of permutations: 999 257s 257s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 257s Df ChiSquare F Pr(>F) 257s Model 4 0.77978 2.1896 0.002 ** 257s Residual 15 1.33549 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s 257s > anova(ord, by = "term", permutations = 199) 257s Permutation test for cca under reduced model 257s Terms added sequentially (first to last) 257s Permutation: free 257s Number of permutations: 199 257s 257s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 257s Df ChiSquare F Pr(>F) 257s A1 1 0.22476 2.5245 0.030 * 257s Management 3 0.55502 2.0780 0.015 * 257s Residual 15 1.33549 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s 257s > anova(ord, by = "mar", permutations = 199) 257s Permutation test for cca under reduced model 257s Marginal effects of terms 257s Permutation: free 257s Number of permutations: 199 257s 257s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 257s Df ChiSquare F Pr(>F) 257s A1 1 0.17594 1.9761 0.045 * 257s Management 3 0.55502 2.0780 0.010 ** 257s Residual 15 1.33549 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s 257s > anova(ord, by = "axis", permutations = 499) 257s Permutation test for cca under reduced model 257s Forward tests for axes 257s Permutation: free 257s Number of permutations: 499 257s 257s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 257s Df ChiSquare F Pr(>F) 257s CCA1 1 0.31875 3.5801 0.006 ** 257s CCA2 1 0.23718 2.6640 0.116 257s CCA3 1 0.13217 1.4845 0.844 257s CCA4 1 0.09168 1.0297 1.000 257s Residual 15 1.33549 257s --- 257s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 257s 257s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 257s + data = dune.env) 258s 258s > ord 258s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 258s data = dune.env) 258s 258s -- Model Summary -- 258s 258s Inertia Proportion Rank 258s Total 2.1153 1.0000 258s Conditional 0.6283 0.2970 3 258s Constrained 0.5109 0.2415 4 258s Unconstrained 0.9761 0.4615 12 258s 258s Inertia is scaled Chi-square 258s 258s -- Eigenvalues -- 258s 258s Eigenvalues for constrained axes: 258s CCA1 CCA2 CCA3 CCA4 258s 0.24932 0.12090 0.08160 0.05904 258s 258s Eigenvalues for unconstrained axes: 258s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 258s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 258s CA10 CA11 CA12 258s 0.02102 0.01254 0.00928 258s 258s 258s > anova(ord, by = "term", permutations = 499) 258s Permutation test for cca under reduced model 258s Terms added sequentially (first to last) 258s Permutation: free 258s Number of permutations: 499 258s 258s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 258s Df ChiSquare F Pr(>F) 258s A1 1 0.11543 1.4190 1.000 258s Management 3 0.39543 1.6205 0.002 ** 258s Residual 12 0.97610 258s --- 258s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 258s 258s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 258s 258s > anova(ord, by = "term", permutations = how) 258s Permutation test for cca under reduced model 258s Terms added sequentially (first to last) 258s Plots: dune.env$Moisture, plot permutation: none 258s Permutation: free 258s Number of permutations: 499 258s 258s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 258s Df ChiSquare F Pr(>F) 258s A1 1 0.11543 1.4190 1.000 258s Management 3 0.39543 1.6205 0.002 ** 258s Residual 12 0.97610 258s --- 258s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 258s 258s > detach(dune.env) 258s > 258s 258s R version 4.4.3 (2025-02-28) -- "Trophy Case" 258s Copyright (C) 2025 The R Foundation for Statistical Computing 258s Platform: x86_64-pc-linux-gnu 258s 258s R is free software and comes with ABSOLUTELY NO WARRANTY. 258s You are welcome to redistribute it under certain conditions. 258s Type 'license()' or 'licence()' for distribution details. 258s 258s R is a collaborative project with many contributors. 258s Type 'contributors()' for more information and 258s 'citation()' on how to cite R or R packages in publications. 258s 258s Type 'demo()' for some demos, 'help()' for on-line help, or 258s 'help.start()' for an HTML browser interface to help. 258s Type 'q()' to quit R. 258s 258s > Stangle("partitioning.Rnw") 258s Writing to file partitioning.R 258s > source("partitioning.R", echo=TRUE) 258s 258s > par(mfrow = c(1, 1)) 258s 258s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 258s 258s > options(SweaveHooks = list(fig = figset)) 258s 258s > library(vegan) 258s Loading required package: permute 258s Loading required package: lattice 259s 259s > labs <- paste("Table", 1:4) 259s 259s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 259s 259s > showvarparts(2, bg = cls, Xnames = labs) 259s 259s > showvarparts(3, bg = cls, Xnames = labs) 259s 259s > showvarparts(4, bg = cls, Xnames = labs) 259s > 266s Test cca-object-tests passed 268s Test oecosimu-tests passed 271s Test vegan-tests passed 271s autopkgtest [22:44:04]: test run-unit-test: -----------------------] 272s autopkgtest [22:44:05]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 272s run-unit-test PASS 272s autopkgtest [22:44:05]: test pkg-r-autopkgtest: preparing testbed 272s Reading package lists... 272s Building dependency tree... 272s Reading state information... 273s Starting pkgProblemResolver with broken count: 0 273s Starting 2 pkgProblemResolver with broken count: 0 273s Done 273s The following NEW packages will be installed: 273s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 273s dctrl-tools g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 273s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-14 273s gfortran-14-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 273s libblas-dev libbz2-dev libcc1-0 libdeflate-dev libgcc-14-dev 273s libgfortran-14-dev libhwasan0 libicu-dev libisl23 libitm1 libjpeg-dev 273s libjpeg-turbo8-dev libjpeg8-dev liblapack-dev liblsan0 liblzma-dev libmpc3 273s libncurses-dev libpcre2-16-0 libpcre2-32-0 libpcre2-dev libpcre2-posix3 273s libpkgconf3 libpng-dev libquadmath0 libreadline-dev libstdc++-14-dev 273s libtirpc-dev libtsan2 libubsan1 pkg-r-autopkgtest pkgconf pkgconf-bin 273s r-base-dev zlib1g-dev 273s 0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded. 273s Need to get 103 MB of archives. 273s After this operation, 363 MB of additional disk space will be used. 273s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 274s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [11.9 MB] 274s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-17ubuntu3 [1030 B] 274s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [5586 B] 274s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.2.0-1ubuntu1 [22.4 kB] 274s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 15-20250222-0ubuntu1 [47.0 kB] 274s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 15-20250222-0ubuntu1 [28.6 kB] 274s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 15-20250222-0ubuntu1 [3055 kB] 274s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 15-20250222-0ubuntu1 [1355 kB] 274s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 15-20250222-0ubuntu1 [2756 kB] 275s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 15-20250222-0ubuntu1 [1205 kB] 275s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 15-20250222-0ubuntu1 [1677 kB] 275s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 15-20250222-0ubuntu1 [152 kB] 275s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-17ubuntu3 [2816 kB] 275s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [23.3 MB] 276s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-17ubuntu3 [536 kB] 276s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1208 B] 276s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.2.0-1ubuntu1 [5004 B] 276s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-17ubuntu3 [2486 kB] 276s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [13.4 MB] 276s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-17ubuntu3 [21.8 kB] 276s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [968 B] 276s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.2.0-1ubuntu1 [1100 B] 276s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 276s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB] 276s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran-14-dev amd64 14.2.0-17ubuntu3 [966 kB] 276s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17ubuntu3 [12.6 MB] 277s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-14 amd64 14.2.0-17ubuntu3 [13.6 kB] 277s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1ubuntu1 [1022 B] 277s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 gfortran amd64 4:14.2.0-1ubuntu1 [1174 B] 277s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 icu-devtools amd64 76.1-1ubuntu2 [237 kB] 277s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas-dev amd64 3.12.1-2 [338 kB] 277s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 libbz2-dev amd64 1.0.8-6 [33.8 kB] 277s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 libdeflate-dev amd64 1.23-1 [71.7 kB] 277s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libicu-dev amd64 76.1-1ubuntu2 [12.6 MB] 278s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-turbo8-dev amd64 2.1.5-3ubuntu2 [324 kB] 278s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] 278s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] 278s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack-dev amd64 3.12.1-2 [6489 kB] 278s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 libncurses-dev amd64 6.5+20250216-2 [424 kB] 278s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-16-0 amd64 10.45-1 [268 kB] 278s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-32-0 amd64 10.45-1 [251 kB] 278s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-posix3 amd64 10.45-1 [7204 B] 278s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libpcre2-dev amd64 10.45-1 [908 kB] 278s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libpkgconf3 amd64 1.8.1-4 [32.3 kB] 278s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu1 [895 kB] 278s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libpng-dev amd64 1.6.47-1 [298 kB] 278s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libreadline-dev amd64 8.2-6 [184 kB] 278s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma-dev amd64 5.6.4-1 [189 kB] 278s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf-bin amd64 1.8.1-4 [21.6 kB] 278s Get:52 http://ftpmaster.internal/ubuntu plucky/main amd64 pkgconf amd64 1.8.1-4 [16.8 kB] 278s Get:53 http://ftpmaster.internal/ubuntu plucky/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB] 278s Get:54 http://ftpmaster.internal/ubuntu plucky/universe amd64 r-base-dev all 4.4.3-1 [4176 B] 278s Get:55 http://ftpmaster.internal/ubuntu plucky/universe amd64 pkg-r-autopkgtest all 20231212ubuntu1 [6448 B] 279s Fetched 103 MB in 5s (20.7 MB/s) 279s Selecting previously unselected package libisl23:amd64. 279s (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 ... 84983 files and directories currently installed.) 279s Preparing to unpack .../00-libisl23_0.27-1_amd64.deb ... 279s Unpacking libisl23:amd64 (0.27-1) ... 279s Selecting previously unselected package libmpc3:amd64. 279s Preparing to unpack .../01-libmpc3_1.3.1-1build2_amd64.deb ... 279s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 279s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 279s Preparing to unpack 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libhwasan0:amd64 (15-20250222-0ubuntu1) ... 279s Selecting previously unselected package libquadmath0:amd64. 280s Preparing to unpack .../13-libquadmath0_15-20250222-0ubuntu1_amd64.deb ... 280s Unpacking libquadmath0:amd64 (15-20250222-0ubuntu1) ... 280s Selecting previously unselected package libgcc-14-dev:amd64. 280s Preparing to unpack .../14-libgcc-14-dev_14.2.0-17ubuntu3_amd64.deb ... 280s Unpacking libgcc-14-dev:amd64 (14.2.0-17ubuntu3) ... 280s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 280s Preparing to unpack .../15-gcc-14-x86-64-linux-gnu_14.2.0-17ubuntu3_amd64.deb ... 280s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-17ubuntu3) ... 280s Selecting previously unselected package gcc-14. 280s Preparing to unpack .../16-gcc-14_14.2.0-17ubuntu3_amd64.deb ... 280s Unpacking gcc-14 (14.2.0-17ubuntu3) ... 280s Selecting previously unselected package gcc-x86-64-linux-gnu. 280s Preparing to unpack .../17-gcc-x86-64-linux-gnu_4%3a14.2.0-1ubuntu1_amd64.deb ... 280s 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unselected package libbz2-dev:amd64. 281s Preparing to unpack .../33-libbz2-dev_1.0.8-6_amd64.deb ... 281s Unpacking libbz2-dev:amd64 (1.0.8-6) ... 281s Selecting previously unselected package libdeflate-dev:amd64. 281s Preparing to unpack .../34-libdeflate-dev_1.23-1_amd64.deb ... 281s Unpacking libdeflate-dev:amd64 (1.23-1) ... 281s Selecting previously unselected package libicu-dev:amd64. 281s Preparing to unpack .../35-libicu-dev_76.1-1ubuntu2_amd64.deb ... 281s Unpacking libicu-dev:amd64 (76.1-1ubuntu2) ... 281s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 281s Preparing to unpack .../36-libjpeg-turbo8-dev_2.1.5-3ubuntu2_amd64.deb ... 281s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-3ubuntu2) ... 281s Selecting previously unselected package libjpeg8-dev:amd64. 281s Preparing to unpack .../37-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... 281s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... 281s Selecting previously unselected package libjpeg-dev:amd64. 281s Preparing 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libtsan2:amd64 (15-20250222-0ubuntu1) ... 282s Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... 282s Setting up libisl23:amd64 (0.27-1) ... 282s Setting up libdeflate-dev:amd64 (1.23-1) ... 282s Setting up libicu-dev:amd64 (76.1-1ubuntu2) ... 282s Setting up libcc1-0:amd64 (15-20250222-0ubuntu1) ... 282s Setting up liblsan0:amd64 (15-20250222-0ubuntu1) ... 282s Setting up libblas-dev:amd64 (3.12.1-2) ... 282s 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 282s Setting up dctrl-tools (2.24-3build3) ... 282s Setting up libitm1:amd64 (15-20250222-0ubuntu1) ... 282s Setting up libbz2-dev:amd64 (1.0.8-6) ... 282s Setting up libpcre2-dev:amd64 (10.45-1) ... 282s Setting up libpng-dev:amd64 (1.6.47-1) ... 282s Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... 282s Setting up pkgconf:amd64 (1.8.1-4) ... 282s Setting up liblapack-dev:amd64 (3.12.1-2) ... 282s update-alternatives: using 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282s Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1ubuntu1) ... 282s Setting up gcc (4:14.2.0-1ubuntu1) ... 282s Setting up g++ (4:14.2.0-1ubuntu1) ... 282s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 282s Setting up build-essential (12.10ubuntu1) ... 282s Setting up gfortran (4:14.2.0-1ubuntu1) ... 282s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode 282s 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 282s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 282s 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 282s Setting up r-base-dev (4.4.3-1) ... 282s Setting up pkg-r-autopkgtest (20231212ubuntu1) ... 282s Processing triggers for libc-bin (2.41-1ubuntu2) ... 282s Processing triggers for man-db (2.13.0-1) ... 284s Processing triggers for install-info (7.1.1-1) ... 285s autopkgtest [22:44:18]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 285s autopkgtest [22:44:18]: test pkg-r-autopkgtest: [----------------------- 285s Test: Try to load the R library vegan 285s 285s R version 4.4.3 (2025-02-28) -- "Trophy Case" 285s Copyright (C) 2025 The R Foundation for Statistical Computing 285s Platform: x86_64-pc-linux-gnu 285s 285s R is free software and comes with ABSOLUTELY NO WARRANTY. 285s You are welcome to redistribute it under certain conditions. 285s Type 'license()' or 'licence()' for distribution details. 285s 285s R is a collaborative project with many contributors. 285s Type 'contributors()' for more information and 285s 'citation()' on how to cite R or R packages in publications. 285s 285s Type 'demo()' for some demos, 'help()' for on-line help, or 285s 'help.start()' for an HTML browser interface to help. 285s Type 'q()' to quit R. 285s 285s > library('vegan') 285s Loading required package: permute 285s Loading required package: lattice 286s > 286s > 286s Other tests are currently unsupported! 286s They will be progressively added. 286s autopkgtest [22:44:19]: test pkg-r-autopkgtest: -----------------------] 287s pkg-r-autopkgtest PASS 287s autopkgtest [22:44:20]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 288s autopkgtest [22:44:21]: @@@@@@@@@@@@@@@@@@@@ summary 288s run-unit-test PASS 288s pkg-r-autopkgtest PASS 294s nova [W] Skipping flock for amd64 294s Creating nova instance adt-plucky-amd64-r-cran-vegan-20250315-223933-juju-7f2275-prod-proposed-migration-environment-20-44daef2f-ad81-4693-9c9d-c5f5e1cf7059 from image adt/ubuntu-plucky-amd64-server-20250304.img (UUID 9c7d4da5-d95f-4c85-ac1f-51eb37e75c4c)... 294s nova [W] Timed out waiting for 1de2a2f4-d681-4d24-addf-076115d514aa to get deleted.