0s autopkgtest [00:42:26]: starting date and time: 2026-02-10 00:42:26+0000 0s autopkgtest [00:42:26]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:42:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.vd6v2jng/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:lattice --apt-upgrade r-cran-vegan --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=lattice/0.22-9-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@sto01-25.secgroup --name adt-resolute-amd64-r-cran-vegan-20260210-004225-juju-7f2275-prod-proposed-migration-environment-2-8e2d3265-a37e-412d-ad41-6e6d6ed20614 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-r-cran-vegan-20260210-004225-juju-7f2275-prod-proposed-migration-environment-2-8e2d3265-a37e-412d-ad41-6e6d6ed20614 from image adt/ubuntu-resolute-amd64-server-20260204.img (UUID fedf54b4-458b-493e-8072-6425c19717b4)... 74s autopkgtest [00:43:40]: testbed dpkg architecture: amd64 75s autopkgtest [00:43:41]: testbed apt version: 3.1.14 75s autopkgtest [00:43:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s autopkgtest [00:43:41]: testbed release detected to be: None 76s autopkgtest [00:43:42]: updating testbed package index (apt update) 76s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 76s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB] 76s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 76s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1637 kB] 76s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [201 kB] 76s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [253 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5996 B] 77s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [316 B] 77s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [1584 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [639 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [33.3 kB] 77s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [4320 B] 77s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [25.2 kB] 77s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [996 B] 77s Fetched 4710 kB in 1s (4490 kB/s) 78s Reading package lists... 79s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 79s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 79s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 79s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 79s Reading package lists... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s Calculating upgrade... 80s The following package was automatically installed and is no longer required: 80s libpython3.13 80s Use 'sudo apt autoremove' to remove it. 80s The following NEW packages will be installed: 80s gcc-16-base libpython3.14 libpython3.14-minimal libpython3.14-stdlib 80s linux-headers-6.19.0-3 linux-headers-6.19.0-3-generic 80s linux-image-6.19.0-3-generic linux-modules-6.19.0-3-generic 80s linux-tools-6.19.0-3 linux-tools-6.19.0-3-generic 80s The following packages will be upgraded: 80s 3cpio amd64-microcode apt bpftool busybox-initramfs busybox-static 80s cryptsetup-bin dash dbus dbus-bin dbus-daemon dbus-session-bus-common 80s dbus-system-bus-common dbus-user-session debianutils dmsetup dracut-install 80s ethtool findutils gir1.2-girepository-3.0 gir1.2-glib-2.0 hwdata iproute2 80s iptables less libapt-pkg7.0 libatomic1 libattr1 libbpf1 libbsd0 80s libcryptsetup12 libdbus-1-3 libdevmapper1.02.1 libdrm-amdgpu1 libdrm-common 80s libdrm2 libevent-core-2.1-7t64 libgcc-s1 libgdbm-compat4t64 libgdbm6t64 80s libgirepository-2.0-0 libglib2.0-0t64 libglib2.0-data libgpm2 libgudev-1.0-0 80s libidn2-0 libip4tc2 libip6tc2 libjansson4 libkeyutils1 liblsof0 80s libmaxminddb0 libnetfilter-conntrack3 libnpth0t64 libonig5 libpcap0.8t64 80s libpci3 libsensors-config libsensors5 libstdc++6 libusb-1.0-0 libwrap0 80s libxau6 libxkbcommon0 libxtables12 linux-generic linux-headers-generic 80s linux-headers-virtual linux-image-generic linux-image-virtual linux-perf 80s linux-tools-common linux-virtual lsof man-db mawk patch pciutils pnp.ids 80s pollinate python3-linkify-it python3-markdown-it python3-referencing sed 80s shared-mime-info tar tcpdump ubuntu-kernel-accessories ubuntu-standard wget 80s 90 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 237 MB of archives. 80s After this operation, 339 MB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 debianutils amd64 5.23.2build1 [93.3 kB] 80s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 dash amd64 0.5.12-12ubuntu3 [96.0 kB] 80s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 findutils amd64 4.10.0-3build2 [307 kB] 80s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 sed amd64 4.9-2build3 [195 kB] 80s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 tar amd64 1.35+dfsg-3.1build2 [257 kB] 80s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libattr1 amd64 1:2.5.2-3build2 [11.4 kB] 80s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-16-base amd64 16-20260208-1ubuntu1 [59.7 kB] 80s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-s1 amd64 16-20260208-1ubuntu1 [80.3 kB] 80s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libbsd0 amd64 0.12.2-2build2 [42.3 kB] 80s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 mawk amd64 1.3.4.20260129-1 [133 kB] 80s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++6 amd64 16-20260208-1ubuntu1 [844 kB] 80s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libapt-pkg7.0 amd64 3.1.15 [1151 kB] 80s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 apt amd64 3.1.15 [1479 kB] 80s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-system-bus-common all 1.16.2-2ubuntu3 [55.8 kB] 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-session-bus-common all 1.16.2-2ubuntu3 [54.4 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-user-session amd64 1.16.2-2ubuntu3 [9696 B] 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-daemon amd64 1.16.2-2ubuntu3 [119 kB] 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus-bin amd64 1.16.2-2ubuntu3 [40.1 kB] 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 dbus amd64 1.16.2-2ubuntu3 [24.2 kB] 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libdbus-1-3 amd64 1.16.2-2ubuntu3 [185 kB] 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libdevmapper1.02.1 amd64 2:1.02.205-2ubuntu3 [142 kB] 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 dmsetup amd64 2:1.02.205-2ubuntu3 [79.4 kB] 80s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 ethtool amd64 1:6.15-3build1 [318 kB] 80s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-girepository-3.0 amd64 2.87.2-2 [25.2 kB] 80s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libgirepository-2.0-0 amd64 2.87.2-2 [76.1 kB] 80s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libatomic1 amd64 16-20260208-1ubuntu1 [11.4 kB] 80s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 gir1.2-glib-2.0 amd64 2.87.2-2 [182 kB] 80s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-0t64 amd64 2.87.2-2 [1613 kB] 80s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 libbpf1 amd64 1:1.6.2-1build1 [184 kB] 80s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 iptables amd64 1.8.11-2ubuntu3 [381 kB] 80s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libip4tc2 amd64 1.8.11-2ubuntu3 [24.2 kB] 80s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libip6tc2 amd64 1.8.11-2ubuntu3 [24.4 kB] 80s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libnetfilter-conntrack3 amd64 1.1.1-1 [47.5 kB] 80s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libxtables12 amd64 1.8.11-2ubuntu3 [36.6 kB] 80s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 iproute2 amd64 6.18.0-1ubuntu1 [1178 kB] 80s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 less amd64 668-1build1 [172 kB] 80s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libcryptsetup12 amd64 2:2.8.0-1ubuntu3 [283 kB] 80s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libglib2.0-data all 2.87.2-2 [58.2 kB] 80s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libidn2-0 amd64 2.3.8-4build1 [67.6 kB] 80s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libkeyutils1 amd64 1.6.3-6ubuntu3 [10.6 kB] 80s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-linkify-it all 2.0.3-1ubuntu3 [19.4 kB] 80s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-markdown-it all 3.0.0-3build1 [54.4 kB] 80s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 shared-mime-info amd64 2.4-5build3 [476 kB] 80s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-static amd64 1:1.37.0-7ubuntu1 [1034 kB] 80s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-common all 2.4.131-1 [9774 B] 80s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm2 amd64 2.4.131-1 [42.3 kB] 80s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm6t64 amd64 1.26-1build1 [36.5 kB] 80s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libgpm2 amd64 1.20.7-12build1 [14.4 kB] 80s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libjansson4 amd64 2.14-2build4 [33.2 kB] 80s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 lsof amd64 4.99.4+dfsg-2build2 [239 kB] 80s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsof0 amd64 4.99.4+dfsg-2build2 [56.5 kB] 80s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 libmaxminddb0 amd64 1.12.2-1build2 [18.9 kB] 80s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcap0.8t64 amd64 1.10.5-2ubuntu3 [154 kB] 80s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 pciutils amd64 1:3.14.0-1build2 [95.5 kB] 80s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libpci3 amd64 1:3.14.0-1build2 [38.1 kB] 80s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors-config all 1:3.6.2-2build1 [6862 B] 80s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 libsensors5 amd64 1:3.6.2-2build1 [28.9 kB] 80s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libusb-1.0-0 amd64 2:1.0.29-2build1 [56.9 kB] 80s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libxau6 amd64 1:1.0.11-1build2 [7502 B] 80s Get:60 http://ftpmaster.internal/ubuntu resolute/main amd64 libxkbcommon0 amd64 1.13.1-1 [159 kB] 80s Get:61 http://ftpmaster.internal/ubuntu resolute/main amd64 man-db amd64 2.13.1-1build1 [1392 kB] 80s Get:62 http://ftpmaster.internal/ubuntu resolute/main amd64 tcpdump amd64 4.99.5-2ubuntu3 [477 kB] 80s Get:63 http://ftpmaster.internal/ubuntu resolute/main amd64 wget amd64 1.25.0-2ubuntu4 [353 kB] 80s Get:64 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-standard amd64 1.564 [13.3 kB] 80s Get:65 http://ftpmaster.internal/ubuntu resolute/main amd64 3cpio amd64 0.14.0-1ubuntu1 [285 kB] 80s Get:66 http://ftpmaster.internal/ubuntu resolute/main amd64 bpftool amd64 7.7.0+6.19.0-3.3 [1229 kB] 80s Get:67 http://ftpmaster.internal/ubuntu resolute/main amd64 busybox-initramfs amd64 1:1.37.0-7ubuntu1 [191 kB] 80s Get:68 http://ftpmaster.internal/ubuntu resolute/main amd64 cryptsetup-bin amd64 2:2.8.0-1ubuntu3 [228 kB] 80s Get:69 http://ftpmaster.internal/ubuntu resolute/main amd64 dracut-install amd64 109-11ubuntu1 [45.8 kB] 80s Get:70 http://ftpmaster.internal/ubuntu resolute/main amd64 hwdata all 0.394-1build1 [1566 B] 80s Get:71 http://ftpmaster.internal/ubuntu resolute/main amd64 pnp.ids all 0.394-1build1 [29.6 kB] 80s Get:72 http://ftpmaster.internal/ubuntu resolute/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [23.2 kB] 80s Get:73 http://ftpmaster.internal/ubuntu resolute/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10build2 [93.1 kB] 80s Get:74 http://ftpmaster.internal/ubuntu resolute/main amd64 libgdbm-compat4t64 amd64 1.26-1build1 [6796 B] 80s Get:75 http://ftpmaster.internal/ubuntu resolute/main amd64 libgudev-1.0-0 amd64 1:238-7build1 [15.9 kB] 80s Get:76 http://ftpmaster.internal/ubuntu resolute/main amd64 libnpth0t64 amd64 1.8-3build1 [9302 B] 80s Get:77 http://ftpmaster.internal/ubuntu resolute/main amd64 libonig5 amd64 6.9.10-1build1 [174 kB] 80s Get:78 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-minimal amd64 3.14.2-1 [920 kB] 80s Get:79 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14-stdlib amd64 3.14.2-1 [2398 kB] 80s Get:80 http://ftpmaster.internal/ubuntu resolute/main amd64 libpython3.14 amd64 3.14.2-1 [2568 kB] 80s Get:81 http://ftpmaster.internal/ubuntu resolute/main amd64 libwrap0 amd64 7.6.q-36build2 [48.5 kB] 80s Get:82 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-modules-6.19.0-3-generic amd64 6.19.0-3.3 [171 MB] 84s Get:83 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-6.19.0-3-generic amd64 6.19.0-3.3+1 [16.8 MB] 84s Get:84 http://ftpmaster.internal/ubuntu resolute/main amd64 amd64-microcode amd64 3.20251202.1ubuntu1 [459 kB] 84s Get:85 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-generic amd64 6.19.0-3.3 [1698 B] 84s Get:86 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-generic amd64 6.19.0-3.3 [12.2 kB] 84s Get:87 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-virtual amd64 6.19.0-3.3 [1700 B] 84s Get:88 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-image-virtual amd64 6.19.0-3.3 [12.1 kB] 84s Get:89 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-virtual amd64 6.19.0-3.3 [1646 B] 84s Get:90 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3 all 6.19.0-3.3 [14.9 MB] 84s Get:91 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-6.19.0-3-generic amd64 6.19.0-3.3 [4330 kB] 84s Get:92 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-headers-generic amd64 6.19.0-3.3 [12.0 kB] 84s Get:93 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-perf amd64 6.19.0-3.3 [4480 kB] 84s Get:94 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-common all 6.19.0-3.3 [345 kB] 84s Get:95 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3 amd64 6.19.0-3.3 [1455 kB] 84s Get:96 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-tools-6.19.0-3-generic amd64 6.19.0-3.3 [1612 B] 84s Get:97 http://ftpmaster.internal/ubuntu resolute/main amd64 patch amd64 2.8-2build1 [95.7 kB] 84s Get:98 http://ftpmaster.internal/ubuntu resolute/main amd64 pollinate all 4.33-4ubuntu5 [14.0 kB] 84s Get:99 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-referencing all 0.36.2-1ubuntu2 [22.2 kB] 84s Get:100 http://ftpmaster.internal/ubuntu resolute/main amd64 ubuntu-kernel-accessories amd64 1.564 [13.1 kB] 85s dpkg-preconfigure: unable to re-open stdin: No such file or directory 85s Fetched 237 MB in 5s (49.5 MB/s) 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../debianutils_5.23.2build1_amd64.deb ... 85s Unpacking debianutils (5.23.2build1) over (5.23.2) ... 85s Setting up debianutils (5.23.2build1) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../dash_0.5.12-12ubuntu3_amd64.deb ... 85s Unpacking dash (0.5.12-12ubuntu3) over (0.5.12-12ubuntu2) ... 85s Setting up dash (0.5.12-12ubuntu3) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../findutils_4.10.0-3build2_amd64.deb ... 85s Unpacking findutils (4.10.0-3build2) over (4.10.0-3build1) ... 85s Setting up findutils (4.10.0-3build2) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../sed_4.9-2build3_amd64.deb ... 85s Unpacking sed (4.9-2build3) over (4.9-2build2) ... 85s Setting up sed (4.9-2build3) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../tar_1.35+dfsg-3.1build2_amd64.deb ... 85s Unpacking tar (1.35+dfsg-3.1build2) over (1.35+dfsg-3.1build1) ... 85s Setting up tar (1.35+dfsg-3.1build2) ... 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../libattr1_1%3a2.5.2-3build2_amd64.deb ... 85s Unpacking libattr1:amd64 (1:2.5.2-3build2) over (1:2.5.2-3build1) ... 85s Setting up libattr1:amd64 (1:2.5.2-3build2) ... 85s Selecting previously unselected package gcc-16-base:amd64. 85s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 83957 files and directories currently installed.) 85s Preparing to unpack .../gcc-16-base_16-20260208-1ubuntu1_amd64.deb ... 85s Unpacking gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 85s Setting up gcc-16-base:amd64 (16-20260208-1ubuntu1) ... 85s (Reading database ... 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(7.7.0+6.19.0-3.3) ... 93s Setting up libip6tc2:amd64 (1.8.11-2ubuntu3) ... 93s Setting up liblsof0 (4.99.4+dfsg-2build2) ... 93s Setting up libmaxminddb0:amd64 (1.12.2-1build2) ... 93s Setting up libpython3.14-minimal:amd64 (3.14.2-1) ... 93s Setting up libsensors-config (1:3.6.2-2build1) ... 93s Setting up less (668-1build1) ... 93s Setting up linux-headers-6.19.0-3 (6.19.0-3.3) ... 93s Setting up libidn2-0:amd64 (2.3.8-4build1) ... 93s Setting up amd64-microcode (3.20251202.1ubuntu1) ... 93s amd64-microcode: microcode will be updated at next boot 93s Setting up man-db (2.13.1-1build1) ... 93s Updating database of manual pages ... 94s man-db.service is a disabled or a static unit not running, not starting it. 94s Setting up libjansson4:amd64 (2.14-2build4) ... 94s Setting up libglib2.0-data (2.87.2-2) ... 94s Setting up pollinate (4.33-4ubuntu5) ... 105s Setting up busybox-static (1:1.37.0-7ubuntu1) ... 105s Setting up libwrap0:amd64 (7.6.q-36build2) ... 105s Setting up linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 106s I: /boot/vmlinuz is now a symlink to vmlinuz-6.19.0-3-generic 106s I: /boot/initrd.img is now a symlink to initrd.img-6.19.0-3-generic 106s Setting up libdbus-1-3:amd64 (1.16.2-2ubuntu3) ... 106s Setting up libatomic1:amd64 (16-20260208-1ubuntu1) ... 106s Setting up patch (2.8-2build1) ... 106s Setting up libsensors5:amd64 (1:3.6.2-2build1) ... 106s Setting up busybox-initramfs (1:1.37.0-7ubuntu1) ... 106s Setting up libxtables12:amd64 (1.8.11-2ubuntu3) ... 106s Setting up lsof (4.99.4+dfsg-2build2) ... 106s Setting up libpci3:amd64 (1:3.14.0-1build2) ... 106s Setting up libdevmapper1.02.1:amd64 (2:1.02.205-2ubuntu3) ... 106s Setting up dracut-install (109-11ubuntu1) ... 106s Setting up dmsetup (2:1.02.205-2ubuntu3) ... 106s Setting up libnetfilter-conntrack3:amd64 (1.1.1-1) ... 106s Setting up pnp.ids (0.394-1build1) ... 106s Setting up dbus-session-bus-common (1.16.2-2ubuntu3) ... 106s Setting up python3-linkify-it (2.0.3-1ubuntu3) ... 106s Setting up libpcap0.8t64:amd64 (1.10.5-2ubuntu3) ... 106s Setting up libcryptsetup12:amd64 (2:2.8.0-1ubuntu3) ... 106s Setting up mawk (1.3.4.20260129-1) ... 106s Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10build2) ... 106s Setting up libusb-1.0-0:amd64 (2:1.0.29-2build1) ... 106s Setting up linux-image-virtual (6.19.0-3.3) ... 106s Setting up dbus-system-bus-common (1.16.2-2ubuntu3) ... 106s Setting up libbsd0:amd64 (0.12.2-2build2) ... 106s Setting up libdrm-common (2.4.131-1) ... 106s Setting up libstdc++6:amd64 (16-20260208-1ubuntu1) ... 106s Setting up dbus-bin (1.16.2-2ubuntu3) ... 106s Setting up libonig5:amd64 (6.9.10-1build1) ... 106s Setting up libbpf1:amd64 (1:1.6.2-1build1) ... 106s Setting up ethtool (1:6.15-3build1) ... 106s Setting up python3-referencing (0.36.2-1ubuntu2) ... 106s Setting up libxkbcommon0:amd64 (1.13.1-1) ... 106s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 106s Setting up linux-headers-6.19.0-3-generic (6.19.0-3.3) ... 106s Setting up tcpdump (4.99.5-2ubuntu3) ... 106s Setting up linux-image-generic (6.19.0-3.3) ... 106s Setting up wget (1.25.0-2ubuntu4) ... 106s Setting up libpython3.14-stdlib:amd64 (3.14.2-1) ... 106s Setting up iptables (1.8.11-2ubuntu3) ... 106s Setting up iproute2 (6.18.0-1ubuntu1) ... 106s Setting up linux-headers-generic (6.19.0-3.3) ... 106s Setting up dbus-daemon (1.16.2-2ubuntu3) ... 106s Setting up hwdata (0.394-1build1) ... 106s Setting up dbus-user-session (1.16.2-2ubuntu3) ... 106s Setting up libglib2.0-0t64:amd64 (2.87.2-2) ... 106s No schema files found: doing nothing. 106s Setting up dbus (1.16.2-2ubuntu3) ... 106s A reboot is required to replace the running dbus-daemon. 106s Please reboot the system when convenient. 107s Setting up shared-mime-info (2.4-5build3) ... 107s Setting up gir1.2-glib-2.0:amd64 (2.87.2-2) ... 107s Setting up pciutils (1:3.14.0-1build2) ... 107s Setting up python3-markdown-it (3.0.0-3build1) ... 107s Setting up libdrm2:amd64 (2.4.131-1) ... 107s Setting up libpython3.14:amd64 (3.14.2-1) ... 107s Setting up libapt-pkg7.0:amd64 (3.1.15) ... 107s Setting up linux-tools-common (6.19.0-3.3) ... 107s Setting up libgudev-1.0-0:amd64 (1:238-7build1) ... 107s Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... 107s Setting up apt (3.1.15) ... 108s Setting up linux-headers-virtual (6.19.0-3.3) ... 108s Setting up linux-generic (6.19.0-3.3) ... 108s Setting up libgirepository-2.0-0:amd64 (2.87.2-2) ... 108s Setting up linux-tools-6.19.0-3 (6.19.0-3.3) ... 108s Setting up ubuntu-standard (1.564) ... 108s Setting up gir1.2-girepository-3.0:amd64 (2.87.2-2) ... 108s Setting up linux-virtual (6.19.0-3.3) ... 108s Setting up linux-perf (6.19.0-3.3) ... 108s Setting up linux-tools-6.19.0-3-generic (6.19.0-3.3) ... 108s Processing triggers for debianutils (5.23.2build1) ... 108s Processing triggers for install-info (7.2-5) ... 108s Processing triggers for initramfs-tools (0.150ubuntu7) ... 108s update-initramfs: Generating /boot/initrd.img-6.18.0-9-generic 113s Processing triggers for libc-bin (2.42-2ubuntu4) ... 113s Processing triggers for linux-image-6.19.0-3-generic (6.19.0-3.3+1) ... 113s /etc/kernel/postinst.d/initramfs-tools: 113s update-initramfs: Generating /boot/initrd.img-6.19.0-3-generic 116s /etc/kernel/postinst.d/zz-update-grub: 116s Sourcing file `/etc/default/grub' 116s Sourcing file `/etc/default/grub.d/50-cloudimg-settings.cfg' 116s Sourcing file `/etc/default/grub.d/90-autopkgtest.cfg' 116s Generating grub configuration file ... 116s Found linux image: /boot/vmlinuz-6.19.0-3-generic 117s Found initrd image: /boot/initrd.img-6.19.0-3-generic 117s Found linux image: /boot/vmlinuz-6.18.0-9-generic 117s Found initrd image: /boot/initrd.img-6.18.0-9-generic 117s Warning: os-prober will not be executed to detect other bootable partitions. 117s Systems on them will not be added to the GRUB boot configuration. 117s Check GRUB_DISABLE_OS_PROBER documentation entry. 117s Adding boot menu entry for UEFI Firmware Settings ... 117s done 117s autopkgtest [00:44:23]: upgrading testbed (apt dist-upgrade and autopurge) 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s The following package was automatically installed and is no longer required: 118s libpython3.13 118s Use 'sudo apt autoremove' to remove it. 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Solving dependencies... 118s The following packages will be REMOVED: 118s libpython3.13* 118s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 118s After this operation, 7599 kB disk space will be freed. 118s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125273 files and directories currently installed.) 118s Removing libpython3.13:amd64 (3.13.11-1) ... 118s Processing triggers for libc-bin (2.42-2ubuntu4) ... 119s autopkgtest [00:44:25]: rebooting testbed after setup commands that affected boot 147s autopkgtest [00:44:53]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 23 20:01:24 UTC 2026 149s autopkgtest [00:44:55]: @@@@@@@@@@@@@@@@@@@@ apt-source r-cran-vegan 151s Get:1 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (dsc) [2211 B] 151s Get:2 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (tar) [1207 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute/universe r-cran-vegan 2.6-10+dfsg-3 (diff) [6396 B] 151s gpgv: Signature made Sat Apr 19 05:22:19 2025 UTC 151s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 151s gpgv: issuer "tille@debian.org" 151s gpgv: Can't check signature: No public key 151s dpkg-source: warning: cannot verify inline signature for ./r-cran-vegan_2.6-10+dfsg-3.dsc: no acceptable signature found 151s autopkgtest [00:44:57]: testing package r-cran-vegan version 2.6-10+dfsg-3 151s autopkgtest [00:44:57]: build not needed 162s autopkgtest [00:45:08]: test run-unit-test: preparing testbed 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Solving dependencies... 163s The following NEW packages will be installed: 163s fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono 163s fonts-glyphicons-halflings fonts-mathjax libblas3 libcairo2 libdatrie1 163s libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 163s libharfbuzz0b libice6 libjbig0 libjpeg-turbo8 libjpeg8 libjs-bootstrap 163s libjs-highlight.js libjs-jquery libjs-jquery-datatables libjs-mathjax 163s liblapack3 liblerc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 163s libpaper-utils libpaper2 libpixman-1-0 libsharpyuv0 libsm6 libtcl8.6 163s libthai-data libthai0 libtiff6 libtk8.6 libwebp7 libxcb-render0 libxcb-shm0 163s libxft2 libxrender1 libxss1 libxt6t64 node-normalize.css r-base-core 163s r-cran-cluster r-cran-commonmark r-cran-evaluate r-cran-highr r-cran-knitr 163s r-cran-lattice r-cran-markdown r-cran-mass r-cran-matrix r-cran-mgcv 163s r-cran-nlme r-cran-permute r-cran-vegan r-cran-xfun r-cran-yaml unzip 163s x11-common xdg-utils zip 163s 0 upgraded, 67 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 67.9 MB of archives. 163s After this operation, 160 MB of additional disk space will be used. 163s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-mono all 2.37-8build1 [502 kB] 163s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-dejavu-core all 2.37-8build1 [834 kB] 163s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig-config amd64 2.17.1-3ubuntu1 [38.5 kB] 163s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libfontconfig1 amd64 2.17.1-3ubuntu1 [144 kB] 163s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 fontconfig amd64 2.17.1-3ubuntu1 [180 kB] 163s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-6 [119 kB] 163s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-mathjax all 2.7.9+dfsg-1build1 [2283 kB] 163s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-7ubuntu1 [260 kB] 163s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 libpixman-1-0 amd64 0.46.4-1 [287 kB] 163s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-render0 amd64 1.17.0-2ubuntu1 [16.2 kB] 163s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 libxcb-shm0 amd64 1.17.0-2ubuntu1 [5808 B] 163s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libxrender1 amd64 1:0.9.12-1 [19.8 kB] 163s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libcairo2 amd64 1.18.4-3 [579 kB] 163s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libdatrie1 amd64 0.2.14-1 [19.8 kB] 163s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate0 amd64 1.23-2build1 [51.6 kB] 163s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 16-20260208-1ubuntu1 [957 kB] 163s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libgomp1 amd64 16-20260208-1ubuntu1 [162 kB] 163s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libgraphite2-3 amd64 1.3.14-11ubuntu1 [73.7 kB] 163s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libharfbuzz0b amd64 12.3.2-1 [519 kB] 163s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 x11-common all 1:7.7+24ubuntu1 [22.4 kB] 163s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 libice6 amd64 2:1.1.1-1build1 [44.0 kB] 163s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8 amd64 2.1.5-4ubuntu3 [156 kB] 163s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8 amd64 8c-2ubuntu12 [2142 B] 163s Get:24 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-bootstrap all 3.4.1+dfsg-6 [129 kB] 163s Get:25 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-highlight.js all 10.7.3+dfsg-2 [144 kB] 163s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 163s Get:27 http://ftpmaster.internal/ubuntu resolute/universe amd64 libjs-jquery-datatables all 1.11.5+dfsg-2build1 [145 kB] 163s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-7ubuntu1 [2739 kB] 163s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 liblerc4 amd64 4.0.0+ds-5ubuntu2 [207 kB] 163s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai-data all 0.1.30-1 [155 kB] 163s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 libthai0 amd64 0.1.30-1 [19.2 kB] 163s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libpango-1.0-0 amd64 1.57.0-1 [241 kB] 163s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangoft2-1.0-0 amd64 1.57.0-1 [53.3 kB] 163s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 libpangocairo-1.0-0 amd64 1.57.0-1 [29.0 kB] 163s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper2 amd64 2.2.5-0.3build1 [17.3 kB] 163s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 libpaper-utils amd64 2.2.5-0.3build1 [15.6 kB] 163s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 libsharpyuv0 amd64 1.5.0-0.1build1 [17.6 kB] 163s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libsm6 amd64 2:1.2.6-1build1 [16.9 kB] 163s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1build1 [1003 kB] 163s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libjbig0 amd64 2.1-6.1ubuntu3 [30.0 kB] 163s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libwebp7 amd64 1.5.0-0.1build1 [264 kB] 163s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libtiff6 amd64 4.7.0-3ubuntu3 [209 kB] 163s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libxft2 amd64 2.3.6-1build2 [45.1 kB] 163s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libxss1 amd64 1:1.2.3-1build4 [7084 B] 163s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 libtk8.6 amd64 8.6.17-1 [823 kB] 163s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libxt6t64 amd64 1:1.2.1-1.3 [173 kB] 163s Get:47 http://ftpmaster.internal/ubuntu resolute/universe amd64 node-normalize.css all 8.0.1-5.1 [10.4 kB] 163s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 zip amd64 3.0-15ubuntu3 [175 kB] 163s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 unzip amd64 6.0-29ubuntu1 [180 kB] 163s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 xdg-utils all 1.2.1-2ubuntu2 [66.1 kB] 163s Get:51 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-core amd64 4.5.2-1ubuntu2 [28.8 MB] 164s Get:52 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-cluster amd64 2.1.8.2-1 [570 kB] 164s Get:53 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-commonmark amd64 1.9.5-1 [138 kB] 164s Get:54 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-evaluate all 1.0.5-1 [117 kB] 164s Get:55 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-xfun amd64 0.55+dfsg-1 [587 kB] 164s Get:56 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-highr all 0.11+dfsg-1 [38.5 kB] 164s Get:57 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-yaml amd64 2.3.10-1 [109 kB] 164s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-mathjax all 2.7.9+dfsg-1build1 [6017 kB] 164s Get:59 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-knitr all 1.51+dfsg-1 [847 kB] 164s Get:60 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 r-cran-lattice amd64 0.22-9-1 [1399 kB] 164s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-markdown all 1.13-1 [162 kB] 164s Get:62 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mass amd64 7.3-65-1 [1116 kB] 164s Get:63 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-matrix amd64 1.7-4-1 [4220 kB] 165s Get:64 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-nlme amd64 3.1.168-1 [2320 kB] 165s Get:65 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-mgcv amd64 1.9-4-1 [3556 kB] 165s Get:66 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-permute all 0.9-8-1 [237 kB] 165s Get:67 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-cran-vegan amd64 2.6-10+dfsg-3 [3137 kB] 165s Preconfiguring packages ... 165s Fetched 67.9 MB in 2s (28.8 MB/s) 165s Selecting previously unselected package fonts-dejavu-mono. 165s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 125269 files and directories currently installed.) 165s Preparing to unpack .../00-fonts-dejavu-mono_2.37-8build1_all.deb ... 165s Unpacking fonts-dejavu-mono (2.37-8build1) ... 165s Selecting previously unselected package fonts-dejavu-core. 165s Preparing to unpack .../01-fonts-dejavu-core_2.37-8build1_all.deb ... 165s Unpacking fonts-dejavu-core (2.37-8build1) ... 165s Selecting previously unselected package fontconfig-config. 165s Preparing to unpack .../02-fontconfig-config_2.17.1-3ubuntu1_amd64.deb ... 165s Unpacking fontconfig-config (2.17.1-3ubuntu1) ... 165s Selecting previously unselected package libfontconfig1:amd64. 165s Preparing to unpack .../03-libfontconfig1_2.17.1-3ubuntu1_amd64.deb ... 165s Unpacking libfontconfig1:amd64 (2.17.1-3ubuntu1) ... 165s Selecting previously unselected package fontconfig. 165s Preparing to unpack .../04-fontconfig_2.17.1-3ubuntu1_amd64.deb ... 165s Unpacking fontconfig (2.17.1-3ubuntu1) ... 165s Selecting previously unselected package fonts-glyphicons-halflings. 165s Preparing to unpack .../05-fonts-glyphicons-halflings_1.009~3.4.1+dfsg-6_all.deb ... 165s Unpacking fonts-glyphicons-halflings (1.009~3.4.1+dfsg-6) ... 165s Selecting previously unselected package fonts-mathjax. 166s Preparing to unpack .../06-fonts-mathjax_2.7.9+dfsg-1build1_all.deb ... 166s Unpacking fonts-mathjax (2.7.9+dfsg-1build1) ... 166s Selecting previously unselected package libblas3:amd64. 166s Preparing to unpack .../07-libblas3_3.12.1-7ubuntu1_amd64.deb ... 166s Unpacking libblas3:amd64 (3.12.1-7ubuntu1) ... 166s Selecting previously unselected package libpixman-1-0:amd64. 166s Preparing to unpack .../08-libpixman-1-0_0.46.4-1_amd64.deb ... 166s Unpacking libpixman-1-0:amd64 (0.46.4-1) ... 166s Selecting previously unselected package libxcb-render0:amd64. 166s Preparing to unpack .../09-libxcb-render0_1.17.0-2ubuntu1_amd64.deb ... 166s Unpacking libxcb-render0:amd64 (1.17.0-2ubuntu1) ... 166s Selecting previously unselected package libxcb-shm0:amd64. 166s Preparing to unpack .../10-libxcb-shm0_1.17.0-2ubuntu1_amd64.deb ... 166s Unpacking libxcb-shm0:amd64 (1.17.0-2ubuntu1) ... 166s Selecting previously unselected package libxrender1:amd64. 166s Preparing to unpack .../11-libxrender1_1%3a0.9.12-1_amd64.deb ... 166s Unpacking libxrender1:amd64 (1:0.9.12-1) ... 166s Selecting previously unselected package libcairo2:amd64. 166s Preparing to unpack .../12-libcairo2_1.18.4-3_amd64.deb ... 166s Unpacking libcairo2:amd64 (1.18.4-3) ... 166s Selecting previously unselected package libdatrie1:amd64. 166s Preparing to unpack .../13-libdatrie1_0.2.14-1_amd64.deb ... 166s Unpacking libdatrie1:amd64 (0.2.14-1) ... 166s Selecting previously unselected package libdeflate0:amd64. 166s Preparing to unpack .../14-libdeflate0_1.23-2build1_amd64.deb ... 166s Unpacking libdeflate0:amd64 (1.23-2build1) ... 166s Selecting previously unselected package libgfortran5:amd64. 166s Preparing to unpack .../15-libgfortran5_16-20260208-1ubuntu1_amd64.deb ... 166s Unpacking libgfortran5:amd64 (16-20260208-1ubuntu1) ... 166s Selecting previously unselected package libgomp1:amd64. 166s Preparing to unpack .../16-libgomp1_16-20260208-1ubuntu1_amd64.deb ... 166s Unpacking libgomp1:amd64 (16-20260208-1ubuntu1) ... 166s Selecting previously unselected package libgraphite2-3:amd64. 166s Preparing to unpack .../17-libgraphite2-3_1.3.14-11ubuntu1_amd64.deb ... 166s Unpacking libgraphite2-3:amd64 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Processing triggers for libc-bin (2.42-2ubuntu4) ... 169s Processing triggers for man-db (2.13.1-1build1) ... 170s Processing triggers for install-info (7.2-5) ... 171s autopkgtest [00:45:17]: test run-unit-test: [----------------------- 171s 171s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 171s Copyright (C) 2025 The R Foundation for Statistical Computing 171s Platform: x86_64-pc-linux-gnu 171s 171s R is free software and comes with ABSOLUTELY NO WARRANTY. 171s You are welcome to redistribute it under certain conditions. 171s Type 'license()' or 'licence()' for distribution details. 171s 171s R is a collaborative project with many contributors. 171s Type 'contributors()' for more information and 171s 'citation()' on how to cite R or R packages in publications. 171s 171s Type 'demo()' for some demos, 'help()' for on-line help, or 171s 'help.start()' for an HTML browser interface to help. 171s Type 'q()' to quit R. 171s 171s > Stangle("decision-vegan.Rnw") 171s Writing to file decision-vegan.R 171s > source("decision-vegan.R", echo=TRUE) 171s 171s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 171s 171s > options(SweaveHooks = list(fig = figset)) 171s 171s > options(prompt = "> ", continue = " ") 171s 171s > options(width = 55) 171s 171s > require(vegan) 171s Loading required package: vegan 171s Loading required package: permute 171s Loading required package: lattice 172s 172s > data(sipoo) 172s 172s > mod <- nestedtemp(sipoo) 172s 172s > plot(mod, "i") 172s 172s > x <- mod$c["Falcsubb"] 172s 172s > y <- 1 - mod$r["Svartholm"] 172s 172s > points(x, y, pch = 16, cex = 1.5) 172s 172s > abline(x + y, -1, lty = 2) 172s 172s > f <- function(x, p) (1 - (1 - x)^p)^(1/p) 172s 172s > cross <- function(x, a, p) f(x, p) - a + x 172s 172s > r <- uniroot(cross, c(0, 1), a = x + y, p = mod$p)$root 172s 172s > arrows(x, y, r, f(r, mod$p), lwd = 4) 172s 172s > library(vegan) 172s 172s > data(varespec) 172s 172s > data(varechem) 172s 172s > orig <- cca(varespec ~ Al + K, varechem) 172s 172s > plot(orig, dis = c("lc", "bp")) 172s 172s > plot(orig, dis = c("lc", "bp")) 172s 172s > i <- sample(nrow(varespec)) 172s 172s > shuff <- cca(varespec[i, ] ~ Al + K, varechem) 172s 172s > plot(shuff, dis = c("lc", "bp")) 172s 172s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 172s + dis = "lc"))) 172s 172s > plot(procrustes(scores(orig, dis = "lc"), scores(shuff, 172s + dis = "lc"))) 172s 172s > tmp1 <- rda(varespec ~ Al + K, varechem) 172s 172s > i <- sample(nrow(varespec)) 172s 172s > tmp2 <- rda(varespec[i, ] ~ Al + K, varechem) 172s 172s > plot(procrustes(scores(tmp1, dis = "lc"), scores(tmp2, 172s + dis = "lc"))) 172s 172s > orig 172s Call: cca(formula = varespec ~ Al + K, data = 172s varechem) 172s 172s -- Model Summary -- 172s 172s Inertia Proportion Rank 172s Total 2.0832 1.0000 172s Constrained 0.4760 0.2285 2 172s Unconstrained 1.6072 0.7715 21 172s 172s Inertia is scaled Chi-square 172s 172s -- Eigenvalues -- 172s 172s Eigenvalues for constrained axes: 172s CCA1 CCA2 172s 0.3608 0.1152 172s 172s Eigenvalues for unconstrained axes: 172s CA1 CA2 CA3 CA4 CA5 CA6 CA7 172s 0.3748 0.2404 0.1970 0.1782 0.1521 0.1184 0.0836 172s CA8 172s 0.0757 172s (Showing 8 of 21 unconstrained eigenvalues) 172s 172s 172s > shuff 172s Call: cca(formula = varespec[i, ] ~ Al + K, data = 172s varechem) 172s 172s -- Model Summary -- 172s 172s Inertia Proportion Rank 172s Total 2.08320 1.00000 172s Constrained 0.18679 0.08967 2 172s Unconstrained 1.89641 0.91033 21 172s 172s Inertia is scaled Chi-square 172s 172s -- Eigenvalues -- 172s 172s Eigenvalues for constrained axes: 172s CCA1 CCA2 172s 0.11465 0.07214 172s 172s Eigenvalues for unconstrained axes: 172s CA1 CA2 CA3 CA4 CA5 CA6 CA7 172s 0.5229 0.2818 0.1970 0.1949 0.1538 0.1167 0.1018 172s CA8 172s 0.0869 172s (Showing 8 of 21 unconstrained eigenvalues) 172s 172s 172s > plot(procrustes(orig, shuff)) 172s 172s > tmp1 <- rda(varespec ~ ., varechem) 172s 172s > tmp2 <- rda(varespec[i, ] ~ ., varechem) 172s 172s > proc <- procrustes(scores(tmp1, dis = "lc", choi = 1:14), 172s + scores(tmp2, dis = "lc", choi = 1:14)) 172s 172s > max(residuals(proc)) 172s [1] 3.073955e-14 172s 172s > data(dune) 172s 172s > data(dune.env) 172s 172s > orig <- cca(dune ~ Moisture, dune.env) 172s 172s > plot(orig, dis = "lc") 172s 172s > plot(orig, display = "wa", type = "points") 172s 172s > ordispider(orig, col = "red") 172s 172s > text(orig, dis = "cn", col = "blue") 172s 172s > plot(orig, display = "wa", type = "points") 172s 172s > ordispider(orig, col = "red") 172s 172s > text(orig, dis = "cn", col = "blue") 172s > 172s 172s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 172s Copyright (C) 2025 The R Foundation for Statistical Computing 172s Platform: x86_64-pc-linux-gnu 172s 172s R is free software and comes with ABSOLUTELY NO WARRANTY. 172s You are welcome to redistribute it under certain conditions. 172s Type 'license()' or 'licence()' for distribution details. 172s 172s R is a collaborative project with many contributors. 172s Type 'contributors()' for more information and 172s 'citation()' on how to cite R or R packages in publications. 172s 172s Type 'demo()' for some demos, 'help()' for on-line help, or 172s 'help.start()' for an HTML browser interface to help. 172s Type 'q()' to quit R. 172s 172s > Stangle("diversity-vegan.Rnw") 172s Writing to file diversity-vegan.R 172s > source("diversity-vegan.R", echo=TRUE) 172s 172s > par(mfrow = c(1, 1)) 172s 172s > options(width = 55) 172s 172s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 172s 172s > options(SweaveHooks = list(fig = figset)) 172s 172s > options(prompt = "> ", continue = " ") 172s 172s > library(vegan) 172s Loading required package: permute 172s Loading required package: lattice 173s 173s > data(BCI) 173s 173s > H <- diversity(BCI) 173s 173s > J <- H/log(specnumber(BCI)) 173s 173s > k <- sample(nrow(BCI), 6) 173s 173s > R <- renyi(BCI[k, ]) 173s 173s > print(plot(R)) 173s 173s > alpha <- fisher.alpha(BCI) 173s 173s > quantile(rowSums(BCI)) 173s 0% 25% 50% 75% 100% 173s 340.0 409.0 428.0 443.5 601.0 173s 173s > Srar <- rarefy(BCI, min(rowSums(BCI))) 173s 173s > S2 <- rarefy(BCI, 2) 173s 173s > all(rank(Srar) == rank(S2)) 173s [1] FALSE 173s 173s > range(diversity(BCI, "simp") - (S2 - 1)) 173s [1] -0.002868298 -0.001330663 173s 173s > data(dune) 173s 173s > data(dune.taxon) 173s 173s > taxdis <- taxa2dist(dune.taxon, varstep = TRUE) 173s 173s > mod <- taxondive(dune, taxdis) 173s 173s > plot(mod) 173s 173s > tr <- hclust(taxdis, "aver") 173s 173s > mod <- treedive(dune, tr) 173s forced matching of 'tree' labels and 'comm' names 173s 173s > k <- sample(nrow(BCI), 1) 173s 173s > fish <- fisherfit(BCI[k, ]) 173s 173s > fish 173s 173s Fisher log series model 173s No. of species: 99 173s Fisher alpha: 41.03649 173s 173s 173s > plot(fish) 173s 173s > prestondistr(BCI[k, ]) 173s 173s Preston lognormal model 173s Method: maximized likelihood to log2 abundances 173s No. of species: 99 173s 173s mode width S0 173s 0.908074 1.642423 27.409254 173s 173s Frequencies by Octave 173s 0 1 2 3 4 173s Observed 19.00000 29.00000 26.50000 8.50000 11.500000 173s Fitted 23.52441 27.36636 21.97452 12.17941 4.659477 173s 5 6 173s Observed 3.500000 1.0000000 173s Fitted 1.230417 0.2242704 173s 173s 173s > rad <- radfit(BCI[k, ]) 173s 173s > rad 173s 173s RAD models, family poisson 173s No. of species 99, total abundance 417 173s 173s par1 par2 par3 Deviance AIC 173s Null 74.926 354.467 173s Preemption 0.042117 76.212 357.753 173s Lognormal 0.82544 1.1247 23.121 306.663 173s Zipf 0.13164 -0.82691 25.994 309.536 173s Mandelbrot 0.4808 -1.1651 3.0985 17.226 302.767 173s BIC 173s Null 354.467 173s Preemption 360.348 173s Lognormal 311.853 173s Zipf 314.726 173s Mandelbrot 310.553 173s 173s > print(radlattice(rad)) 173s 173s > sac <- specaccum(BCI) 173s 173s > plot(sac, ci.type = "polygon", ci.col = "yellow") 173s 173s > sac <- specaccum(BCI) 173s 173s > plot(sac, ci.type = "polygon", ci.col = "yellow") 173s 173s > ncol(BCI)/mean(specnumber(BCI)) - 1 173s [1] 1.478519 173s 173s > beta <- vegdist(BCI, binary = TRUE) 173s 173s > mean(beta) 173s [1] 0.3399075 173s 173s > betadiver(help = TRUE) 173s 1 "w" = (b+c)/(2*a+b+c) 173s 2 "-1" = (b+c)/(2*a+b+c) 173s 3 "c" = (b+c)/2 173s 4 "wb" = b+c 173s 5 "r" = 2*b*c/((a+b+c)^2-2*b*c) 173s 6 "I" = log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) - 173s ((a+b)*log(a+b) + (a+c)*log(a+c)) / (2*a+b+c) 173s 7 "e" = exp(log(2*a+b+c) - 2*a*log(2)/(2*a+b+c) 173s - ((a+b)*log(a+b) + (a+c)*log(a+c)) / 173s (2*a+b+c))-1 173s 8 "t" = (b+c)/(2*a+b+c) 173s 9 "me" = (b+c)/(2*a+b+c) 173s 10 "j" = a/(a+b+c) 173s 11 "sor" = 2*a/(2*a+b+c) 173s 12 "m" = (2*a+b+c)*(b+c)/(a+b+c) 173s 13 "-2" = pmin.int(b,c)/(pmax.int(b,c)+a) 173s 14 "co" = (a*c+a*b+2*b*c)/(2*(a+b)*(a+c)) 173s 15 "cc" = (b+c)/(a+b+c) 173s 16 "g" = (b+c)/(a+b+c) 173s 17 "-3" = pmin.int(b,c)/(a+b+c) 173s 18 "l" = (b+c)/2 173s 19 "19" = 2*(b*c+1)/(a+b+c)/(a+b+c-1) 173s 20 "hk" = (b+c)/(2*a+b+c) 173s 21 "rlb" = a/(a+c) 173s 22 "sim" = pmin.int(b,c)/(pmin.int(b,c)+a) 173s 23 "gl" = 2*abs(b-c)/(2*a+b+c) 173s 24 "z" = (log(2)-log(2*a+b+c)+log(a+b+c))/log(2) 173s 173s > z <- betadiver(BCI, "z") 173s 173s > quantile(z) 173s 0% 25% 50% 75% 100% 173s 0.2732845 0.3895024 0.4191536 0.4537180 0.5906091 173s 173s > data(dune) 173s 173s > data(dune.env) 173s 173s > z <- betadiver(dune, "z") 173s 173s > mod <- with(dune.env, betadisper(z, Management)) 173s 173s > mod 173s 173s Homogeneity of multivariate dispersions 173s 173s Call: betadisper(d = z, group = Management) 173s 173s No. of Positive Eigenvalues: 12 173s No. of Negative Eigenvalues: 7 173s 173s Average distance to median: 173s BF HF NM SF 173s 0.2532 0.2512 0.4406 0.3635 173s 173s Eigenvalues for PCoA axes: 173s (Showing 8 of 19 eigenvalues) 173s PCoA1 PCoA2 PCoA3 PCoA4 PCoA5 PCoA6 173s 1.65466 0.88696 0.53336 0.37435 0.28725 0.22445 173s PCoA7 PCoA8 173s 0.16128 0.08099 173s 173s > boxplot(mod) 173s 173s > specpool(BCI) 173s Species chao chao.se jack1 jack1.se jack2 173s All 225 236.3732 6.54361 245.58 5.650522 247.8722 173s boot boot.se n 173s All 235.6862 3.468888 50 173s 173s > s <- sample(nrow(BCI), 25) 173s 173s > specpool(BCI[s, ]) 173s Species chao chao.se jack1 jack1.se jack2 173s All 208 225.28 9.257905 231.04 6.575591 239.0133 173s boot boot.se n 173s All 219.3669 3.99796 25 173s 173s > estimateR(BCI[k, ]) 173s 27 173s S.obs 99.000000 173s S.chao1 132.476190 173s se.chao1 14.332686 173s S.ACE 146.364277 173s se.ACE 6.934629 173s 173s > veiledspec(prestondistr(BCI[k, ])) 173s Extrapolated Observed Veiled 173s 112.84236 99.00000 13.84236 173s 173s > veiledspec(BCI[k, ]) 173s Extrapolated Observed Veiled 173s 122.34765 99.00000 23.34765 173s 173s > smo <- beals(BCI) 173s 173s > j <- which(colnames(BCI) == "Ceiba.pentandra") 173s 173s > plot(beals(BCI, species = j, include = FALSE), BCI[, 173s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 173s 173s > j <- which(colnames(BCI) == "Ceiba.pentandra") 173s 173s > plot(beals(BCI, species = j, include = FALSE), BCI[, 173s + j], ylab = "Occurrence", main = "Ceiba pentandra", xlab = "Probability of occurrence") 173s > 173s Warning messages: 173s 1: In cor(x > 0) : the standard deviation is zero 173s 2: In cor(x > 0) : the standard deviation is zero 173s 3: In betadisper(z, Management) : 173s some squared distances are negative and changed to zero 173s 173s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 173s Copyright (C) 2025 The R Foundation for Statistical Computing 173s Platform: x86_64-pc-linux-gnu 173s 173s R is free software and comes with ABSOLUTELY NO WARRANTY. 173s You are welcome to redistribute it under certain conditions. 173s Type 'license()' or 'licence()' for distribution details. 173s 173s R is a collaborative project with many contributors. 173s Type 'contributors()' for more information and 173s 'citation()' on how to cite R or R packages in publications. 173s 173s Type 'demo()' for some demos, 'help()' for on-line help, or 173s 'help.start()' for an HTML browser interface to help. 173s Type 'q()' to quit R. 173s 173s > Stangle("intro-vegan.Rnw") 173s Writing to file intro-vegan.R 173s > source("intro-vegan.R", echo=TRUE) 173s 173s > par(mfrow = c(1, 1)) 173s 173s > options(width = 72) 173s 173s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 173s 173s > options(SweaveHooks = list(fig = figset)) 173s 173s > options(prompt = "> ", continue = " ") 173s 173s > library(vegan) 173s Loading required package: permute 173s Loading required package: lattice 174s 174s > data(dune) 174s 174s > ord <- decorana(dune) 174s 174s > ord 174s 174s Call: 174s decorana(veg = dune) 174s 174s Detrended correspondence analysis with 26 segments. 174s Rescaling of axes with 4 iterations. 174s Total inertia (scaled Chi-square): 2.1153 174s 174s DCA1 DCA2 DCA3 DCA4 174s Eigenvalues 0.5117 0.3036 0.12125 0.14267 174s Additive Eigenvalues 0.5117 0.2985 0.12242 0.12984 174s Decorana values 0.5360 0.2869 0.08136 0.04814 174s Axis lengths 3.7004 3.1166 1.30055 1.47888 174s 174s 174s > ord <- metaMDS(dune, trace = FALSE) 174s 174s > ord 174s 174s Call: 174s metaMDS(comm = dune, trace = FALSE) 174s 174s global Multidimensional Scaling using monoMDS 174s 174s Data: dune 174s Distance: bray 174s 174s Dimensions: 2 174s Stress: 0.1183186 174s Stress type 1, weak ties 174s Best solution was repeated 4 times in 20 tries 174s The best solution was from try 1 (random start) 174s Scaling: centring, PC rotation, halfchange scaling 174s Species: expanded scores based on ‘dune’ 174s 174s 174s > plot(ord) 174s 174s > plot(ord) 174s 174s > plot(ord, type = "n") 174s 174s > points(ord, display = "sites", cex = 0.8, pch = 21, 174s + col = "red", bg = "yellow") 174s 174s > text(ord, display = "species", cex = 0.7, col = "blue") 174s 174s > plot(ord, type = "n") 174s 174s > points(ord, display = "sites", cex = 0.8, pch = 21, 174s + col = "red", bg = "yellow") 174s 174s > text(ord, display = "species", cex = 0.7, col = "blue") 174s 174s > text(points(plot(ord, type = "n"), "sites", cex = 0.8, 174s + pch = 21, col = "red", bg = "yellow"), "species", cex = 0.7, 174s + col = "blue") 174s 174s > data(dune.env) 174s 174s > attach(dune.env) 174s 174s > plot(ord, disp = "sites", type = "n") 174s 174s > ordihull(ord, Management, col = 1:4, lwd = 3) 174s 174s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 174s + lwd = 3) 174s 174s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 174s 174s > ordispider(ord, Management, col = 1:4, label = TRUE) 174s 174s > points(ord, disp = "sites", pch = 21, col = "red", 174s + bg = "yellow", cex = 1.3) 174s 174s > plot(ord, disp = "sites", type = "n") 174s 174s > ordihull(ord, Management, col = 1:4, lwd = 3) 174s 174s > ordiellipse(ord, Management, col = 1:4, kind = "ehull", 174s + lwd = 3) 174s 174s > ordiellipse(ord, Management, col = 1:4, draw = "polygon") 174s 174s > ordispider(ord, Management, col = 1:4, label = TRUE) 174s 174s > points(ord, disp = "sites", pch = 21, col = "red", 174s + bg = "yellow", cex = 1.3) 174s 174s > ord.fit <- envfit(ord ~ A1 + Management, data = dune.env, 174s + perm = 999) 174s 174s > ord.fit 174s 174s ***VECTORS 174s 174s NMDS1 NMDS2 r2 Pr(>r) 174s A1 0.96474 0.26322 0.3649 0.02 * 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s Permutation: free 174s Number of permutations: 999 174s 174s ***FACTORS: 174s 174s Centroids: 174s NMDS1 NMDS2 174s ManagementBF -0.4534 -0.0102 174s ManagementHF -0.2636 -0.1282 174s ManagementNM 0.2958 0.5790 174s ManagementSF 0.1506 -0.4670 174s 174s Goodness of fit: 174s r2 Pr(>r) 174s Management 0.4134 0.005 ** 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s Permutation: free 174s Number of permutations: 999 174s 174s 174s 174s > plot(ord, dis = "site") 174s 174s > plot(ord.fit) 174s 174s > ordisurf(ord, A1, add = TRUE) 174s 174s Family: gaussian 174s Link function: identity 174s 174s Formula: 174s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 174s 174s Estimated degrees of freedom: 174s 1.59 total = 2.59 174s 174s REML score: 41.58727 174s 174s > plot(ord, dis = "site") 174s 174s > plot(ord.fit) 174s 174s > ordisurf(ord, A1, add = TRUE) 174s 174s Family: gaussian 174s Link function: identity 174s 174s Formula: 174s y ~ s(x1, x2, k = 10, bs = "tp", fx = FALSE) 174s 174s Estimated degrees of freedom: 174s 1.59 total = 2.59 174s 174s REML score: 41.58727 174s 174s > ord <- cca(dune ~ A1 + Management, data = dune.env) 174s 174s > ord 174s Call: cca(formula = dune ~ A1 + Management, data = dune.env) 174s 174s -- Model Summary -- 174s 174s Inertia Proportion Rank 174s Total 2.1153 1.0000 174s Constrained 0.7798 0.3686 4 174s Unconstrained 1.3355 0.6314 15 174s 174s Inertia is scaled Chi-square 174s 174s -- Eigenvalues -- 174s 174s Eigenvalues for constrained axes: 174s CCA1 CCA2 CCA3 CCA4 174s 0.3187 0.2372 0.1322 0.0917 174s 174s Eigenvalues for unconstrained axes: 174s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 CA10 174s 0.3620 0.2029 0.1527 0.1345 0.1110 0.0800 0.0767 0.0553 0.0444 0.0415 174s CA11 CA12 CA13 CA14 CA15 174s 0.0317 0.0178 0.0116 0.0087 0.0047 174s 174s 174s > plot(ord) 174s 174s > plot(ord) 174s 174s > cca(dune ~ ., data = dune.env) 174s 174s Some constraints or conditions were aliased because they were 174s redundant. This can happen if terms are linearly dependent (collinear): 174s ‘Manure^4’ 174s Call: cca(formula = dune ~ A1 + Moisture + Management + Use + 174s Manure, data = dune.env) 174s 174s -- Model Summary -- 174s 174s Inertia Proportion Rank 174s Total 2.1153 1.0000 174s Constrained 1.5032 0.7106 12 174s Unconstrained 0.6121 0.2894 7 174s 174s Inertia is scaled Chi-square 174s 174s -- Note -- 174s 174s Some constraints or conditions were aliased because they were 174s redundant. This can happen if terms are linearly dependent 174s (collinear): ‘Manure^4’ 174s 174s -- Eigenvalues -- 174s 174s Eigenvalues for constrained axes: 174s CCA1 CCA2 CCA3 CCA4 CCA5 CCA6 CCA7 CCA8 CCA9 CCA10 174s 0.4671 0.3410 0.1761 0.1532 0.0953 0.0703 0.0589 0.0499 0.0318 0.0260 174s CCA11 CCA12 174s 0.0228 0.0108 174s 174s Eigenvalues for unconstrained axes: 174s CA1 CA2 CA3 CA4 CA5 CA6 CA7 174s 0.27237 0.10876 0.08975 0.06305 0.03489 0.02529 0.01798 174s 174s 174s > anova(ord) 174s Permutation test for cca under reduced model 174s Permutation: free 174s Number of permutations: 999 174s 174s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 174s Df ChiSquare F Pr(>F) 174s Model 4 0.77978 2.1896 0.002 ** 174s Residual 15 1.33549 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > anova(ord, by = "term", permutations = 199) 174s Permutation test for cca under reduced model 174s Terms added sequentially (first to last) 174s Permutation: free 174s Number of permutations: 199 174s 174s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 174s Df ChiSquare F Pr(>F) 174s A1 1 0.22476 2.5245 0.015 * 174s Management 3 0.55502 2.0780 0.005 ** 174s Residual 15 1.33549 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > anova(ord, by = "mar", permutations = 199) 174s Permutation test for cca under reduced model 174s Marginal effects of terms 174s Permutation: free 174s Number of permutations: 199 174s 174s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 174s Df ChiSquare F Pr(>F) 174s A1 1 0.17594 1.9761 0.055 . 174s Management 3 0.55502 2.0780 0.005 ** 174s Residual 15 1.33549 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > anova(ord, by = "axis", permutations = 499) 174s Permutation test for cca under reduced model 174s Forward tests for axes 174s Permutation: free 174s Number of permutations: 499 174s 174s Model: cca(formula = dune ~ A1 + Management, data = dune.env) 174s Df ChiSquare F Pr(>F) 174s CCA1 1 0.31875 3.5801 0.010 ** 174s CCA2 1 0.23718 2.6640 0.150 174s CCA3 1 0.13217 1.4845 0.848 174s CCA4 1 0.09168 1.0297 1.000 174s Residual 15 1.33549 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > ord <- cca(dune ~ A1 + Management + Condition(Moisture), 174s + data = dune.env) 174s 174s > ord 174s Call: cca(formula = dune ~ A1 + Management + Condition(Moisture), 174s data = dune.env) 174s 174s -- Model Summary -- 174s 174s Inertia Proportion Rank 174s Total 2.1153 1.0000 174s Conditional 0.6283 0.2970 3 174s Constrained 0.5109 0.2415 4 174s Unconstrained 0.9761 0.4615 12 174s 174s Inertia is scaled Chi-square 174s 174s -- Eigenvalues -- 174s 174s Eigenvalues for constrained axes: 174s CCA1 CCA2 CCA3 CCA4 174s 0.24932 0.12090 0.08160 0.05904 174s 174s Eigenvalues for unconstrained axes: 174s CA1 CA2 CA3 CA4 CA5 CA6 CA7 CA8 CA9 174s 0.30637 0.13191 0.11516 0.10947 0.07724 0.07575 0.04871 0.03758 0.03106 174s CA10 CA11 CA12 174s 0.02102 0.01254 0.00928 174s 174s 174s > anova(ord, by = "term", permutations = 499) 174s Permutation test for cca under reduced model 174s Terms added sequentially (first to last) 174s Permutation: free 174s Number of permutations: 499 174s 174s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 174s Df ChiSquare F Pr(>F) 174s A1 1 0.11543 1.4190 1.000 174s Management 3 0.39543 1.6205 0.002 ** 174s Residual 12 0.97610 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > how <- how(nperm = 499, plots = Plots(strata = dune.env$Moisture)) 174s 174s > anova(ord, by = "term", permutations = how) 174s Permutation test for cca under reduced model 174s Terms added sequentially (first to last) 174s Plots: dune.env$Moisture, plot permutation: none 174s Permutation: free 174s Number of permutations: 499 174s 174s Model: cca(formula = dune ~ A1 + Management + Condition(Moisture), data = dune.env) 174s Df ChiSquare F Pr(>F) 174s A1 1 0.11543 1.4190 1.000 174s Management 3 0.39543 1.6205 0.002 ** 174s Residual 12 0.97610 174s --- 174s Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 174s 174s > detach(dune.env) 174s > 174s 174s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 174s Copyright (C) 2025 The R Foundation for Statistical Computing 174s Platform: x86_64-pc-linux-gnu 174s 174s R is free software and comes with ABSOLUTELY NO WARRANTY. 174s You are welcome to redistribute it under certain conditions. 174s Type 'license()' or 'licence()' for distribution details. 174s 174s R is a collaborative project with many contributors. 174s Type 'contributors()' for more information and 174s 'citation()' on how to cite R or R packages in publications. 174s 174s Type 'demo()' for some demos, 'help()' for on-line help, or 174s 'help.start()' for an HTML browser interface to help. 174s Type 'q()' to quit R. 174s 174s > Stangle("partitioning.Rnw") 174s Writing to file partitioning.R 174s > source("partitioning.R", echo=TRUE) 174s 174s > par(mfrow = c(1, 1)) 174s 174s > figset <- function() par(mar = c(4, 4, 1, 1) + 0.1) 174s 174s > options(SweaveHooks = list(fig = figset)) 174s 174s > library(vegan) 174s Loading required package: permute 174s Loading required package: lattice 175s 175s > labs <- paste("Table", 1:4) 175s 175s > cls <- c("hotpink", "skyblue", "orange", "limegreen") 175s 175s > showvarparts(2, bg = cls, Xnames = labs) 175s 175s > showvarparts(3, bg = cls, Xnames = labs) 175s 175s > showvarparts(4, bg = cls, Xnames = labs) 175s > 181s Test cca-object-tests passed 181s Test oecosimu-tests passed 183s Test vegan-tests passed 184s autopkgtest [00:45:30]: test run-unit-test: -----------------------] 184s run-unit-test PASS 184s autopkgtest [00:45:30]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 184s autopkgtest [00:45:30]: test pkg-r-autopkgtest: preparing testbed 185s Reading package lists... 185s Building dependency tree... 185s Reading state information... 185s Solving dependencies... 185s The following NEW packages will be installed: 185s build-essential cpp cpp-15 cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu 185s dctrl-tools g++ g++-15 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 185s gcc-15 gcc-15-x86-64-linux-gnu gcc-x86-64-linux-gnu gfortran gfortran-15 185s gfortran-15-x86-64-linux-gnu gfortran-x86-64-linux-gnu icu-devtools libasan8 185s libblas-dev libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcrypt-dev 185s libdeflate-dev libgcc-15-dev libgfortran-15-dev libhwasan0 libicu-dev 185s libisl23 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev liblapack-dev 185s liblsan0 liblzma-dev libmpc3 libncurses-dev libpcre2-16-0 libpcre2-32-0 185s libpcre2-dev libpcre2-posix3 libpkgconf3 libpng-dev libquadmath0 185s libreadline-dev libstdc++-15-dev libtirpc-dev libtsan2 libubsan1 libzstd-dev 185s linux-libc-dev pkg-r-autopkgtest pkgconf pkgconf-bin r-base-dev rpcsvc-proto 185s zlib1g-dev 185s 0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded. 185s Need to get 112 MB of archives. 185s After this operation, 402 MB of additional disk space will be used. 185s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 libc-dev-bin amd64 2.42-2ubuntu4 [23.3 kB] 185s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 linux-libc-dev amd64 6.19.0-3.3 [1846 kB] 185s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libcrypt-dev amd64 1:4.5.1-1 [122 kB] 185s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 rpcsvc-proto amd64 1.4.3-1build1 [68.3 kB] 185s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libc6-dev amd64 2.42-2ubuntu4 [2207 kB] 185s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 libisl23 amd64 0.27-1build1 [691 kB] 185s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 libmpc3 amd64 1.3.1-2 [54.8 kB] 185s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [12.9 MB] 186s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-15 amd64 15.2.0-12ubuntu1 [1034 B] 186s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [5746 B] 186s Get:11 http://ftpmaster.internal/ubuntu resolute/main amd64 cpp amd64 4:15.2.0-4ubuntu1 [22.4 kB] 186s Get:12 http://ftpmaster.internal/ubuntu resolute/main amd64 libcc1-0 amd64 16-20260208-1ubuntu1 [51.2 kB] 186s Get:13 http://ftpmaster.internal/ubuntu resolute/main amd64 libitm1 amd64 16-20260208-1ubuntu1 [30.2 kB] 186s Get:14 http://ftpmaster.internal/ubuntu resolute/main amd64 libasan8 amd64 16-20260208-1ubuntu1 [3182 kB] 186s Get:15 http://ftpmaster.internal/ubuntu resolute/main amd64 liblsan0 amd64 16-20260208-1ubuntu1 [1392 kB] 186s Get:16 http://ftpmaster.internal/ubuntu resolute/main amd64 libtsan2 amd64 16-20260208-1ubuntu1 [2838 kB] 186s Get:17 http://ftpmaster.internal/ubuntu resolute/main amd64 libubsan1 amd64 16-20260208-1ubuntu1 [1238 kB] 186s Get:18 http://ftpmaster.internal/ubuntu resolute/main amd64 libhwasan0 amd64 16-20260208-1ubuntu1 [1729 kB] 186s Get:19 http://ftpmaster.internal/ubuntu resolute/main amd64 libquadmath0 amd64 16-20260208-1ubuntu1 [155 kB] 186s Get:20 http://ftpmaster.internal/ubuntu resolute/main amd64 libgcc-15-dev amd64 15.2.0-12ubuntu1 [2866 kB] 186s Get:21 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [25.4 MB] 187s Get:22 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-15 amd64 15.2.0-12ubuntu1 [530 kB] 187s Get:23 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1208 B] 187s Get:24 http://ftpmaster.internal/ubuntu resolute/main amd64 gcc amd64 4:15.2.0-4ubuntu1 [5024 B] 187s Get:25 http://ftpmaster.internal/ubuntu resolute/main amd64 libstdc++-15-dev amd64 15.2.0-12ubuntu1 [2553 kB] 187s Get:26 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [14.4 MB] 187s Get:27 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-15 amd64 15.2.0-12ubuntu1 [25.3 kB] 187s Get:28 http://ftpmaster.internal/ubuntu resolute/main amd64 g++-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [966 B] 187s Get:29 http://ftpmaster.internal/ubuntu resolute/main amd64 g++ amd64 4:15.2.0-4ubuntu1 [1100 B] 187s Get:30 http://ftpmaster.internal/ubuntu resolute/main amd64 build-essential amd64 12.12ubuntu2 [5256 B] 187s Get:31 http://ftpmaster.internal/ubuntu resolute/main amd64 dctrl-tools amd64 2.24-3build4 [104 kB] 187s Get:32 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran-15-dev amd64 15.2.0-12ubuntu1 [973 kB] 187s Get:33 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-12ubuntu1 [13.6 MB] 187s Get:34 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-15 amd64 15.2.0-12ubuntu1 [18.1 kB] 187s Get:35 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4ubuntu1 [1014 B] 187s Get:36 http://ftpmaster.internal/ubuntu resolute/main amd64 gfortran amd64 4:15.2.0-4ubuntu1 [1172 B] 187s Get:37 http://ftpmaster.internal/ubuntu resolute/main amd64 icu-devtools amd64 78.2-1ubuntu1 [214 kB] 187s Get:38 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas-dev amd64 3.12.1-7ubuntu1 [235 kB] 187s Get:39 http://ftpmaster.internal/ubuntu resolute/main amd64 libbz2-dev amd64 1.0.8-6build2 [36.2 kB] 187s Get:40 http://ftpmaster.internal/ubuntu resolute/main amd64 libdeflate-dev amd64 1.23-2build1 [58.8 kB] 187s Get:41 http://ftpmaster.internal/ubuntu resolute/main amd64 libicu-dev amd64 78.2-1ubuntu1 [12.5 MB] 188s Get:42 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-turbo8-dev amd64 2.1.5-4ubuntu3 [300 kB] 188s Get:43 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg8-dev amd64 8c-2ubuntu12 [1480 B] 188s Get:44 http://ftpmaster.internal/ubuntu resolute/main amd64 libjpeg-dev amd64 8c-2ubuntu12 [1480 B] 188s Get:45 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack-dev amd64 3.12.1-7ubuntu1 [5433 kB] 188s Get:46 http://ftpmaster.internal/ubuntu resolute/main amd64 libncurses-dev amd64 6.6+20251231-1 [389 kB] 188s Get:47 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-16-0 amd64 10.46-1 [243 kB] 188s Get:48 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-32-0 amd64 10.46-1 [230 kB] 188s Get:49 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-posix3 amd64 10.46-1 [7354 B] 188s Get:50 http://ftpmaster.internal/ubuntu resolute/main amd64 libpcre2-dev amd64 10.46-1 [832 kB] 188s Get:51 http://ftpmaster.internal/ubuntu resolute/main amd64 libpkgconf3 amd64 1.8.1-4build1 [32.8 kB] 188s Get:52 http://ftpmaster.internal/ubuntu resolute/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1ubuntu2 [898 kB] 188s Get:53 http://ftpmaster.internal/ubuntu resolute/main amd64 libpng-dev amd64 1.6.54-1 [273 kB] 188s Get:54 http://ftpmaster.internal/ubuntu resolute/main amd64 libreadline-dev amd64 8.3-3 [189 kB] 188s Get:55 http://ftpmaster.internal/ubuntu resolute/main amd64 libzstd-dev amd64 1.5.7+dfsg-3 [376 kB] 188s Get:56 http://ftpmaster.internal/ubuntu resolute/main amd64 liblzma-dev amd64 5.8.2-2 [179 kB] 188s Get:57 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf-bin amd64 1.8.1-4build1 [21.7 kB] 188s Get:58 http://ftpmaster.internal/ubuntu resolute/main amd64 pkgconf amd64 1.8.1-4build1 [16.8 kB] 188s Get:59 http://ftpmaster.internal/ubuntu resolute/main amd64 libtirpc-dev amd64 1.3.6+ds-1 [195 kB] 188s Get:60 http://ftpmaster.internal/ubuntu resolute/universe amd64 r-base-dev all 4.5.2-1ubuntu2 [1880 B] 188s Get:61 http://ftpmaster.internal/ubuntu resolute/universe amd64 pkg-r-autopkgtest all 20250812 [6158 B] 188s Fetched 112 MB in 3s (36.8 MB/s) 188s Selecting previously unselected package libc-dev-bin. 188s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 133296 files and directories currently installed.) 188s Preparing to unpack .../00-libc-dev-bin_2.42-2ubuntu4_amd64.deb ... 188s Unpacking libc-dev-bin (2.42-2ubuntu4) ... 188s Selecting previously unselected package linux-libc-dev:amd64. 188s Preparing to unpack .../01-linux-libc-dev_6.19.0-3.3_amd64.deb ... 188s Unpacking linux-libc-dev:amd64 (6.19.0-3.3) ... 188s Selecting previously unselected package libcrypt-dev:amd64. 188s Preparing to unpack .../02-libcrypt-dev_1%3a4.5.1-1_amd64.deb ... 188s Unpacking libcrypt-dev:amd64 (1:4.5.1-1) ... 188s Selecting previously unselected package rpcsvc-proto. 188s Preparing to unpack .../03-rpcsvc-proto_1.4.3-1build1_amd64.deb ... 188s Unpacking rpcsvc-proto (1.4.3-1build1) ... 188s Selecting previously unselected package libc6-dev:amd64. 188s Preparing to unpack .../04-libc6-dev_2.42-2ubuntu4_amd64.deb ... 188s Unpacking libc6-dev:amd64 (2.42-2ubuntu4) ... 188s Selecting previously unselected package libisl23:amd64. 188s Preparing to unpack .../05-libisl23_0.27-1build1_amd64.deb ... 188s Unpacking libisl23:amd64 (0.27-1build1) ... 188s Selecting previously unselected package libmpc3:amd64. 188s Preparing to unpack .../06-libmpc3_1.3.1-2_amd64.deb ... 188s Unpacking libmpc3:amd64 (1.3.1-2) ... 188s Selecting previously unselected package cpp-15-x86-64-linux-gnu. 188s Preparing to unpack .../07-cpp-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 188s Unpacking cpp-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package cpp-15. 189s Preparing to unpack .../08-cpp-15_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package cpp-x86-64-linux-gnu. 189s Preparing to unpack .../09-cpp-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking cpp-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package cpp. 189s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking cpp (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package libcc1-0:amd64. 189s Preparing to unpack .../11-libcc1-0_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libcc1-0:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libitm1:amd64. 189s Preparing to unpack .../12-libitm1_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libitm1:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libasan8:amd64. 189s Preparing to unpack .../13-libasan8_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libasan8:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package liblsan0:amd64. 189s Preparing to unpack .../14-liblsan0_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking liblsan0:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libtsan2:amd64. 189s Preparing to unpack .../15-libtsan2_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libtsan2:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libubsan1:amd64. 189s Preparing to unpack .../16-libubsan1_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libubsan1:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libhwasan0:amd64. 189s Preparing to unpack .../17-libhwasan0_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libhwasan0:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libquadmath0:amd64. 189s Preparing to unpack .../18-libquadmath0_16-20260208-1ubuntu1_amd64.deb ... 189s Unpacking libquadmath0:amd64 (16-20260208-1ubuntu1) ... 189s Selecting previously unselected package libgcc-15-dev:amd64. 189s Preparing to unpack .../19-libgcc-15-dev_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking libgcc-15-dev:amd64 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package gcc-15-x86-64-linux-gnu. 189s Preparing to unpack .../20-gcc-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking gcc-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package gcc-15. 189s Preparing to unpack .../21-gcc-15_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package gcc-x86-64-linux-gnu. 189s Preparing to unpack .../22-gcc-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking gcc-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package gcc. 189s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking gcc (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package libstdc++-15-dev:amd64. 189s Preparing to unpack .../24-libstdc++-15-dev_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking libstdc++-15-dev:amd64 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package g++-15-x86-64-linux-gnu. 189s Preparing to unpack .../25-g++-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking g++-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package g++-15. 189s Preparing to unpack .../26-g++-15_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking g++-15 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package g++-x86-64-linux-gnu. 189s Preparing to unpack .../27-g++-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking g++-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package g++. 189s Preparing to unpack .../28-g++_4%3a15.2.0-4ubuntu1_amd64.deb ... 189s Unpacking g++ (4:15.2.0-4ubuntu1) ... 189s Selecting previously unselected package build-essential. 189s Preparing to unpack .../29-build-essential_12.12ubuntu2_amd64.deb ... 189s Unpacking build-essential (12.12ubuntu2) ... 189s Selecting previously unselected package dctrl-tools. 189s Preparing to unpack .../30-dctrl-tools_2.24-3build4_amd64.deb ... 189s Unpacking dctrl-tools (2.24-3build4) ... 189s Selecting previously unselected package libgfortran-15-dev:amd64. 189s Preparing to unpack .../31-libgfortran-15-dev_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking libgfortran-15-dev:amd64 (15.2.0-12ubuntu1) ... 189s Selecting previously unselected package gfortran-15-x86-64-linux-gnu. 189s Preparing to unpack .../32-gfortran-15-x86-64-linux-gnu_15.2.0-12ubuntu1_amd64.deb ... 189s Unpacking gfortran-15-x86-64-linux-gnu (15.2.0-12ubuntu1) ... 190s Selecting previously unselected package gfortran-15. 190s Preparing to unpack .../33-gfortran-15_15.2.0-12ubuntu1_amd64.deb ... 190s Unpacking gfortran-15 (15.2.0-12ubuntu1) ... 190s Selecting previously unselected package gfortran-x86-64-linux-gnu. 190s Preparing to unpack .../34-gfortran-x86-64-linux-gnu_4%3a15.2.0-4ubuntu1_amd64.deb ... 190s Unpacking gfortran-x86-64-linux-gnu (4:15.2.0-4ubuntu1) ... 190s Selecting previously unselected package gfortran. 190s Preparing to unpack .../35-gfortran_4%3a15.2.0-4ubuntu1_amd64.deb ... 190s Unpacking gfortran (4:15.2.0-4ubuntu1) ... 190s Selecting previously unselected package icu-devtools. 190s Preparing to unpack .../36-icu-devtools_78.2-1ubuntu1_amd64.deb ... 190s Unpacking icu-devtools (78.2-1ubuntu1) ... 190s Selecting previously unselected package libblas-dev:amd64. 190s Preparing to unpack .../37-libblas-dev_3.12.1-7ubuntu1_amd64.deb ... 190s Unpacking libblas-dev:amd64 (3.12.1-7ubuntu1) ... 190s Selecting previously unselected package libbz2-dev:amd64. 190s Preparing to unpack .../38-libbz2-dev_1.0.8-6build2_amd64.deb ... 190s Unpacking libbz2-dev:amd64 (1.0.8-6build2) ... 190s Selecting previously unselected package libdeflate-dev:amd64. 190s Preparing to unpack .../39-libdeflate-dev_1.23-2build1_amd64.deb ... 190s Unpacking libdeflate-dev:amd64 (1.23-2build1) ... 190s Selecting previously unselected package libicu-dev:amd64. 190s Preparing to unpack .../40-libicu-dev_78.2-1ubuntu1_amd64.deb ... 190s Unpacking libicu-dev:amd64 (78.2-1ubuntu1) ... 190s Selecting previously unselected package libjpeg-turbo8-dev:amd64. 190s Preparing to unpack .../41-libjpeg-turbo8-dev_2.1.5-4ubuntu3_amd64.deb ... 190s Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-4ubuntu3) ... 190s Selecting previously unselected package libjpeg8-dev:amd64. 190s Preparing to unpack .../42-libjpeg8-dev_8c-2ubuntu12_amd64.deb ... 190s Unpacking libjpeg8-dev:amd64 (8c-2ubuntu12) ... 190s Selecting previously unselected package libjpeg-dev:amd64. 190s Preparing to unpack .../43-libjpeg-dev_8c-2ubuntu12_amd64.deb ... 190s Unpacking libjpeg-dev:amd64 (8c-2ubuntu12) ... 190s Selecting previously unselected package liblapack-dev:amd64. 190s Preparing to unpack .../44-liblapack-dev_3.12.1-7ubuntu1_amd64.deb ... 190s Unpacking liblapack-dev:amd64 (3.12.1-7ubuntu1) ... 190s Selecting previously unselected package libncurses-dev:amd64. 190s Preparing to unpack .../45-libncurses-dev_6.6+20251231-1_amd64.deb ... 190s Unpacking libncurses-dev:amd64 (6.6+20251231-1) ... 190s Selecting previously unselected package libpcre2-16-0:amd64. 190s Preparing to unpack .../46-libpcre2-16-0_10.46-1_amd64.deb ... 190s Unpacking libpcre2-16-0:amd64 (10.46-1) ... 190s Selecting previously unselected package libpcre2-32-0:amd64. 190s Preparing to unpack .../47-libpcre2-32-0_10.46-1_amd64.deb ... 190s Unpacking libpcre2-32-0:amd64 (10.46-1) ... 190s Selecting previously unselected package libpcre2-posix3:amd64. 190s Preparing to unpack .../48-libpcre2-posix3_10.46-1_amd64.deb ... 190s Unpacking libpcre2-posix3:amd64 (10.46-1) ... 190s Selecting previously unselected package libpcre2-dev:amd64. 190s Preparing to unpack .../49-libpcre2-dev_10.46-1_amd64.deb ... 190s Unpacking libpcre2-dev:amd64 (10.46-1) ... 190s Selecting previously unselected package libpkgconf3:amd64. 190s Preparing to unpack .../50-libpkgconf3_1.8.1-4build1_amd64.deb ... 190s Unpacking libpkgconf3:amd64 (1.8.1-4build1) ... 190s Selecting previously unselected package zlib1g-dev:amd64. 190s Preparing to unpack .../51-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu2_amd64.deb ... 190s Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1ubuntu2) ... 190s Selecting previously unselected package libpng-dev:amd64. 190s Preparing to unpack .../52-libpng-dev_1.6.54-1_amd64.deb ... 190s Unpacking libpng-dev:amd64 (1.6.54-1) ... 190s Selecting previously unselected package libreadline-dev:amd64. 190s Preparing to unpack .../53-libreadline-dev_8.3-3_amd64.deb ... 190s Unpacking libreadline-dev:amd64 (8.3-3) 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doesn't exist 190s update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode 190s 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 190s Setting up g++ (4:15.2.0-4ubuntu1) ... 190s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 190s Setting up build-essential (12.12ubuntu2) ... 190s Setting up r-base-dev (4.5.2-1ubuntu2) ... 190s Setting up pkg-r-autopkgtest (20250812) ... 190s Processing triggers for libc-bin (2.42-2ubuntu4) ... 190s Processing triggers for man-db (2.13.1-1build1) ... 191s Processing triggers for install-info (7.2-5) ... 192s autopkgtest [00:45:38]: test pkg-r-autopkgtest: /usr/share/dh-r/pkg-r-autopkgtest 192s autopkgtest [00:45:38]: test pkg-r-autopkgtest: [----------------------- 192s Test: Try to load the R library vegan 192s 192s R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 192s Copyright (C) 2025 The R Foundation for Statistical Computing 192s Platform: x86_64-pc-linux-gnu 192s 192s R is free software and comes with ABSOLUTELY NO WARRANTY. 192s You are welcome to redistribute it under certain conditions. 192s Type 'license()' or 'licence()' for distribution details. 192s 192s R is a collaborative project with many contributors. 192s Type 'contributors()' for more information and 192s 'citation()' on how to cite R or R packages in publications. 192s 192s Type 'demo()' for some demos, 'help()' for on-line help, or 192s 'help.start()' for an HTML browser interface to help. 192s Type 'q()' to quit R. 192s 192s > library('vegan') 192s Loading required package: permute 192s Loading required package: lattice 193s > 193s autopkgtest [00:45:39]: test pkg-r-autopkgtest: -----------------------] 193s autopkgtest [00:45:39]: test pkg-r-autopkgtest: - - - - - - - - - - results - - - - - - - - - - 193s pkg-r-autopkgtest PASS 194s autopkgtest [00:45:40]: @@@@@@@@@@@@@@@@@@@@ summary 194s run-unit-test PASS 194s pkg-r-autopkgtest PASS